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Baruah B, Dutta MP, Banerjee S, Bhattacharyya DK. EnsemBic: An effective ensemble of biclustering to identify potential biomarkers of esophageal squamous cell carcinoma. Comput Biol Chem 2024; 110:108090. [PMID: 38759483 DOI: 10.1016/j.compbiolchem.2024.108090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/28/2024] [Accepted: 04/29/2024] [Indexed: 05/19/2024]
Abstract
The development of functionally enriched and biologically competent biclustering algorithm is essential for extracting hidden information from massive biological datasets. This paper presents a novel biclustering ensemble called EnsemBic based on p-value, which calculates the functional similarity of genetic associations. To validate the effectiveness and robustness of EnsemBic, we apply three well-known biclustering techniques, viz. Laplace Prior, iBBiG, and xMotif to implement EnsemBic and have been compared using different leading parameters. It is observed that the EnsemBic outperforms its competing algorithms in several prominent functional and biological measures. Next, the biclusters obtained from EnsemBic are used to identify potential biomarkers of Esophageal Squamous Cell Carcinoma (ESCC) by exploring topological and biological relevance with reference to the elite genes, attained from genecards. Finally, we discover that the genes F2RL3, APPL1, CALM1, IFNGR1, LPAR1, ANGPT2, ARPC2, CGN, CLDN7, ATP6V1C2, CEACAM1, FTL, PLAU,PSMB4, and EPHB2 carry both the topological and biological significance of previously established ESCC elite genes. Therefore, we declare the aforementioned genes as potential biomarkers of ESCC.
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Affiliation(s)
- Bikash Baruah
- Dept. of Computer Science and Engineering, NIT Arunachal Pradesh, India
| | - Manash P Dutta
- Dept. of Computer Science & Information Technology, Cotton University, Guwahati, Assam, India.
| | | | - Dhruba K Bhattacharyya
- Dept. of Computer Science and Engineering, Tezpur University, School of Engineering, Tezpur, India
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Chang LY, Lee MZ, Wu Y, Lee WK, Ma CL, Chang JM, Chen CW, Huang TC, Lee CH, Lee JC, Tseng YY, Lin CY. Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles. Nucleic Acids Res 2024; 52:e17. [PMID: 38096046 PMCID: PMC10853793 DOI: 10.1093/nar/gkad1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 02/10/2024] Open
Abstract
Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge.
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Affiliation(s)
- Lan-Yun Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Meng-Zhan Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Yujia Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Kai Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chia-Liang Ma
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Jun-Mao Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Ciao-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Tzu-Chun Huang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chia-Hwa Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, New Taipei City 235, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, New Taipei City 235, Taiwan
| | - Jih-Chin Lee
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 110, Taiwan
| | - Yu-Yao Tseng
- Department of Food Science, Nutrition, and Nutraceutical Biotechnology, Shih Chien University, Taipei 104, Taiwan
| | - Chun-Yu Lin
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Data Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Payra AK, Saha B, Ghosh A. MEM-FET: Essential protein prediction using membership feature and machine learning approach. Proteins 2024; 92:60-75. [PMID: 37638618 DOI: 10.1002/prot.26577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 02/21/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023]
Abstract
Proteins are played key roles in different functionalities in our daily life. All functional roles of a protein are a bit enhanced in interaction compared to individuals. Identification of essential proteins of an organism is a time consume and costly task during observation in the wet lab. The results of observation in wet lab always ensure high reliability and accuracy in the biological ground. Essential protein prediction using computational approaches is an alternative choice in research. It proves its significance rapidly in day-to-day life as well as reduces the experimental cost of wet lab effectively. Existing computational methods were implemented using Protein interaction networks (PPIN), Sequence, Gene Expression Dataset (GED), Gene Ontology (GO), Orthologous groups, and Subcellular localized datasets. Machine learning has diverse categories of features that enable to model and predict essential macromolecules of understudied organisms. A novel methodology MEM-FET (membership feature) is predicted based on features, that is, edge clustering coefficient, Average clustering coefficient, subcellular localization, and Gene Ontology within a compartment of common neighbors. The accuracy (ACC) values of the predicted true positive (TP) essential proteins are 0.79, 0.74, 0.78, and 0.71 for YHQ, YMIPS, YDIP, and YMBD datasets. An enriched set of essential proteins are also predicted using the MEM-FET algorithm. Ensemble ML also validated the proposed model with an accuracy of 60%. It has been predicted that MEM-FET algorithms outperform other existing algorithms with an ACC value of 80% for the yeast dataset.
