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Le Bars S, Glaab E. Single-Cell Cortical Transcriptomics Reveals Common and Distinct Changes in Cell-Cell Communication in Alzheimer's and Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04419-7. [PMID: 39143450 DOI: 10.1007/s12035-024-04419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) cause significant neuronal loss and severely impair daily living. Despite different clinical manifestations, these disorders share common pathological molecular hallmarks, including mitochondrial dysfunction and synaptic degeneration. A detailed comparison of molecular changes at single-cell resolution in the cortex, as one of the main brain regions affected in both disorders, may reveal common susceptibility factors and disease mechanisms. We performed single-cell transcriptomic analyses of post-mortem cortical tissue from AD and PD subjects and controls to identify common and distinct disease-associated changes in individual genes, cellular pathways, molecular networks, and cell-cell communication events, and to investigate common mechanisms. The results revealed significant disease-specific, shared, and opposing gene expression changes, including cell type-specific signatures for both diseases. Hypoxia signaling and lipid metabolism emerged as significantly modulated cellular processes in both AD and PD, with contrasting expression alterations between the two diseases. Furthermore, both pathway and cell-cell communication analyses highlighted shared significant alterations involving the JAK-STAT signaling pathway, which has been implicated in the inflammatory response in several neurodegenerative disorders. Overall, the analyses revealed common and distinct alterations in gene signatures, pathway activities, and gene regulatory subnetworks in AD and PD. The results provide insights into coordinated changes in pathway activity and cell-cell communication that may guide future diagnostics and therapeutics.
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Affiliation(s)
- Sophie Le Bars
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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2
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Al-Odat OS, Nelson E, Budak-Alpdogan T, Jonnalagadda SC, Desai D, Pandey MK. Discovering Potential in Non-Cancer Medications: A Promising Breakthrough for Multiple Myeloma Patients. Cancers (Basel) 2024; 16:2381. [PMID: 39001443 PMCID: PMC11240591 DOI: 10.3390/cancers16132381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
MM is a common type of cancer that unfortunately leads to a significant number of deaths each year. The majority of the reported MM cases are detected in the advanced stages, posing significant challenges for treatment. Additionally, all MM patients eventually develop resistance or experience relapse; therefore, advances in treatment are needed. However, developing new anti-cancer drugs, especially for MM, requires significant financial investment and a lengthy development process. The study of drug repurposing involves exploring the potential of existing drugs for new therapeutic uses. This can significantly reduce both time and costs, which are typically a major concern for MM patients. The utilization of pre-existing non-cancer drugs for various myeloma treatments presents a highly efficient and cost-effective strategy, considering their prior preclinical and clinical development. The drugs have shown promising potential in targeting key pathways associated with MM progression and resistance. Thalidomide exemplifies the success that can be achieved through this strategy. This review delves into the current trends, the challenges faced by conventional therapies for MM, and the importance of repurposing drugs for MM. This review highlights a noncomprehensive list of conventional therapies that have potentially significant anti-myeloma properties and anti-neoplastic effects. Additionally, we offer valuable insights into the resources that can help streamline and accelerate drug repurposing efforts in the field of MM.
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Affiliation(s)
- Omar S. Al-Odat
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA;
| | - Emily Nelson
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA;
| | | | | | - Dhimant Desai
- Department of Pharmacology, Penn State Neuroscience Institute, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Manoj K. Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (O.S.A.-O.); (E.N.)
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3
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Ali M, Garcia P, Lunkes LP, Sciortino A, Thomas M, Heurtaux T, Grzyb K, Halder R, Coowar D, Skupin A, Buée L, Blum D, Buttini M, Glaab E. Single cell transcriptome analysis of the THY-Tau22 mouse model of Alzheimer's disease reveals sex-dependent dysregulations. Cell Death Discov 2024; 10:119. [PMID: 38453894 PMCID: PMC10920792 DOI: 10.1038/s41420-024-01885-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Alzheimer's disease (AD) progression and pathology show pronounced sex differences, but the factors driving these remain poorly understood. To gain insights into early AD-associated molecular changes and their sex dependency for tau pathology in the cortex, we performed single-cell RNA-seq in the THY-Tau22 AD mouse model. By examining cell type-specific and cell type-agnostic AD-related gene activity changes and their sex-dimorphism for individual genes, pathways and cellular sub-networks, we identified both statistically significant alterations and interpreted the upstream mechanisms controlling them. Our results confirm several significant sex-dependent alterations in gene activity in the THY-Tau22 model mice compared to controls, with more pronounced alterations in females. Both changes shared across multiple cell types and cell type-specific changes were observed. The differential genes showed significant over-representation of known AD-relevant processes, such as pathways associated with neuronal differentiation, programmed cell death and inflammatory responses. Regulatory network analysis of these genes revealed upstream regulators that modulate many of the downstream targets with sex-dependent changes. Most key regulators have been previously implicated in AD, such as Egr1, Klf4, Chchd2, complement system genes, and myelin-associated glycoproteins. Comparing with similar data from the Tg2576 AD mouse model and human AD patients, we identified multiple genes with consistent, cell type-specific and sex-dependent alterations across all three datasets. These shared changes were particularly evident in the expression of myelin-associated genes such as Mbp and Plp1 in oligodendrocytes. In summary, we observed significant cell type-specific transcriptomic changes in the THY-Tau22 mouse model, with a strong over-representation of known AD-associated genes and processes. These include both sex-neutral and sex-specific patterns, characterized by consistent shifts in upstream master regulators and downstream target genes. Collectively, these findings provide insights into mechanisms influencing sex-specific susceptibility to AD and reveal key regulatory proteins that could be targeted for developing treatments addressing sex-dependent AD pathology.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Laetitia P Lunkes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Alessia Sciortino
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Melanie Thomas
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Tony Heurtaux
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, 8 avenue du Swing, L-4367, Belvaux, Luxembourg
- Luxembourg Center of Neuropathology, L-3555, Dudelange, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Djalil Coowar
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Alex Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, UMR-S1172 Lille Neuroscience & Cognition (LilNCog), Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - David Blum
- University of Lille, Inserm, CHU Lille, UMR-S1172 Lille Neuroscience & Cognition (LilNCog), Lille, France
- Alzheimer and Tauopathies, LabEx DISTALZ, Lille, France
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.
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Cruchaga C, Ali M, Shen Y, Do A, Wang L, Western D, Liu M, Beric A, Budde J, Gentsch J, Schindler S, Morris J, Holtzman D, Fernández M, Ruiz A, Alvarez I, Aguilar M, Pastor P, Rutledge J, Oh H, Wilson E, Le Guen Y, Khalid R, Robins C, Pulford D, Ibanez L, Wyss-Coray T, Ju Sung Y. Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures for asymptomatic and symptomatic Alzheimer's disease. RESEARCH SQUARE 2024:rs.3.rs-3631708. [PMID: 38410465 PMCID: PMC10896368 DOI: 10.21203/rs.3.rs-3631708/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Changes in Amyloid-β (A), hyperphosphorylated Tau (T) in brain and cerebrospinal fluid (CSF) precedes AD symptoms, making CSF proteome a potential avenue to understand the pathophysiology and facilitate reliable diagnostics and therapies. Using the AT framework and a three-stage study design (discovery, replication, and meta-analysis), we identified 2,173 proteins dysregulated in AD, that were further validated in a third totally independent cohort. Machine learning was implemented to create and validate highly accurate and replicable (AUC>0.90) models that predict AD biomarker positivity and clinical status. These models can also identify people that will convert to AD and those AD cases with faster progression. The associated proteins cluster in four different protein pseudo-trajectories groups spanning the AD continuum and were enrichment in specific pathways including neuronal death, apoptosis and tau phosphorylation (early stages), microglia dysregulation and endolysosomal dysfuncton(mid-stages), brain plasticity and longevity (mid-stages) and late microglia-neuron crosstalk (late stages).
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Affiliation(s)
| | | | | | - Anh Do
- Washington University School of Medicine
| | - Lihua Wang
- Washington University School of Medicine
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | | | | | | | | | | | - Ignacio Alvarez
- Fundació Docència i Recerca MútuaTerrassa, Terrassa, Barcelona, Spain
| | | | - Pau Pastor
- University Hospital Germans Trias i Pujol
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Ali M, Huarte OU, Heurtaux T, Garcia P, Rodriguez BP, Grzyb K, Halder R, Skupin A, Buttini M, Glaab E. Single-Cell Transcriptional Profiling and Gene Regulatory Network Modeling in Tg2576 Mice Reveal Gender-Dependent Molecular Features Preceding Alzheimer-Like Pathologies. Mol Neurobiol 2024; 61:541-566. [PMID: 35980567 PMCID: PMC10861719 DOI: 10.1007/s12035-022-02985-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 07/29/2022] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) onset and progression is influenced by a complex interplay of several environmental and genetic factors, one of them gender. Pronounced gender differences have been observed both in the relative risk of developing AD and in clinical disease manifestations. A molecular level understanding of these gender disparities is still missing, but could provide important clues on cellular mechanisms modulating the disease and reveal new targets for gender-oriented disease-modifying precision therapies. We therefore present here a comprehensive single-cell analysis of disease-associated molecular gender differences in transcriptomics data from the neocortex, one of the brain regions most susceptible to AD, in one of the most widely used AD mouse models, the Tg2576 model. Cortical areas are also most commonly used in studies of post-mortem AD brains. To identify disease-linked molecular processes that occur before the onset of detectable neuropathology, we focused our analyses on an age with no detectable plaques and microgliosis. Cell-type specific alterations were investigated at the level of individual genes, pathways, and gene regulatory networks. The number of differentially expressed genes (DEGs) was not large enough to build context-specific gene regulatory networks for each individual cell type, and thus, we focused on the study of cell types with dominant changes and included analyses of changes across the combination of cell types. We observed significant disease-associated gender differences in cellular processes related to synapse organization and reactive oxygen species metabolism, and identified a limited set of transcription factors, including Egr1 and Klf6, as key regulators of many of the disease-associated and gender-dependent gene expression changes in the model. Overall, our analyses revealed significant cell-type specific gene expression changes in individual genes, pathways and sub-networks, including gender-specific and gender-dimorphic changes in both upstream transcription factors and their downstream targets, in the Tg2576 AD model before the onset of overt disease. This opens a window into molecular events that could determine gender-susceptibility to AD, and uncovers tractable target candidates for potential gender-specific precision medicine for AD.
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Affiliation(s)
- Muhammad Ali
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, 6200, Maastricht, the Netherlands
| | - Oihane Uriarte Huarte
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
| | - Tony Heurtaux
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, L‑4362, Esch-Sur-Alzette, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
| | - Beatriz Pardo Rodriguez
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
- University of the Basque Country, Cell Biology and Histology Department, 48940, Leioa, Vizcaya, Basque Country, Spain
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Physics and Materials Science, University of Luxembourg, 162a av. de la Faïencerie, 1511, Luxembourg, Luxembourg
- Department of Neuroscience, University of California San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.
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Sameni M, Mirmotalebisohi SA, Dehghan Z, Abooshahab R, Khazaei-Poul Y, Mozafar M, Zali H. Deciphering molecular mechanisms of SARS-CoV-2 pathogenesis and drug repurposing through GRN motifs: a comprehensive systems biology study. 3 Biotech 2023; 13:117. [PMID: 37070032 PMCID: PMC10090260 DOI: 10.1007/s13205-023-03518-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/13/2023] [Indexed: 03/28/2023] Open
Abstract
The world has recently been plagued by a new coronavirus infection called SARS-CoV-2. This virus may lead to severe acute respiratory syndrome followed by multiple organ failure. SARS-CoV-2 has approximately 80-90% genetic similarity to SARS-CoV. Given the limited omics data available for host response to the viruses (more limited data for SARS-CoV-2), we attempted to unveil the crucial molecular mechanisms underlying the SARS-CoV-2 pathogenesis by comparing its regulatory network motifs with SARS-CoV. We also attempted to identify the non-shared crucial molecules and their functions to predict the specific mechanisms for each infection and the processes responsible for their different manifestations. Deciphering the crucial shared and non-shared mechanisms at the molecular level and signaling pathways underlying both diseases may help shed light on their pathogenesis and pave the way for other new drug repurposing against COVID-19. We constructed the GRNs for host response to SARS-CoV and SARS-CoV-2 pathogens (in vitro) and identified the significant 3-node regulatory motifs by analyzing them topologically and functionally. We attempted to identify the shared and non-shared regulatory elements and signaling pathways between their host responses. Interestingly, our findings indicated that NFKB1, JUN, STAT1, FOS, KLF4, and EGR1 were the critical shared TFs between motif-related subnetworks in both SARS and COVID-1, which are considered genes with specific functions in the immune response. Enrichment analysis revealed that the NOD-like receptor signaling, TNF signaling, and influenza A pathway were among the first significant pathways shared between SARS and COVID-19 up-regulated DEGs networks, and the term "metabolic pathways" (hsa01100) among the down-regulated DEGs networks. WEE1, PMAIP1, and TSC22D2 were identified as the top three hubs specific to SARS. However, MYPN, SPRY4, and APOL6 were the tops specific to COVID-19 in vitro. The term "Complement and coagulation cascades" pathway was identified as the first top non-shared pathway for COVID-19 and the MAPK signaling pathway for SARS. We used the identified crucial DEGs to construct a drug-gene interaction network to propose some drug candidates. Zinc chloride, Fostamatinib, Copper, Tirofiban, Tretinoin, and Levocarnitine were the six drugs with higher scores in our drug-gene network analysis. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03518-x.
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Affiliation(s)
- Marzieh Sameni
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Yalda Khazaei-Poul
- Student Research Committee, Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Hakimeh Zali
- Proteomics Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Shah I, Bundy J, Chambers B, Everett LJ, Haggard D, Harrill J, Judson RS, Nyffeler J, Patlewicz G. Navigating Transcriptomic Connectivity Mapping Workflows to Link Chemicals with Bioactivities. Chem Res Toxicol 2022; 35:1929-1949. [PMID: 36301716 PMCID: PMC10483698 DOI: 10.1021/acs.chemrestox.2c00245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Screening new compounds for potential bioactivities against cellular targets is vital for drug discovery and chemical safety. Transcriptomics offers an efficient approach for assessing global gene expression changes, but interpreting chemical mechanisms from these data is often challenging. Connectivity mapping is a potential data-driven avenue for linking chemicals to mechanisms based on the observation that many biological processes are associated with unique gene expression signatures (gene signatures). However, mining the effects of a chemical on gene signatures for biological mechanisms is challenging because transcriptomic data contain thousands of noisy genes. New connectivity mapping approaches seeking to distinguish signal from noise continue to be developed, spurred by the promise of discovering chemical mechanisms, new drugs, and disease targets from burgeoning transcriptomic data. Here, we analyze these approaches in terms of diverse transcriptomic technologies, public databases, gene signatures, pattern-matching algorithms, and statistical evaluation criteria. To navigate the complexity of connectivity mapping, we propose a harmonized scheme to coherently organize and compare published workflows. We first standardize concepts underlying transcriptomic profiles and gene signatures based on various transcriptomic technologies such as microarrays, RNA-Seq, and L1000 and discuss the widely used data sources such as Gene Expression Omnibus, ArrayExpress, and MSigDB. Next, we generalize connectivity mapping as a pattern-matching task for finding similarity between a query (e.g., transcriptomic profile for new chemical) and a reference (e.g., gene signature of known target). Published pattern-matching approaches fall into two main categories: vector-based use metrics like correlation, Jaccard index, etc., and aggregation-based use parametric and nonparametric statistics (e.g., gene set enrichment analysis). The statistical methods for evaluating the performance of different approaches are described, along with comparisons reported in the literature on benchmark transcriptomic data sets. Lastly, we review connectivity mapping applications in toxicology and offer guidance on evaluating chemical-induced toxicity with concentration-response transcriptomic data. In addition to serving as a high-level guide and tutorial for understanding and implementing connectivity mapping workflows, we hope this review will stimulate new algorithms for evaluating chemical safety and drug discovery using transcriptomic data.
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Affiliation(s)
- Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Joseph Bundy
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Bryant Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Logan J. Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Derik Haggard
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Joshua Harrill
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Richard S. Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Johanna Nyffeler
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
- Oak Ridge Institute for Science and Education (ORISE) Postdoctoral Fellow, Oak Ridge, Tennessee, 37831, US
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure, Office of Research and Development, US. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
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Yang B, Bao W, Chen B, Song D. Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data. BioData Min 2022; 15:13. [PMID: 35690842 PMCID: PMC9188720 DOI: 10.1186/s13040-022-00297-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/22/2022] [Indexed: 11/30/2022] Open
Abstract
Single-cell RNA-seq overcomes the shortcomings of conventional transcriptome sequencing technology and could provide a powerful tool for distinguishing the transcriptome characteristics of various cell types in biological tissues, and comprehensively revealing the heterogeneity of gene expression between cells. Many Intelligent Computing methods have been presented to infer gene regulatory network (GRN) with single-cell RNA-seq data. In this paper, we investigate the performances of seven classifiers including support vector machine (SVM), random forest (RF), Naive Bayesian (NB), GBDT, logical regression (LR), decision tree (DT) and K-Nearest Neighbor (KNN) for solving the binary classification problems of GRN inference with single-cell RNA-seq data (Single_cell_GRN). In SVM, three different kernel functions (linear, polynomial and radial basis function) are utilized, respectively. Three real single-cell RNA-seq datasets from mouse and human are utilized. The experiment results prove that in most cases supervised learning methods (SVM, RF, NB, GBDT, LR, DT and KNN) perform better than unsupervised learning method (GENIE3) in terms of AUC. SVM, RF and KNN have the better performances than other four classifiers. In SVM, linear and polynomial kernels are more fit to model single-cell RNA-seq data.
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Affiliation(s)
- Bin Yang
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China
| | - Wenzheng Bao
- School of Information and Electrical Engineering, Xuzhou University of Technology, Xuzhou, 221018, China.
| | - Baitong Chen
- Xuzhou First People's Hospital, Xuzhou, 221000, China
| | - Dan Song
- School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, China.
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease. Nat Commun 2021; 12:4246. [PMID: 34253728 PMCID: PMC8275683 DOI: 10.1038/s41467-021-24470-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents. Traditional drug discovery process use differential, Bayesian and other network based approaches. We developed a Boolean approach for building disease maps and prioritizing pre-clinical models to discover a first-in-class therapy to restore and protect the leaky gut barrier in inflammatory bowel disease.
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10
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Gopal J, Prakash Sinnarasan VS, Venkatesan A. Identification of Repurpose Drugs by Computational Analysis of Disease-Gene-Drug Associations. J Comput Biol 2021; 28:975-984. [PMID: 34242526 DOI: 10.1089/cmb.2020.0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repurposing of marketed drugs to find new indications has become an alternative to circumvent the risk of traditional drug development by its productivity quality. Despite many approaches, computational analysis has great potential to fuel the development of all-rounder drugs to find new classes of medicine for neglected and rare disease. The genes that can explain variations in drug response associated to disease are more important and significant in drug therapeutics necessitate elucidating the relationships of a gene, drug, and disease. The proposed computational analysis facilitates the discovery of knowledge on both target and disease-based relationships from large sources of biomedical literature spread over different platforms. It uses the utility of text mining for automatic extraction of valuable aggregated biomedical entities (disease, gene, and drug) from PubMed to serves as an input to the analysis of association prediction. The top-ranked associations considered for identification of repurposing drugs and also the hidden associations identified using concurrence principle to extrapolate the new relationships. Such findings are reported as novel and contribute to the knowledge base for pharmacogenomics, would immensely support the discovery and progress of novel therapeutic pathways and patient segment biomarkers.