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Affiliation(s)
- Anjan Kumar Payra
- Department of Computer Science and Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, Kolkata, India
| | - Banani Saha
- Department of Computer Science and Engineering, University of Calcutta, Kolkata, India
| | - Anupam Ghosh
- Department of Computer Science and Engineering, Netaji Subhash Engineering College, Kolkata, India
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Zhu X, Zhang Q, Du X, Jiang Y, Niu Y, Wei Y, Zhang Y, Chillrud SN, Liang D, Li H, Chen R, Kan H, Cai J. Respiratory Effects of Traffic-Related Air Pollution: A Randomized, Crossover Analysis of Lung Function, Airway Metabolome, and Biomarkers of Airway Injury. Environ Health Perspect 2023; 131:57002. [PMID: 37141245 PMCID: PMC10159268 DOI: 10.1289/ehp11139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 02/19/2023] [Accepted: 03/20/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Exposure to traffic-related air pollution (TRAP) has been associated with increased risks of respiratory diseases, but the biological mechanisms are not yet fully elucidated. OBJECTIVES Our aim was to evaluate the respiratory responses and explore potential biological mechanisms of TRAP exposure in a randomized crossover trial. METHODS We conducted a randomized crossover trial in 56 healthy adults. Each participant was exposed to high- and low-TRAP exposure sessions by walking in a park and down a road with high traffic volume for 4 h in random order. Respiratory symptoms and lung function, including forced expiratory volume in the first second (FEV 1 ), forced vital capacity (FVC), the ratio of FEV 1 to FVC, and maximal mid-expiratory flow (MMEF), were measured before and after each exposure session. Markers of 8-isoprostane, tumor necrosis factor- α (TNF- α ), and ezrin in exhaled breath condensate (EBC), and surfactant proteins D (SP-D) in serum were also measured. We used linear mixed-effects models to estimate the associations, adjusted for age, sex, body mass index, meteorological condition, and batch (only for biomarkers). Liquid chromatography-mass spectrometry was used to profile the EBC metabolome. Untargeted metabolome-wide association study (MWAS) analysis and pathway enrichment analysis using mummichog were performed to identify critical metabolomic features and pathways associated with TRAP exposure. RESULTS Participants had two to three times higher exposure to traffic-related air pollutants except for fine particulate matter while walking along the road compared with in the park. Compared with the low-TRAP exposure at the park, high-TRAP exposure at the road was associated with a higher score of respiratory symptoms [2.615 (95% CI: 0.605, 4.626), p = 1.2 × 10 - 2 ] and relatively lower lung function indicators [- 0.075 L (95% CI: - 0.138 , - 0.012 ), p = 2.1 × 10 - 2 ] for FEV 1 and - 0.190 L / s (95% CI: - 0.351 , - 0.029 ; p = 2.4 × 10 - 2 ) for MMEF]. Exposure to TRAP was significantly associated with changes in some, but not all, biomarkers, particularly with a 0.494 -ng / mL (95% CI: 0.297, 0.691; p = 9.5 × 10 - 6 ) increase for serum SP-D and a 0.123 -ng / mL (95% CI: - 0.208 , - 0.037 ; p = 7.2 × 10 - 3 ) decrease for EBC ezrin. Untargeted MWAS analysis revealed that elevated TRAP exposure was significantly associated with perturbations in 23 and 32 metabolic pathways under positive- and negative-ion modes, respectively. These pathways were most related to inflammatory response, oxidative stress, and energy use metabolism. CONCLUSIONS This study suggests that TRAP exposure might lead to lung function impairment and respiratory symptoms. Possible underlying mechanisms include lung epithelial injury, inflammation, oxidative stress, and energy metabolism disorders. https://doi.org/10.1289/EHP11139.