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Affiliation(s)
- Jeyakodi Gopal
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Amouda Venkatesan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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11
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Zhao BW, You ZH, Wong L, Zhang P, Li HY, Wang L. MGRL: Predicting Drug-Disease Associations Based on Multi-Graph Representation Learning. Front Genet 2021; 12:657182. [PMID: 34054920 PMCID: PMC8153989 DOI: 10.3389/fgene.2021.657182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Drug repositioning is an application-based solution based on mining existing drugs to find new targets, quickly discovering new drug-disease associations, and reducing the risk of drug discovery in traditional medicine and biology. Therefore, it is of great significance to design a computational model with high efficiency and accuracy. In this paper, we propose a novel computational method MGRL to predict drug-disease associations based on multi-graph representation learning. More specifically, MGRL first uses the graph convolution network to learn the graph representation of drugs and diseases from their self-attributes. Then, the graph embedding algorithm is used to represent the relationships between drugs and diseases. Finally, the two kinds of graph representation learning features were put into the random forest classifier for training. To the best of our knowledge, this is the first work to construct a multi-graph to extract the characteristics of drugs and diseases to predict drug-disease associations. The experiments show that the MGRL can achieve a higher AUC of 0.8506 based on five-fold cross-validation, which is significantly better than other existing methods. Case study results show the reliability of the proposed method, which is of great significance for practical applications.
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Affiliation(s)
- Bo-Wei Zhao
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China.,University of Chinese Academy of Sciences, Beijing, China.,Xinjiang Laboratory of Minority Speech and Language Information Processing, Ürümqi, China
| | - Zhu-Hong You
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China.,University of Chinese Academy of Sciences, Beijing, China.,Xinjiang Laboratory of Minority Speech and Language Information Processing, Ürümqi, China
| | - Leon Wong
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China.,University of Chinese Academy of Sciences, Beijing, China.,Xinjiang Laboratory of Minority Speech and Language Information Processing, Ürümqi, China
| | - Ping Zhang
- The School of Computer Sciences, BaoJi University of Arts and Sciences, Baoji, China
| | - Hao-Yuan Li
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
| | - Lei Wang
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Ürümqi, China.,University of Chinese Academy of Sciences, Beijing, China.,Xinjiang Laboratory of Minority Speech and Language Information Processing, Ürümqi, China
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12
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Guo Z, Fu Y, Huang C, Zheng C, Wu Z, Chen X, Gao S, Ma Y, Shahen M, Li Y, Tu P, Zhu J, Wang Z, Xiao W, Wang Y. NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:549-564. [PMID: 33744433 PMCID: PMC9040018 DOI: 10.1016/j.gpb.2020.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/04/2020] [Accepted: 09/24/2020] [Indexed: 10/31/2022]
Abstract
Rapid development of high-throughput technologies has permitted the identification of an increasing number of disease-associated genes (DAGs), which are important for understanding disease initiation and developing precision therapeutics. However, DAGs often contain large amounts of redundant or false positive information, leading to difficulties in quantifying and prioritizing potential relationships between these DAGs and human diseases. In this study, a network-oriented gene entropy approach (NOGEA) is proposed for accurately inferring master genes that contribute to specific diseases by quantitatively calculating their perturbation abilities on directed disease-specific gene networks. In addition, we confirmed that the master genes identified by NOGEA have a high reliability for predicting disease-specific initiation events and progression risk. Master genes may also be used to extract the underlying information of different diseases, thus revealing mechanisms of disease comorbidity. More importantly, approved therapeutic targets are topologically localized in a small neighborhood of master genes on the interactome network, which provides a new way for predicting drug-disease associations. Through this method, 11 old drugs were newly identified and predicted to be effective for treating pancreatic cancer and then validated by in vitro experiments. Collectively, the NOGEA was useful for identifying master genes that control disease initiation and co-occurrence, thus providing a valuable strategy for drug efficacy screening and repositioning. NOGEA codes are publicly available at https://github.com/guozihuaa/NOGEA.
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Affiliation(s)
- Zihu Guo
- College of Life Science, Northwest University, Xi'an 710069, China; College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Yingxue Fu
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Chao Huang
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Chunli Zheng
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Ziyin Wu
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Xuetong Chen
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Shuo Gao
- College of Life Science, Northwest A & F University, Yangling 712100, China
| | - Yaohua Ma
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Mohamed Shahen
- Zoology Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Faculty of Chemical, Environmental and Biological Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Pengfei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jingbo Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Zhenzhong Wang
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China
| | - Wei Xiao
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China.
| | - Yonghua Wang
- College of Life Science, Northwest University, Xi'an 710069, China; College of Life Science, Northwest A & F University, Yangling 712100, China; State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Lianyungang 222001, China.
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13
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Giovagnoni C, Ali M, Eijssen LMT, Maes R, Choe K, Mulder M, Kleinjans J, Del Sol A, Glaab E, Mastroeni D, Delvaux E, Coleman P, Losen M, Pishva E, Martinez-Martinez P, van den Hove DLA. Altered sphingolipid function in Alzheimer's disease; a gene regulatory network approach. Neurobiol Aging 2021; 102:178-187. [PMID: 33773368 DOI: 10.1016/j.neurobiolaging.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/04/2020] [Accepted: 02/02/2021] [Indexed: 10/22/2022]
Abstract
Sphingolipids (SLs) are bioactive lipids involved in various important physiological functions. The SL pathway has been shown to be affected in several brain-related disorders, including Alzheimer's disease (AD). Recent evidence suggests that epigenetic dysregulation plays an important role in the pathogenesis of AD as well. Here, we use an integrative approach to better understand the relationship between epigenetic and transcriptomic processes in regulating SL function in the middle temporal gyrus of AD patients. Transcriptomic analysis of 252 SL-related genes, selected based on GO term annotations, from 46 AD patients and 32 healthy age-matched controls, revealed 103 differentially expressed SL-related genes in AD patients. Additionally, methylomic analysis of the same subjects revealed parallel hydroxymethylation changes in PTGIS, GBA, and ITGB2 in AD. Subsequent gene regulatory network-based analysis identified 3 candidate genes, that is, SELPLG, SPHK1 and CAV1 whose alteration holds the potential to revert the gene expression program from a diseased towards a healthy state. Together, this epigenomic and transcriptomic approach highlights the importance of SL-related genes in AD, and may provide novel biomarkers and therapeutic alternatives to traditionally investigated biological pathways in AD.
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Affiliation(s)
- Caterina Giovagnoni
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands.
| | - Muhammad Ali
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Lars M T Eijssen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Richard Maes
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Monique Mulder
- Department of Internal Medicine, Division of Pharmacology, Vascular and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, the Netherlands
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Diego Mastroeni
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Elaine Delvaux
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Paul Coleman
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Mario Losen
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Ehsan Pishva
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Pilar Martinez-Martinez
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNs), Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Wuerzburg, Germany
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14
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Yang K, Lu K, Wu Y, Yu J, Liu B, Zhao Y, Chen J, Zhou X. A network-based machine-learning framework to identify both functional modules and disease genes. Hum Genet 2021; 140:897-913. [PMID: 33409574 DOI: 10.1007/s00439-020-02253-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
Disease gene identification is a critical step towards uncovering the molecular mechanisms of diseases and systematically investigating complex disease phenotypes. Despite considerable efforts to develop powerful computing methods, candidate gene identification remains a severe challenge owing to the connectivity of an incomplete interactome network, which hampers the discovery of true novel candidate genes. We developed a network-based machine-learning framework to identify both functional modules and disease candidate genes. In this framework, we designed a semi-supervised non-negative matrix factorization model to obtain the functional modules related to the diseases and genes. Of note, we proposed a disease gene-prioritizing method called MapGene that integrates the correlations from both functional modules and network closeness. Our framework identified a set of functional modules with highly functional homogeneity and close gene interactions. Experiments on a large-scale benchmark dataset showed that MapGene performs significantly better than the state-of-the-art algorithms. Further analysis demonstrates MapGene can effectively relieve the impact of the incompleteness of interactome networks and obtain highly reliable rankings of candidate genes. In addition, disease cases on Parkinson's disease and diabetes mellitus confirmed the generalization of MapGene for novel candidate gene identification. This work proposed, for the first time, an integrated computing framework to predict both functional modules and disease candidate genes. The methodology and results support that our framework has the potential to help discover underlying functional modules and reliable candidate genes in human disease.
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Affiliation(s)
- Kuo Yang
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China.,Institute for TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, 10084, China
| | - Kezhi Lu
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China.,imec-DistriNet, KU Leuven, Leuven, 3001, Belgium
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jian Yu
- Beijing Key Laboratory of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, Beijing, 100044, China
| | - Baoyan Liu
- Data Center of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jianxin Chen
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xuezhong Zhou
- School of Computer and Information Technology, Institute of Medical Intelligence, Beijing Jiaotong University, Beijing, 100044, China. .,Data Center of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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15
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Yu Z, Huang F, Zhao X, Xiao W, Zhang W. Predicting drug-disease associations through layer attention graph convolutional network. Brief Bioinform 2020; 22:5918381. [PMID: 33078832 DOI: 10.1093/bib/bbaa243] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/16/2020] [Accepted: 08/31/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Determining drug-disease associations is an integral part in the process of drug development. However, the identification of drug-disease associations through wet experiments is costly and inefficient. Hence, the development of efficient and high-accuracy computational methods for predicting drug-disease associations is of great significance. RESULTS In this paper, we propose a novel computational method named as layer attention graph convolutional network (LAGCN) for the drug-disease association prediction. Specifically, LAGCN first integrates the known drug-disease associations, drug-drug similarities and disease-disease similarities into a heterogeneous network, and applies the graph convolution operation to the network to learn the embeddings of drugs and diseases. Second, LAGCN combines the embeddings from multiple graph convolution layers using an attention mechanism. Third, the unobserved drug-disease associations are scored based on the integrated embeddings. Evaluated by 5-fold cross-validations, LAGCN achieves an area under the precision-recall curve of 0.3168 and an area under the receiver-operating characteristic curve of 0.8750, which are better than the results of existing state-of-the-art prediction methods and baseline methods. The case study shows that LAGCN can discover novel associations that are not curated in our dataset. CONCLUSION LAGCN is a useful tool for predicting drug-disease associations. This study reveals that embeddings from different convolution layers can reflect the proximities of different orders, and combining the embeddings by the attention mechanism can improve the prediction performances.
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Affiliation(s)
- Zhouxin Yu
- College of Informatics, Huazhong Agricultural University
| | - Feng Huang
- College of Informatics, Huazhong Agricultural University
| | - Xiaohan Zhao
- College of Informatics, Huazhong Agricultural University
| | | | - Wen Zhang
- College of Informatics, Huazhong Agricultural University
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16
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Fernando PC, Mabee PM, Zeng E. Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. BMC Bioinformatics 2020; 21:442. [PMID: 33028186 PMCID: PMC7542696 DOI: 10.1186/s12859-020-03773-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 09/22/2020] [Indexed: 01/04/2023] Open
Abstract
Background Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein–protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. Moreover, PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes. Therefore, we developed an integrative framework to improve the candidate gene prediction accuracy for anatomical entities by combining existing experimental knowledge about gene-anatomical entity relationships with PPI networks using anatomy ontology annotations. We hypothesized that this integration improves the quality of the PPI networks by reducing the number of false positive and false negative interactions and is better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These anatomy-based gene networks were semantic networks, as they were constructed based on the anatomy ontology annotations that were obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions. Results According to evaluations of candidate gene prediction performance tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks, which were semantically improved PPI networks, showed better performances by having higher area under the curve values for receiver operating characteristic and precision-recall curves than PPI networks for both zebrafish and mouse. Conclusion Integration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improved the candidate gene prediction accuracy and optimized them for predicting candidate genes for anatomical entities.
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Affiliation(s)
- Pasan C Fernando
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA.,National Ecological Observatory Network, Battelle Memorial Institute, 1685 38th St., Suite 100, Boulder, CO, 80301, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA. .,Department of Preventive and Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA. .,Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA. .,Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA.
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17
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Khorsand B, Savadi A, Naghibzadeh M. Comprehensive host-pathogen protein-protein interaction network analysis. BMC Bioinformatics 2020; 21:400. [PMID: 32912135 PMCID: PMC7488060 DOI: 10.1186/s12859-020-03706-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Infectious diseases are a cruel assassin with millions of victims around the world each year. Understanding infectious mechanism of viruses is indispensable for their inhibition. One of the best ways of unveiling this mechanism is to investigate the host-pathogen protein-protein interaction network. In this paper we try to disclose many properties of this network. We focus on human as host and integrate experimentally 32,859 interaction between human proteins and virus proteins from several databases. We investigate different properties of human proteins targeted by virus proteins and find that most of them have a considerable high centrality scores in human intra protein-protein interaction network. Investigating human proteins network properties which are targeted by different virus proteins can help us to design multipurpose drugs. RESULTS As host-pathogen protein-protein interaction network is a bipartite network and centrality measures for this type of networks are scarce, we proposed seven new centrality measures for analyzing bipartite networks. Applying them to different virus strains reveals unrandomness of attack strategies of virus proteins which could help us in drug design hence elevating the quality of life. They could also be used in detecting host essential proteins. Essential proteins are those whose functions are critical for survival of its host. One of the proposed centralities named diversity of predators, outperforms the other existing centralities in terms of detecting essential proteins and could be used as an optimal essential proteins' marker. CONCLUSIONS Different centralities were applied to analyze human protein-protein interaction network and to detect characteristics of human proteins targeted by virus proteins. Moreover, seven new centralities were proposed to analyze host-pathogen protein-protein interaction network and to detect pathogens' favorite host protein victims. Comparing different centralities in detecting essential proteins reveals that diversity of predator (one of the proposed centralities) is the best essential protein marker.
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Affiliation(s)
- Babak Khorsand
- Computer Engineering Department, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abdorreza Savadi
- Computer Engineering Department, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
- Ferdowsi University of Mashhad, Azadi Square, Mashhad, 9177948974 Iran
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18
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Li Q, Dai W, Liu J, Sang Q, Li YX, Li YY. Gene dysregulation analysis builds a mechanistic signature for prognosis and therapeutic benefit in colorectal cancer. J Mol Cell Biol 2020; 12:881-893. [PMID: 32717065 PMCID: PMC7883816 DOI: 10.1093/jmcb/mjaa041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/09/2022] Open
Abstract
The implementation of cancer precision medicine requires biomarkers or signatures for predicting prognosis and therapeutic benefits. Most of current efforts in this field are paying much more attention to predictive accuracy than to molecular mechanistic interpretability. Mechanism-driven strategy has recently emerged, aiming to build signatures with both predictive power and explanatory power. Driven by this strategy, we developed a robust gene dysregulation analysis framework with machine learning algorithms, which is capable of exploring gene dysregulations underlying carcinogenesis from high-dimensional data with cooperativity and synergy between regulators and several other transcriptional regulation rules taken into consideration. We then applied the framework to a colorectal cancer (CRC) cohort from The Cancer Genome Atlas. The identified CRC-related dysregulations significantly covered known carcinogenic processes and exhibited good prognostic effect. By choosing dysregulations with greedy strategy, we built a four-dysregulation (4-DysReg) signature, which has the capability of predicting prognosis and adjuvant chemotherapy benefit. 4-DysReg has the potential to explain carcinogenesis in terms of dysfunctional transcriptional regulation. These results demonstrate that our gene dysregulation analysis framework could be used to develop predictive signature with mechanistic interpretability for cancer precision medicine, and furthermore, elucidate the mechanisms of carcinogenesis.
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Affiliation(s)
- Quanxue Li
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Wentao Dai
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Jixiang Liu
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Qingqing Sang
- Department of Surgery, Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi-Xue Li
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
| | - Yuan-Yuan Li
- Shanghai Center for Bioinformation Technology, Shanghai 201203, China.,Shanghai Engineering Research Center of Pharmaceutical Translation and Shanghai Industrial Technology Institute, Shanghai 201203, China
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19
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Shafiekhani S, Shafiekhani M, Rahbar S, Jafari AH. Extended Robust Boolean Network of Budding Yeast Cell Cycle. JOURNAL OF MEDICAL SIGNALS & SENSORS 2020; 10:94-104. [PMID: 32676445 PMCID: PMC7359953 DOI: 10.4103/jmss.jmss_40_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/22/2019] [Accepted: 10/20/2019] [Indexed: 11/17/2022]
Abstract
Background: How to explore the dynamics of transition probabilities between phases of budding yeast cell cycle (BYCC) network based on the dynamics of protein activities that control this network? How to identify the robust structure of protein interactions of BYCC Boolean network (BN)? Budding yeast allows scientists to put experiments into effect in order to discover the intracellular cell cycle regulating structures which are well simulated by mathematical modeling. Methods: We extended an available deterministic BN of proteins responsible for the cell cycle to a Markov chain model containing apoptosis besides G1, S, G2, M, and stationary G1. Using genetic algorithm (GA), we estimated the kinetic parameters of the extended BN model so that the subsequent transition probabilities derived using Markov chain model of cell states as normal cell cycle becomes the maximum while the structure of chemical interactions of extended BN of cell cycle becomes more stable. Results: Using kinetic parameters optimized by GA, the probability of the subsequent transitions between cell cycle phases is maximized. The relative basin size of stationary G1 increased from 86% to 96.48% while the number of attractors decreased from 7 in the original model to 5 in the extended one. Hence, an increase in the robustness of the system has been achieved. Conclusion: The structure of interacting proteins in cell cycle network affects its robustness and probabilities of transitions between different cell cycle phases. Markov chain and BN are good approaches to study the stability and dynamics of the cell cycle network.
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Affiliation(s)
- Sajad Shafiekhani
- Department of Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Biomedical Technologies and Robotics, Tehran University of Medical Sciences, Tehran, Iran.,Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojtaba Shafiekhani
- Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Sara Rahbar
- Department of Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Biomedical Technologies and Robotics, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Homayoun Jafari
- Department of Biomedical Engineering, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Biomedical Technologies and Robotics, Tehran University of Medical Sciences, Tehran, Iran
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20
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Zhang S, Li X, Lin Q, Lin J, Wong KC. Uncovering the key dimensions of high-throughput biomolecular data using deep learning. Nucleic Acids Res 2020; 48:e56. [PMID: 32232416 PMCID: PMC7261195 DOI: 10.1093/nar/gkaa191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 01/09/2023] Open
Abstract
Recent advances in high-throughput single-cell RNA-seq have enabled us to measure thousands of gene expression levels at single-cell resolution. However, the transcriptomic profiles are high-dimensional and sparse in nature. To address it, a deep learning framework based on auto-encoder, termed DeepAE, is proposed to elucidate high-dimensional transcriptomic profiling data in an encode-decode manner. Comparative experiments were conducted on nine transcriptomic profiling datasets to compare DeepAE with four benchmark methods. The results demonstrate that the proposed DeepAE outperforms the benchmark methods with robust performance on uncovering the key dimensions of single-cell RNA-seq data. In addition, we also investigate the performance of DeepAE in other contexts and platforms such as mass cytometry and metabolic profiling in a comprehensive manner. Gene ontology enrichment and pathology analysis are conducted to reveal the mechanisms behind the robust performance of DeepAE by uncovering its key dimensions.