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Affiliation(s)
- Xinlei Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingli Zhang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xihao Du
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yixuan Jiang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yongjie Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yang Zhang
- Department of Systems Biology for Medicine, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Steven N. Chillrud
- Division of Geochemistry, Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Huichu Li
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- National Center for Children’s Health, Children’s Hospital of Fudan University, Shanghai, China
| | - Jing Cai
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Lu Y, Pang Z, Xia J. Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data. Brief Bioinform 2023; 24:bbac553. [PMID: 36572652 PMCID: PMC9851290 DOI: 10.1093/bib/bbac553] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/31/2022] [Accepted: 11/15/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses to exposures or interactions with microbial communities. However, biological interpretation of global metabolomics data remains a daunting task. Recent years have seen growing applications of pathway enrichment analysis based on putative annotations of liquid chromatography coupled with mass spectrometry (LC-MS) peaks for functional interpretation of LC-MS-based global metabolomics data. However, due to intricate peak-metabolite and metabolite-pathway relationships, considerable variations are observed among results obtained using different approaches. There is an urgent need to benchmark these approaches to inform the best practices. RESULTS We have conducted a benchmark study of common peak annotation approaches and pathway enrichment methods in current metabolomics studies. Representative approaches, including three peak annotation methods and four enrichment methods, were selected and benchmarked under different scenarios. Based on the results, we have provided a set of recommendations regarding peak annotation, ranking metrics and feature selection. The overall better performance was obtained for the mummichog approach. We have observed that a ~30% annotation rate is sufficient to achieve high recall (~90% based on mummichog), and using semi-annotated data improves functional interpretation. Based on the current platforms and enrichment methods, we further propose an identifiability index to indicate the possibility of a pathway being reliably identified. Finally, we evaluated all methods using 11 COVID-19 and 8 inflammatory bowel diseases (IBD) global metabolomics datasets.
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Affiliation(s)
- Yao Lu
- Department of Microbiology and Immunology, McGill University, Quebec, Canada
| | - Zhiqiang Pang
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Jianguo Xia
- Department of Microbiology and Immunology, McGill University, Quebec, Canada
- Institute of Parasitology, McGill University, Quebec, Canada
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Payra AK, Saha B, Ghosh A. MM-CCNB: Essential protein prediction using MAX-MIN strategies and compartment of common neighboring approach. Comput Methods Programs Biomed 2023; 228:107247. [PMID: 36427433 DOI: 10.1016/j.cmpb.2022.107247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/16/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND OBJECTIVE Proteins are indispensable for the flow of the life of living organisms. Protein pairs in interaction exhibit more functional activities than individuals. These activities have been considered an essential measure in predicting their essentiality. Neighborhood approaches have been used frequently in the prediction of essentiality scores. All paired neighbors of the essential proteins are nominated for the suitable candidate seeds for prediction. Still now Jaccard's coefficient is limited to predicting functions, homologous groups, sequence analysis, etc. It really motivate us to predict essential proteins efficiently using different computational approaches. METHODS In our work, we proposed modified Jaccard's coefficient to predict essential proteins. We have proposed a novel methodology for predicting essential proteins using MAX-MIN strategies and modified Jaccard's coefficient approach. RESULTS The performance of our proposed methodology has been analyzed for Saccharomyces cerevisiae datasets with an accuracy of more than 80%. It has been observed that the proposed algorithm is outperforms with an accuracy of 0.78, 0.74, 0.79, and 0.862 for YDIP, YMIPS, YHQ, and YMBD datasets respectivly. CONCLUSIONS There are several computational approaches in the existing state-of-art model of essential protein prediction. It has been noted that our predicted methodology outperforms other existing models viz. different centralities, local interaction density combined with protein complexes, modified monkey algorithm and ortho_sim_loc methods.