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Affiliation(s)
- Shixiong Zhang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin 132000, China
| | - Qiuzhen Lin
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
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21
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Kale VP, Habib H, Chitren R, Patel M, Pramanik KC, Jonnalagadda SC, Challagundla K, Pandey MK. Old drugs, new uses: Drug repurposing in hematological malignancies. Semin Cancer Biol 2020; 68:242-248. [PMID: 32151704 DOI: 10.1016/j.semcancer.2020.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/16/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022]
Abstract
Discovery and development of novel anti-cancer drugs are expensive and time consuming. Systems biology approaches have revealed that a drug being developed for a non-cancer indication can hit other targets as well, which play critical roles in cancer progression. Since drugs for non-cancer indications would have already gone through the preclinical and partial or full clinical development, repurposing such drugs for hematological malignancies would cost much less, and drastically reduce the development time, which is evident in case of thalidomide. Here, we have reviewed some of the drugs for their potential to repurpose for treating the hematological malignancies. We have also enlisted resources that can be helpful in drug repurposing.
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Affiliation(s)
- Vijay P Kale
- Clinical and Nonclinical Research, Battelle Memorial Institute, Columbus, OH, USA
| | - Hasan Habib
- School of Osteopathic Medicine, Stratford, NJ, USA
| | - Robert Chitren
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA; Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ, USA
| | - Milan Patel
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Kartick C Pramanik
- Department of Pharmacology, Kentucky College of Osteopathic Medicine (KYCOM), University of Pikeville, KY, USA
| | | | - Kishore Challagundla
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Manoj K Pandey
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
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22
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Yang K, Wang R, Liu G, Shu Z, Wang N, Zhang R, Yu J, Chen J, Li X, Zhou X. HerGePred: Heterogeneous Network Embedding Representation for Disease Gene Prediction. IEEE J Biomed Health Inform 2020; 23:1805-1815. [PMID: 31283472 DOI: 10.1109/jbhi.2018.2870728] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The discovery of disease-causing genes is a critical step towards understanding the nature of a disease and determining a possible cure for it. In recent years, many computational methods to identify disease genes have been proposed. However, making full use of disease-related (e.g., symptoms) and gene-related (e.g., gene ontology and protein-protein interactions) information to improve the performance of disease gene prediction is still an issue. Here, we develop a heterogeneous disease-gene-related network (HDGN) embedding representation framework for disease gene prediction (called HerGePred). Based on this framework, a low-dimensional vector representation (LVR) of the nodes in the HDGN can be obtained. Then, we propose two specific algorithms, namely, an LVR-based similarity prediction and a random walk with restart on a reconstructed heterogeneous disease-gene network (RW-RDGN), to predict disease genes with high performance. First, to validate the rationality of the framework, we analyze the similarity-based overlap distribution of disease pairs and design an experiment for disease-gene association recovery, the results of which revealed that the LVR of nodes performs well at preserving the local and global network structure of the HDGN. Then, we apply tenfold cross validation and external validation to compare our methods with other well-known disease gene prediction algorithms. The experimental results show that the RW-RDGN performs better than the state-of-the-art algorithm. The prediction results of disease candidate genes are essential for molecular mechanism investigation and experimental validation. The source codes of HerGePred and experimental data are available at https://github.com/yangkuoone/HerGePred.
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23
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Basha O, Argov CM, Artzy R, Zoabi Y, Hekselman I, Alfandari L, Chalifa-Caspi V, Yeger-Lotem E. Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes. Bioinformatics 2020; 36:2821-2828. [DOI: 10.1093/bioinformatics/btaa034] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 01/07/2020] [Accepted: 01/16/2020] [Indexed: 01/19/2023] Open
Abstract
Abstract
Motivation
Differential network analysis, designed to highlight network changes between conditions, is an important paradigm in network biology. However, differential network analysis methods have been typically designed to compare between two conditions and were rarely applied to multiple protein interaction networks (interactomes). Importantly, large-scale benchmarks for their evaluation have been lacking.
Results
Here, we present a framework for assessing the ability of differential network analysis of multiple human tissue interactomes to highlight tissue-selective processes and disorders. For this, we created a benchmark of 6499 curated tissue-specific Gene Ontology biological processes. We applied five methods, including four differential network analysis methods, to construct weighted interactomes for 34 tissues. Rigorous assessment of this benchmark revealed that differential analysis methods perform well in revealing tissue-selective processes (AUCs of 0.82–0.9). Next, we applied differential network analysis to illuminate the genes underlying tissue-selective hereditary disorders. For this, we curated a dataset of 1305 tissue-specific hereditary disorders and their manifesting tissues. Focusing on subnetworks containing the top 1% differential interactions in disease-relevant tissue interactomes revealed significant enrichment for disorder-causing genes in 18.6% of the cases, with a significantly high success rate for blood, nerve, muscle and heart diseases.
Summary
Altogether, we offer a framework that includes expansive manually curated datasets of tissue-selective processes and disorders to be used as benchmarks or to illuminate tissue-selective processes and genes. Our results demonstrate that differential analysis of multiple human tissue interactomes is a powerful tool for highlighting processes and genes with tissue-selective functionality and clinical impact.
Availability and implementation
Datasets are available as part of the Supplementary data.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Chanan M Argov
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Raviv Artzy
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Yazeed Zoabi
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Idan Hekselman
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Liad Alfandari
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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24
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Gomez-Giro G, Arias-Fuenzalida J, Jarazo J, Zeuschner D, Ali M, Possemis N, Bolognin S, Halder R, Jäger C, Kuper WFE, van Hasselt PM, Zaehres H, del Sol A, van der Putten H, Schöler HR, Schwamborn JC. Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis. Acta Neuropathol Commun 2019; 7:222. [PMID: 31888773 PMCID: PMC6937812 DOI: 10.1186/s40478-019-0871-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022] Open
Abstract
The juvenile form of neuronal ceroid Lipofuscinosis (JNCL) is the most common form within this group of rare lysosomal storage disorders, causing pediatric neurodegeneration. The genetic disorder, which is caused by recessive mutations affecting the CLN3 gene, features progressive vision loss, cognitive and motor decline and other psychiatric conditions, seizure episodes, leading to premature death. Animal models have traditionally aid the understanding of the disease mechanisms and pathology and are very relevant for biomarker research and therapeutic testing. Nevertheless, there is a need for establishing reliable and predictive human cellular models to study the disease. Since patient material, particularly from children, is scarce and difficult to obtain, we generated an engineered a CLN3-mutant isogenic human induced pluripotent stem cell (hiPSC) line carrying the c.1054C → T pathologic variant, using state of the art CRISPR/Cas9 technology. To prove the suitability of the isogenic pair to model JNCL, we screened for disease-specific phenotypes in non-neuronal two-dimensional cell culture models as well as in cerebral brain organoids. Our data demonstrates that the sole introduction of the pathogenic variant gives rise to classical hallmarks of JNCL in vitro. Additionally, we discovered an alteration of the splicing caused by this particular mutation. Next, we derived cerebral organoids and used them as a neurodevelopmental model to study the particular effects of the CLN3Q352X mutation during brain formation in the disease context. About half of the mutation -carrying cerebral organoids completely failed to develop normally. The other half, which escaped this severe defect were used for the analysis of more subtle alterations. In these escapers, whole-transcriptome analysis demonstrated early disease signatures, affecting pathways related to development, corticogenesis and synapses. Complementary metabolomics analysis confirmed decreased levels of cerebral tissue metabolites, some particularly relevant for synapse formation and neurotransmission, such as gamma-amino butyric acid (GABA). Our data suggests that a mutation in CLN3 severely affects brain development. Furthermore, before disease onset, disease -associated neurodevelopmental changes, particular concerning synapse formation and function, occur.
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25
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Lardenoije R, Roubroeks JAY, Pishva E, Leber M, Wagner H, Iatrou A, Smith AR, Smith RG, Eijssen LMT, Kleineidam L, Kawalia A, Hoffmann P, Luck T, Riedel-Heller S, Jessen F, Maier W, Wagner M, Hurlemann R, Kenis G, Ali M, del Sol A, Mastroeni D, Delvaux E, Coleman PD, Mill J, Rutten BPF, Lunnon K, Ramirez A, van den Hove DLA. Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood. Clin Epigenetics 2019; 11:164. [PMID: 31775875 PMCID: PMC6880587 DOI: 10.1186/s13148-019-0755-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/26/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Late-onset Alzheimer's disease (AD) is a complex multifactorial affliction, the pathogenesis of which is thought to involve gene-environment interactions that might be captured in the epigenome. The present study investigated epigenome-wide patterns of DNA methylation (5-methylcytosine, 5mC) and hydroxymethylation (5-hydroxymethylcytosine, 5hmC), as well as the abundance of unmodified cytosine (UC), in relation to AD. RESULTS We identified epigenetic differences in AD patients (n = 45) as compared to age-matched controls (n = 35) in the middle temporal gyrus, pertaining to genomic regions close to or overlapping with genes such as OXT (- 3.76% 5mC, pŠidák = 1.07E-06), CHRNB1 (+ 1.46% 5hmC, pŠidák = 4.01E-04), RHBDF2 (- 3.45% UC, pŠidák = 4.85E-06), and C3 (- 1.20% UC, pŠidák = 1.57E-03). In parallel, in an independent cohort, we compared the blood methylome of converters to AD dementia (n = 54) and non-converters (n = 42), at a preclinical stage. DNA methylation in the same region of the OXT promoter as found in the brain was found to be associated with subsequent conversion to AD dementia in the blood of elderly, non-demented individuals (+ 3.43% 5mC, pŠidák = 7.14E-04). CONCLUSIONS The implication of genome-wide significant differential methylation of OXT, encoding oxytocin, in two independent cohorts indicates it is a promising target for future studies on early biomarkers and novel therapeutic strategies in AD.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Janou A. Y. Roubroeks
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Markus Leber
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
| | - Holger Wagner
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Adam R. Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G. Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Lars M. T. Eijssen
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Luca Kleineidam
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Amit Kawalia
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
- Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH-4058 Basel, Switzerland
| | - Tobias Luck
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Frank Jessen
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
| | - Wolfgang Maier
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Michael Wagner
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - René Hurlemann
- Department of Psychiatry and Division of Medical Psychology, University of Bonn, 53105 Bonn, Germany
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Muhammad Ali
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Antonio del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russian Federation
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Dolgoprudny Bilbao, Spain
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Elaine Delvaux
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Paul D. Coleman
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
- Institute of Psychiatry, King’s College London, London, UK
| | - Bart P. F. Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Daniël L. A. van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
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Saganowski S, Bródka P, Koziarski M, Kazienko P. Analysis of group evolution prediction in complex networks. PLoS One 2019; 14:e0224194. [PMID: 31661495 PMCID: PMC6818769 DOI: 10.1371/journal.pone.0224194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 10/07/2019] [Indexed: 11/25/2022] Open
Abstract
In the world, in which acceptance and the identification with social communities are highly desired, the ability to predict the evolution of groups over time appears to be a vital but very complex research problem. Therefore, we propose a new, adaptable, generic, and multistage method for Group Evolution Prediction (GEP) in complex networks, that facilitates reasoning about the future states of the recently discovered groups. The precise GEP modularity enabled us to carry out extensive and versatile empirical studies on many real-world complex / social networks to analyze the impact of numerous setups and parameters like time window type and size, group detection method, evolution chain length, prediction models, etc. Additionally, many new predictive features reflecting the group state at a given time have been identified and tested. Some other research problems like enriching learning evolution chains with external data have been analyzed as well.
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Affiliation(s)
- Stanisław Saganowski
- Department of Computational Intelligence, Faculty of Computer Science and Management, Wrocław University of Science and Technology, Wrocław, Poland
- * E-mail:
| | - Piotr Bródka
- Department of Computational Intelligence, Faculty of Computer Science and Management, Wrocław University of Science and Technology, Wrocław, Poland
| | - Michał Koziarski
- Department of Electronics, Faculty of Computer Science, Electronics and Telecommunications, AGH University of Science and Technology, Kraków, Poland
| | - Przemysław Kazienko
- Department of Computational Intelligence, Faculty of Computer Science and Management, Wrocław University of Science and Technology, Wrocław, Poland
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27
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Sabetian S, Shamsir MS. Computer aided analysis of disease linked protein networks. Bioinformation 2019; 15:513-522. [PMID: 31485137 PMCID: PMC6704336 DOI: 10.6026/97320630015513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/26/2022] Open
Abstract
Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and analyzing the protein interaction network is being developed as a powerful approach to create network pharmacology toward detecting unknown genes and proteins associated with diseases. Discovery drug targets regarding therapeutic decisions are exciting outcomes of studying disease networks. Protein connections may be identified by experimental and recent new computational approaches. Due to difficulties in analyzing in-vivo proteins interactions, many researchers have encouraged improving computational methods to design protein interaction network. In this review, the experimental and computational approaches and also advantages and disadvantages of these methods regarding the identification of new interactions in a molecular mechanism have been reviewed. Systematic analysis of complex biological systems including network pharmacology and disease network has also been discussed in this review.
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Affiliation(s)
- Soudabeh Sabetian
- Department of Biological and Health Sciences, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia
- Infertility Research Center, Shiraz University, Shiraz 71454, Iran, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohd Shahir Shamsir
- Department of Biological and Health Sciences, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia
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28
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Sachdev K, Gupta MK. A comprehensive review of feature based methods for drug target interaction prediction. J Biomed Inform 2019; 93:103159. [PMID: 30926470 DOI: 10.1016/j.jbi.2019.103159] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/22/2022]
Abstract
Drug target interaction is a prominent research area in the field of drug discovery. It refers to the recognition of interactions between chemical compounds and the protein targets in the human body. Wet lab experiments to identify these interactions are expensive as well as time consuming. The computational methods of interaction prediction help limit the search space for these experiments. These computational methods can be divided into ligand based approaches, docking approaches and chemogenomic approaches. In this review, we aim to describe the various feature based chemogenomic methods for drug target interaction prediction. It provides a comprehensive overview of the various techniques, datasets, tools and metrics. The feature based methods have been categorized, explained and compared. A novel framework for drug target interaction prediction has also been proposed that aims to improve the performance of existing methods. To the best of our knowledge, this is the first comprehensive review focusing only on feature based methods of drug target interaction.
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Affiliation(s)
- Kanica Sachdev
- Computer Science and Engineering Department, SMVDU, J&K, India.
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29
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Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Dai P. A Comparative Study of Cluster Detection Algorithms in Protein-Protein Interaction for Drug Target Discovery and Drug Repurposing. Front Pharmacol 2019; 10:109. [PMID: 30837876 PMCID: PMC6389713 DOI: 10.3389/fphar.2019.00109] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
The interactions between drugs and their target proteins induce altered expression of genes involved in complex intracellular networks. The properties of these functional network modules are critical for the identification of drug targets, for drug repurposing, and for understanding the underlying mode of action of the drug. The topological modules generated by a computational approach are defined as functional clusters. However, the functions inferred for these topological modules extracted from a large-scale molecular interaction network, such as a protein–protein interaction (PPI) network, could differ depending on different cluster detection algorithms. Moreover, the dynamic gene expression profiles among tissues or cell types causes differential functional interaction patterns between the molecular components. Thus, the connections in the PPI network should be modified by the transcriptomic landscape of specific cell lines before producing topological clusters. Here, we systematically investigated the clusters of a cell-based PPI network by using four cluster detection algorithms. We subsequently compared the performance of these algorithms for target gene prediction, which integrates gene perturbation data with the cell-based PPI network using two drug target prioritization methods, shortest path and diffusion correlation. In addition, we validated the proportion of perturbed genes in clusters by finding candidate anti-breast cancer drugs and confirming our predictions using literature evidence and cases in the ClinicalTrials.gov. Our results indicate that the Walktrap (CW) clustering algorithm achieved the best performance overall in our comparative study.
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Affiliation(s)
- Jun Ma
- National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, China.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jenny Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Xin Men
- Shaanxi Microbiology Institute, Xi'an, China
| | | | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, China
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30
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Ma S, Jiang T, Jiang R. Constructing tissue-specific transcriptional regulatory networks via a Markov random field. BMC Genomics 2018; 19:884. [PMID: 30598101 PMCID: PMC6311931 DOI: 10.1186/s12864-018-5277-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recent advances in sequencing technologies have enabled parallel assays of chromatin accessibility and gene expression for major human cell lines. Such innovation provides a great opportunity to decode phenotypic consequences of genetic variation via the construction of predictive gene regulatory network models. However, there still lacks a computational method to systematically integrate chromatin accessibility information with gene expression data to recover complicated regulatory relationships between genes in a tissue-specific manner. RESULTS We propose a Markov random field (MRF) model for constructing tissue-specific transcriptional regulatory networks via integrative analysis of DNase-seq and RNA-seq data. Our method, named CSNets (cell-line specific regulatory networks), first infers regulatory networks for individual cell lines using chromatin accessibility information, and then fine-tunes these networks using the MRF based on pairwise similarity between cell lines derived from gene expression data. Using this method, we constructed regulatory networks specific to 110 human cell lines and 13 major tissues with the use of ENCODE data. We demonstrated the high quality of these networks via comprehensive statistical analysis based on ChIP-seq profiles, functional annotations, taxonomic analysis, and literature surveys. We further applied these networks to analyze GWAS data of Crohn's disease and prostate cancer. Results were either consistent with the literature or provided biological insights into regulatory mechanisms of these two complex diseases. The website of CSNets is freely available at http://bioinfo.au.tsinghua.edu.cn/jianglab/CSNETS/ . CONCLUSIONS CSNets demonstrated the power of joint analysis on epigenomic and transcriptomic data towards the accurate construction of gene regulatory network. Our work provides not only a useful resource of regulatory networks to the community, but also valuable experiences in methodology development for multi-omics data integration.
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Affiliation(s)
- Shining Ma
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program Stanford University, Stanford, CA 94305 USA
| | - Tao Jiang
- Ministry of Education Key Laboratory of Bioinformatics; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084 China
- Department of Computer Science and Engineering, University of California, Riverside, CA 92521 USA
| | - Rui Jiang
- Ministry of Education Key Laboratory of Bioinformatics; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084 China
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Duran‐Frigola M, Fernández‐Torras A, Bertoni M, Aloy P. Formatting biological big data for modern machine learning in drug discovery. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Miquel Duran‐Frigola
- Joint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology Barcelona Spain
| | - Adrià Fernández‐Torras
- Joint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology Barcelona Spain
| | - Martino Bertoni
- Joint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology Barcelona Spain
| | - Patrick Aloy
- Joint IRB‐BSC‐CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain
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32
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Wang F, Lei X, Wu FX. A Review of Drug Repositioning Based Chemical-induced Cell Line Expression Data. Curr Med Chem 2018; 27:5340-5350. [PMID: 30381060 DOI: 10.2174/0929867325666181101115801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 08/10/2018] [Accepted: 10/21/2018] [Indexed: 12/14/2022]
Abstract
Drug repositioning is an important area of biomedical research. The drug repositioning studies have shifted to computational approaches. Large-scale perturbation databases, such as the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures, contain a number of chemical-induced gene expression profiles and provide great opportunities for computational biology and drug repositioning. One reason is that the profiles provided by the Connectivity Map and the Library of Integrated Network-Based Cellular Signatures databases show an overall view of biological mechanism in drugs, diseases and genes. In this article, we provide a review of the two databases and their recent applications in drug repositioning.