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Affiliation(s)
- Anjan Kumar Payra
- Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata 700074, India.
| | - Banani Saha
- Department of Computer Science & Engineering, University of Calcutta, Saltlake City Kolkata 700073, India
| | - Anupam Ghosh
- Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata 700152, India.
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Maghsoudi Z, Nguyen H, Tavakkoli A, Nguyen T. A comprehensive survey of the approaches for pathway analysis using multi-omics data integration. Brief Bioinform 2022; 23:6761962. [PMID: 36252928 PMCID: PMC9677478 DOI: 10.1093/bib/bbac435] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 02/07/2023] Open
Abstract
Pathway analysis has been widely used to detect pathways and functions associated with complex disease phenotypes. The proliferation of this approach is due to better interpretability of its results and its higher statistical power compared with the gene-level statistics. A plethora of pathway analysis methods that utilize multi-omics setup, rather than just transcriptomics or proteomics, have recently been developed to discover novel pathways and biomarkers. Since multi-omics gives multiple views into the same problem, different approaches are employed in aggregating these views into a comprehensive biological context. As a result, a variety of novel hypotheses regarding disease ideation and treatment targets can be formulated. In this article, we review 32 such pathway analysis methods developed for multi-omics and multi-cohort data. We discuss their availability and implementation, assumptions, supported omics types and databases, pathway analysis techniques and integration strategies. A comprehensive assessment of each method's practicality, and a thorough discussion of the strengths and drawbacks of each technique will be provided. The main objective of this survey is to provide a thorough examination of existing methods to assist potential users and researchers in selecting suitable tools for their data and analysis purposes, while highlighting outstanding challenges in the field that remain to be addressed for future development.
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Affiliation(s)
- Zeynab Maghsoudi
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Ha Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Alireza Tavakkoli
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557, Nevada, USA
| | - Tin Nguyen
- Corresponding author: Tin Nguyen, Department of Computer Science and Engineering, University of Nevada, Reno, NV, USA. Tel.: +1-775-784-6619;
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Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE. Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. Skelet Muscle 2022; 12:20. [PMID: 35971133 PMCID: PMC9377060 DOI: 10.1186/s13395-022-00303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in adult muscle satellite cells (SCs) within hours following muscle damage and is required for effective stem cell activation and muscle repair. However, why FOS is rapidly downregulated before SCs enter cell cycle as progenitor cells (i.e., transiently expressed) remains unclear. Further, whether boosting FOS levels in the proliferating progeny of SCs can enhance their myogenic properties needs further evaluation. METHODS We established an inducible, FOS expression system to evaluate the impact of persistent FOS activity in muscle progenitor cells ex vivo. We performed various assays to measure cellular proliferation and differentiation, as well as uncover changes in RNA levels and three-dimensional (3D) chromatin interactions. RESULTS Persistent FOS activity in primary muscle progenitor cells severely antagonizes their ability to differentiate and form myotubes within the first 2 weeks in culture. RNA-seq analysis revealed that ectopic FOS activity in muscle progenitor cells suppressed a global pro-myogenic transcriptional program, while activating a stress-induced, mitogen-activated protein kinase (MAPK) transcriptional signature. Additionally, we observed various FOS-dependent, chromosomal re-organization events in A/B compartments, topologically associated domains (TADs), and genomic loops near FOS-regulated genes. CONCLUSIONS Our results suggest that elevated FOS activity in recently activated muscle progenitor cells perturbs cellular differentiation by altering the 3D chromosome organization near critical pro-myogenic genes. This work highlights the crucial importance of tightly controlling FOS expression in the muscle lineage and suggests that in states of chronic stress or disease, persistent FOS activity in muscle precursor cells may disrupt the muscle-forming process.
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Affiliation(s)
- A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Gabriel Elizalde
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alfredo E Gonzalez
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kartik Soni
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: BioFrontiers and Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Albert E Almada
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA.