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Affiliation(s)
- Fei Wang
- Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Fang-Xiang Wu
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, China
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33
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Skraly FA, Ambavaram MMR, Peoples O, Snell KD. Metabolic engineering to increase crop yield: From concept to execution. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:23-32. [PMID: 29907305 DOI: 10.1016/j.plantsci.2018.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 05/18/2023]
Abstract
Although the return on investment over the last 20 years for mass screening of individual plant genes to improve crop performance has been low, the investment in these activities was essential to establish the infrastructure and tools of modern plant genomics. Complex traits such as crop yield are likely multigenic, and the exhaustive screening of random gene combinations to achieve yield gains is not realistic. Clearly, smart approaches must be developed. In silico analyses of plant metabolism and gene networks can move a trait discovery program beyond trial-and-error approaches and towards rational design strategies. Metabolic models employing flux-balance analysis are useful to determine the contribution of individual genes to a trait, or to compare, optimize, or even design metabolic pathways. Regulatory association networks provide a transcriptome-based view of the plant and can lead to the identification of transcription factors that control expression of multiple genes affecting a trait. In this review, the use of these models from the perspective of an Ag innovation company's trait discovery and development program will be discussed. Important decisions that can have significant impacts on the cost and timeline to develop a commercial trait will also be presented.
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Affiliation(s)
- Frank A Skraly
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | | | - Oliver Peoples
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | - Kristi D Snell
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States.
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34
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De Bastiani MA, Pfaffenseller B, Klamt F. Master Regulators Connectivity Map: A Transcription Factors-Centered Approach to Drug Repositioning. Front Pharmacol 2018; 9:697. [PMID: 30034338 PMCID: PMC6043797 DOI: 10.3389/fphar.2018.00697] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/08/2018] [Indexed: 01/09/2023] Open
Abstract
Drug discovery is a very expensive and time-consuming endeavor. Fortunately, recent omics technologies and Systems Biology approaches introduced interesting new tools to achieve this task, facilitating the repurposing of already known drugs to new therapeutic assignments using gene expression data and bioinformatics. The inherent role of transcription factors in gene expression modulation makes them strong candidates for master regulators of phenotypic transitions. However, transcription factors expression itself usually does not reflect its activity changes due to post-transcriptional modifications and other complications. In this aspect, the use of high-throughput transcriptomic data may be employed to infer transcription factors-targets interactions and assess their activity through co-expression networks, which can be further used to search for drugs capable of reverting the gene expression profile of pathological phenotypes employing the connectivity maps paradigm. Following this idea, we argue that a module-oriented connectivity map approach using transcription factors-centered networks would aid the query for new repositioning candidates. Through a brief case study, we explored this idea in bipolar disorder, retrieving known drugs used in the usual clinical scenario as well as new candidates with potential therapeutic application in this disease. Indeed, the results of the case study indicate just how promising our approach may be to drug repositioning.
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Affiliation(s)
- Marco A De Bastiani
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Science and Technology for Translational Medicine, Porto Alegre, Brazil
| | - Bianca Pfaffenseller
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Molecular Psychiatry, Clinicas Hospital of Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabio Klamt
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Science and Technology for Translational Medicine, Porto Alegre, Brazil
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35
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Vasilevich A, de Boer J. Robot-scientists will lead tomorrow's biomaterials discovery. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018. [DOI: 10.1016/j.cobme.2018.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Jung S, Hartmann A, Del Sol A. RefBool: a reference-based algorithm for discretizing gene expression data. Bioinformatics 2018; 33:1953-1962. [PMID: 28334101 DOI: 10.1093/bioinformatics/btx111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
Motivation The identification of genes or molecular regulatory mechanisms implicated in biological processes often requires the discretization, and in particular booleanization, of gene expression measurements. However, currently used methods mostly classify each measurement into an active or inactive state regardless of its statistical support possibly leading to downstream analysis conclusions based on spurious booleanization results. Results In order to overcome the lack of certainty inherent in current methodologies and to improve the process of discretization, we introduce RefBool, a reference-based algorithm for discretizing gene expression data. Instead of requiring each measurement to be classified as active or inactive, RefBool allows for the classification of a third state that can be interpreted as an intermediate expression of genes. Furthermore, each measurement is associated to a p- and q-value indicating the significance of each classification. Validation of RefBool on a neuroepithelial differentiation study and subsequent qualitative and quantitative comparison against 10 currently used methods supports its advantages and shows clear improvements of resulting clusterings. Availability and Implementation The software is available as MATLAB files in the Supplementary Information and as an online repository ( https://github.com/saschajung/RefBool ). Contact antonio.delsol@uni.lu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sascha Jung
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Andras Hartmann
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
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37
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Lakiotaki K, Vorniotakis N, Tsagris M, Georgakopoulos G, Tsamardinos I. BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. Database (Oxford) 2018; 2018:4917852. [PMID: 29688366 PMCID: PMC5836265 DOI: 10.1093/database/bay011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 01/12/2023]
Abstract
Biotechnology revolution generates a plethora of omics data with an exponential growth pace. Therefore, biological data mining demands automatic, 'high quality' curation efforts to organize biomedical knowledge into online databases. BioDataome is a database of uniformly preprocessed and disease-annotated omics data with the aim to promote and accelerate the reuse of public data. We followed the same preprocessing pipeline for each biological mart (microarray gene expression, RNA-Seq gene expression and DNA methylation) to produce ready for downstream analysis datasets and automatically annotated them with disease-ontology terms. We also designate datasets that share common samples and automatically discover control samples in case-control studies. Currently, BioDataome includes ∼5600 datasets, ∼260 000 samples spanning ∼500 diseases and can be easily used in large-scale massive experiments and meta-analysis. All datasets are publicly available for querying and downloading via BioDataome web application. We demonstrate BioDataome's utility by presenting exploratory data analysis examples. We have also developed BioDataome R package found in: https://github.com/mensxmachina/BioDataome/.Database URL: http://dataome.mensxmachina.org/.
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Affiliation(s)
- Kleanthi Lakiotaki
- Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece
| | - Nikolaos Vorniotakis
- Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece
| | - Michail Tsagris
- Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece
| | - Georgios Georgakopoulos
- Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece
| | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Voutes Campus, 70013 Heraklion, Crete, Greece
- Gnosis Data Analysis PC, Palaiokapa 64, 71305 Heraklion, Crete, Greece
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38
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Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW. Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. Genome Res 2017; 27:1783-1794. [PMID: 29030469 PMCID: PMC5668937 DOI: 10.1101/gr.223313.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
Abstract
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators. Our data revealed the bifurcation and developmental tracks of the two NPC subpopulations, and we captured an early (24 h) transition phase that leads to alternative neuronal specifications. The consequent up-regulation and down-regulation of stage- and subpopulation-specific gene groups during the course of maturation revealed biological insights with regard to key regulatory transcription factors and lincRNAs that control cellular programs in the identified neuronal subpopulations.
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Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
| | - Piroon Jenjaroenpun
- Genome and Gene expression Data Analysis Division, Bioinformatics Institute, Singapore 138671
| | - Akshay Bhinge
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, Campus Belval, University of Luxembourg, L-4367 Luxembourg
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Vladimir A Kuznetsov
- Genome and Gene expression Data Analysis Division, Bioinformatics Institute, Singapore 138671
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
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39
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Angarica VE, Del Sol A. Bioinformatics Tools for Genome-Wide Epigenetic Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:489-512. [PMID: 28523562 DOI: 10.1007/978-3-319-53889-1_25] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epigenetics play a central role in the regulation of many important cellular processes, and dysregulations at the epigenetic level could be the source of serious pathologies, such as neurological disorders affecting brain development, neurodegeneration, and intellectual disability. Despite significant technological advances for epigenetic profiling, there is still a need for a systematic understanding of how epigenetics shapes cellular circuitry, and disease pathogenesis. The development of accurate computational approaches for analyzing complex epigenetic profiles is essential for disentangling the mechanisms underlying cellular development, and the intricate interaction networks determining and sensing chromatin modifications and DNA methylation to control gene expression. In this chapter, we review the recent advances in the field of "computational epigenetics," including computational methods for processing different types of epigenetic data, prediction of chromatin states, and study of protein dynamics. We also discuss how "computational epigenetics" has complemented the fast growth in the generation of epigenetic data for uncovering the main differences and similarities at the epigenetic level between individuals and the mechanisms underlying disease onset and progression.
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Affiliation(s)
- Vladimir Espinosa Angarica
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg.
| | - Antonio Del Sol
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, 4366 Belvaux, Luxembourg
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40
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Anderson WD, Vadigepalli R. Modeling cytokine regulatory network dynamics driving neuroinflammation in central nervous system disorders. DRUG DISCOVERY TODAY. DISEASE MODELS 2017; 19:59-67. [PMID: 28947907 PMCID: PMC5609716 DOI: 10.1016/j.ddmod.2017.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A central goal of pharmacological efforts to treat central nervous system (CNS) diseases is to develop systemic therapeutics that can restore CNS homeostasis. Achieving this goal requires a fundamental understanding of CNS function within the organismal context so as to leverage the mechanistic insights on the molecular basis of cellular and tissue functions towards novel drug target identification. The immune system constitutes a key link between the periphery and CNS, and many neurological disorders and neurodegenerative diseases are characterized by immune dysfunction. We review the salient opportunities for applying computational models to CNS disease research, and summarize relevant approaches from studies of immune function and neuroinflammation. While the accurate prediction of disease-related phenomena is often considered the central goal of modeling studies, we highlight the utility of computational modeling applications beyond making predictions, particularly for drawing counterintuitive insights from model-based analysis of multi-parametric and time series data sets.