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA.
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Byrne DJ, Garcia-Pardo ME, Cole NB, Batnasan B, Heneghan S, Sohail A, Blackstone C, O'Sullivan NC. Liver X receptor-agonist treatment rescues degeneration in a Drosophila model of hereditary spastic paraplegia. Acta Neuropathol Commun 2022; 10:40. [PMID: 35346366 PMCID: PMC8961908 DOI: 10.1186/s40478-022-01343-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022] Open
Abstract
Hereditary spastic paraplegias (HSPs) are a group of inherited, progressive neurodegenerative conditions characterised by prominent lower-limb spasticity and weakness, caused by a length-dependent degeneration of the longest corticospinal upper motor neurons. While more than 80 spastic paraplegia genes (SPGs) have been identified, many cases arise from mutations in genes encoding proteins which generate and maintain tubular endoplasmic reticulum (ER) membrane organisation. The ER-shaping proteins are essential for the health and survival of long motor neurons, however the mechanisms by which mutations in these genes cause the axonopathy observed in HSP have not been elucidated. To further develop our understanding of the ER-shaping proteins, this study outlines the generation of novel in vivo and in vitro models, using CRISPR/Cas9-mediated gene editing to knockout the ER-shaping protein ADP-ribosylation factor-like 6 interacting protein 1 (ARL6IP1), mutations in which give rise to the HSP subtype SPG61. Loss of Arl6IP1 in Drosophila results in progressive locomotor deficits, emulating a key aspect of HSP in patients. ARL6IP1 interacts with ER-shaping proteins and is required for regulating the organisation of ER tubules, particularly within long motor neuron axons. Unexpectedly, we identified physical and functional interactions between ARL6IP1 and the phospholipid transporter oxysterol-binding protein-related protein 8 in both human and Drosophila model systems, pointing to a conserved role for ARL6IP1 in lipid homeostasis. Furthermore, loss of Arl6IP1 from Drosophila neurons results in a cell non-autonomous accumulation of lipid droplets in axonal glia. Importantly, treatment with lipid regulating liver X receptor-agonists blocked lipid droplet accumulation, restored axonal ER organisation, and improved locomotor function in Arl6IP1 knockout Drosophila. Our findings indicate that disrupted lipid homeostasis contributes to neurodegeneration in HSP, identifying a potential novel therapeutic avenue for the treatment of this disorder.
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Affiliation(s)
- Dwayne J Byrne
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - M Elena Garcia-Pardo
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Nelson B Cole
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Belguun Batnasan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sophia Heneghan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Anood Sohail
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Niamh C O'Sullivan
- UCD School of Biomolecular and Biomedical Sciences, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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Baruah B, Dutta MP, Bhattacharyya DK. Identification of ESCC potential biomarkers using biclustering algorithms. Gene Reports 2022. [DOI: 10.1016/j.genrep.2022.101563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022; 220:6516514. [PMID: 35380657 PMCID: PMC8982048 DOI: 10.1093/genetics/iyac005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.
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Affiliation(s)
- Mahima Vedi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L Hill
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ketaki Thorat
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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12
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Liany H, Lin Y, Jeyasekharan A, Rajan V. An Algorithm to Mine Therapeutic Motifs for Cancer from Networks of Genetic Interactions. IEEE J Biomed Health Inform 2022; 26:2830-2838. [PMID: 34990373 DOI: 10.1109/jbhi.2022.3141076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Study of pairwise genetic interactions, such as mutually exclusive mutations, has led to understanding of underlying mechanisms in cancer. Investigation of various combinatorial motifs within networks of such interactions can lead to deeper insights into its mutational landscape and inform therapy development. One such motif called the Between-Pathway Model (BPM) represents redundant or compensatory pathways that can be therapeutically exploited. Finding such BPM motifs is challenging since most formulations require solving variants of the NP-complete maximum weight bipartite subgraph problem. In this paper we design an algorithm based on Integer Linear Programming (ILP) to solve this problem. In our experiments, our approach outperforms the best previous method to mine BPM motifs. Further, our ILP-based approach allows us to easily model additional application-specific constraints. We illustrate this advantage through a new application of BPM motifs that can potentially aid in finding combination therapies to combat cancer.