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Affiliation(s)
- Warren D. Anderson
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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41
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Ayyildiz D, Gov E, Sinha R, Arga KY. Ovarian Cancer Differential Interactome and Network Entropy Analysis Reveal New Candidate Biomarkers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:285-294. [PMID: 28375712 DOI: 10.1089/omi.2017.0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ovarian cancer is one of the most common cancers and has a high mortality rate due to insidious symptoms and lack of robust diagnostics. A hitherto understudied concept in cancer pathogenesis may offer new avenues for innovation in ovarian cancer biomarker development. Cancer cells are characterized by an increase in network entropy, and several studies have exploited this concept to identify disease-associated gene and protein modules. We report in this study the changes in protein-protein interactions (PPIs) in ovarian cancer within a differential network (interactome) analysis framework utilizing the entropy concept and gene expression data. A compendium of six transcriptome datasets that included 140 samples from laser microdissected epithelial cells of ovarian cancer patients and 51 samples from healthy population was obtained from Gene Expression Omnibus, and the high confidence human protein interactome (31,465 interactions among 10,681 proteins) was used. The uncertainties of the up- or downregulation of PPIs in ovarian cancer were estimated through an entropy formulation utilizing combined expression levels of genes, and the interacting protein pairs with minimum uncertainty were identified. We identified 105 proteins with differential PPI patterns scattered in 11 modules, each indicating significantly affected biological pathways in ovarian cancer such as DNA repair, cell proliferation-related mechanisms, nucleoplasmic translocation of estrogen receptor, extracellular matrix degradation, and inflammation response. In conclusion, we suggest several PPIs as biomarker candidates for ovarian cancer and discuss their future biological implications as potential molecular targets for pharmaceutical development as well. In addition, network entropy analysis is a concept that deserves greater research attention for diagnostic innovation in oncology and tumor pathogenesis.
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Affiliation(s)
- Dilara Ayyildiz
- 1 Department of Bioengineering, Marmara University , Istanbul, Turkey .,2 Department of Biomedical Sciences and Biotechnology, University of Udine , Udine, Italy
| | - Esra Gov
- 1 Department of Bioengineering, Marmara University , Istanbul, Turkey .,3 Department of Bioengineering, Adana Science and Technology University , Adana, Turkey
| | - Raghu Sinha
- 4 Department of Biochemistry and Molecular Biology, Penn State College of Medicine , Hershey, Pennsylvania
| | - Kazim Yalcin Arga
- 1 Department of Bioengineering, Marmara University , Istanbul, Turkey
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42
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Manivannan J, Prashanth M, Saravana Kumar V, Shairam M, Subburaj J. Systems biological understanding of the regulatory network and the possible therapeutic strategies for vascular calcification. MOLECULAR BIOSYSTEMS 2016; 12:3683-3694. [PMID: 27752677 DOI: 10.1039/c6mb00557h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since there is no precise therapy for treating vascular calcification by directly targeting the vascular wall, we aim to unveil novel drug targets through mining the molecular effect of a high phosphate environment on vascular cells through computational methods. Here, we hypothesize that manipulation of the vascular pathogenic network by small molecule therapeutics predicted from prior knowledge might offer great promise. With this, we intend to understand the publicly available transcriptomic data of vascular smooth muscle cells and endothelial cells exposed to the high phosphate induced vascular calcification milieu and to re-examine the above published experiments for reasons different from those examined in the previous studies through multilevel systems biological understanding. Hence, in this study the differentially expressed genes were subjected to both upstream and downstream network analysis through multiple standalone software and web servers. To provide an insight into causal signaling, we simultaneously predicted upstream regulatory layers through transcription factor and kinome enrichment analysis. Moreover the possible systems pharmacological choices were presented in three ways as (1) drug induced expression modulation, (2) drugs that interact with upstream and downstream regulatory targets, (3) possible natural product therapeutics from target-compound relationship. Furthermore for validating the current study we have specifically evaluated the preventive effect of two predicted natural compounds in a bovine aortic calcification model. The overall observation predicts a few novel mechanisms that might be involved in vascular dysfunction and calcification in both cell types. Also, the systems pharmacological investigation provides clues for the possible therapeutic options along with validation. In conclusion, the current study indicates that reanalysis of transcriptomic data propels us to reposition the approved drugs and use natural compounds as novel therapeutic agents for vascular calcification.
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Affiliation(s)
- Jeganathan Manivannan
- AU-KBC Research Centre, MIT Campus-Anna University, Chrompet, Chennai-600044, Tamil Nadu, India.
| | - Manjunath Prashanth
- AU-KBC Research Centre, MIT Campus-Anna University, Chrompet, Chennai-600044, Tamil Nadu, India.
| | | | - Manickaraj Shairam
- AU-KBC Research Centre, MIT Campus-Anna University, Chrompet, Chennai-600044, Tamil Nadu, India.
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43
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He FQ, Ollert M. Network-Guided Key Gene Discovery for a Given Cellular Process. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016. [PMID: 27783134 DOI: 10.1007/10_2016_39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Identification of key genes for a given physiological or pathological process is an essential but still very challenging task for the entire biomedical research community. Statistics-based approaches, such as genome-wide association study (GWAS)- or quantitative trait locus (QTL)-related analysis have already made enormous contributions to identifying key genes associated with a given disease or phenotype, the success of which is however very much dependent on a huge number of samples. Recent advances in network biology, especially network inference directly from genome-scale data and the following-up network analysis, opens up new avenues to predict key genes driving a given biological process or cellular function. Here we review and compare the current approaches in predicting key genes, which have no chances to stand out by classic differential expression analysis, from gene-regulatory, protein-protein interaction, or gene expression correlation networks. We elaborate these network-based approaches mainly in the context of immunology and infection, and urge more usage of correlation network-based predictions. Such network-based key gene discovery approaches driven by information-enriched 'omics' data should be very useful for systematic key gene discoveries for any given biochemical process or cellular function, and also valuable for novel drug target discovery and novel diagnostic, prognostic and therapeutic-efficiency marker prediction for a specific disease or disorder.
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Affiliation(s)
- Feng Q He
- Department of Infection and Immunity, Group of Immune Systems Biology, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg.
| | - Markus Ollert
- Department of Infection and Immunity, Group of Allergy and Clinical Immunology, Luxembourg Institute of Health, 29, rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5000, Odense C, Denmark
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44
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Martin AJM, Dominguez C, Contreras-Riquelme S, Holmes DS, Perez-Acle T. Graphlet Based Metrics for the Comparison of Gene Regulatory Networks. PLoS One 2016; 11:e0163497. [PMID: 27695050 PMCID: PMC5047442 DOI: 10.1371/journal.pone.0163497] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/10/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding the control of gene expression remains one of the main challenges in the post-genomic era. Accordingly, a plethora of methods exists to identify variations in gene expression levels. These variations underlay almost all relevant biological phenomena, including disease and adaptation to environmental conditions. However, computational tools to identify how regulation changes are scarce. Regulation of gene expression is usually depicted in the form of a gene regulatory network (GRN). Structural changes in a GRN over time and conditions represent variations in the regulation of gene expression. Like other biological networks, GRNs are composed of basic building blocks called graphlets. As a consequence, two new metrics based on graphlets are proposed in this work: REConstruction Rate (REC) and REC Graphlet Degree (RGD). REC determines the rate of graphlet similarity between different states of a network and RGD identifies the subset of nodes with the highest topological variation. In other words, RGD discerns how th GRN was rewired. REC and RGD were used to compare the local structure of nodes in condition-specific GRNs obtained from gene expression data of Escherichia coli, forming biofilms and cultured in suspension. According to our results, most of the network local structure remains unaltered in the two compared conditions. Nevertheless, changes reported by RGD necessarily imply that a different cohort of regulators (i.e. transcription factors (TFs)) appear on the scene, shedding light on how the regulation of gene expression occurs when E. coli transits from suspension to biofilm. Consequently, we propose that both metrics REC and RGD should be adopted as a quantitative approach to conduct differential analyses of GRNs. A tool that implements both metrics is available as an on-line web server (http://dlab.cl/loto).
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Affiliation(s)
- Alberto J. M. Martin
- Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Chile
- * E-mail: (AJMM); (TPA)
| | - Calixto Dominguez
- Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Tomas Perez-Acle
- Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Chile
- * E-mail: (AJMM); (TPA)
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Espinosa Angarica V, del Sol A. Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation. Bioessays 2016; 38:758-68. [PMID: 27321053 PMCID: PMC5094535 DOI: 10.1002/bies.201600103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pluripotency can be considered a functional characteristic of pluripotent stem cells (PSCs) populations and their niches, rather than a property of individual cells. In this view, individual cells within the population independently adopt a variety of different expression states, maintained by different signaling, transcriptional, and epigenetics regulatory networks. In this review, we propose that generation of integrative network models from single cell data will be essential for getting a better understanding of the regulation of self-renewal and differentiation. In particular, we suggest that the identification of network stability determinants in these integrative models will provide important insights into the mechanisms mediating the transduction of signals from the niche, and how these signals can trigger differentiation. In this regard, the differential use of these stability determinants in subpopulation-specific regulatory networks would mediate differentiation into different cell fates. We suggest that this approach could offer a promising avenue for the development of novel strategies for increasing the efficiency and fidelity of differentiation, which could have a strong impact on regenerative medicine.
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Affiliation(s)
- Vladimir Espinosa Angarica
- Luxembourg Center for Systems Biomedicine (LCSB)University of Luxembourg, Campus BelvalBelvauxLuxembourg
| | - Antonio del Sol
- Luxembourg Center for Systems Biomedicine (LCSB)University of Luxembourg, Campus BelvalBelvauxLuxembourg
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