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13
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Gundogdu P, Loucera C, Alamo-Alvarez I, Dopazo J, Nepomuceno I. Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data. BioData Min 2022; 15:1. [PMID: 34980200 PMCID: PMC8722116 DOI: 10.1186/s13040-021-00285-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background Single-cell RNA sequencing (scRNA-seq) data provide valuable insights into cellular heterogeneity which is significantly improving the current knowledge on biology and human disease. One of the main applications of scRNA-seq data analysis is the identification of new cell types and cell states. Deep neural networks (DNNs) are among the best methods to address this problem. However, this performance comes with the trade-off for a lack of interpretability in the results. In this work we propose an intelligible pathway-driven neural network to correctly solve cell-type related problems at single-cell resolution while providing a biologically meaningful representation of the data. Results In this study, we explored the deep neural networks constrained by several types of prior biological information, e.g. signaling pathway information, as a way to reduce the dimensionality of the scRNA-seq data. We have tested the proposed biologically-based architectures on thousands of cells of human and mouse origin across a collection of public datasets in order to check the performance of the model. Specifically, we tested the architecture across different validation scenarios that try to mimic how unknown cell types are clustered by the DNN and how it correctly annotates cell types by querying a database in a retrieval problem. Moreover, our approach demonstrated to be comparable to other less interpretable DNN approaches constrained by using protein-protein interactions gene regulation data. Finally, we show how the latent structure learned by the network could be used to visualize and to interpret the composition of human single cell datasets. Conclusions Here we demonstrate how the integration of pathways, which convey fundamental information on functional relationships between genes, with DNNs, that provide an excellent classification framework, results in an excellent alternative to learn a biologically meaningful representation of scRNA-seq data. In addition, the introduction of prior biological knowledge in the DNN reduces the size of the network architecture. Comparative results demonstrate a superior performance of this approach with respect to other similar approaches. As an additional advantage, the use of pathways within the DNN structure enables easy interpretability of the results by connecting features to cell functionalities by means of the pathway nodes, as demonstrated with an example with human melanoma tumor cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13040-021-00285-4.
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Affiliation(s)
- Pelin Gundogdu
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Inmaculada Alamo-Alvarez
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain
| | - Joaquin Dopazo
- Clinical Bioinformatics Area. Fundación Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain. .,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, 41013, Sevilla, Spain. .,Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, 41013, Sevilla, Spain. .,FPS/ELIXIR-es, Hospital Virgen del Rocío, 42013, Sevilla, Spain.
| | - Isabel Nepomuceno
- Department of Computer Languages and Systems, Universidad de Sevilla, Sevilla, Spain.
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14
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La Ferlita A, Alaimo S, Ferro A, Pulvirenti A. Pathway Analysis for Cancer Research and Precision Oncology Applications. Advances in Experimental Medicine and Biology 2022; 1361:143-161. [DOI: 10.1007/978-3-030-91836-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Pascual G, Domínguez D, Elosúa-Bayes M, Beckedorff F, Laudanna C, Bigas C, Douillet D, Greco C, Symeonidi A, Hernández I, Gil SR, Prats N, Bescós C, Shiekhattar R, Amit M, Heyn H, Shilatifard A, Benitah SA. Dietary palmitic acid promotes a prometastatic memory via Schwann cells. Nature 2021; 599:485-490. [PMID: 34759321 DOI: 10.1038/s41586-021-04075-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/30/2021] [Indexed: 11/09/2022]
Abstract
Fatty acid uptake and altered metabolism constitute hallmarks of metastasis1,2, yet evidence of the underlying biology, as well as whether all dietary fatty acids are prometastatic, is lacking. Here we show that dietary palmitic acid (PA), but not oleic acid or linoleic acid, promotes metastasis in oral carcinomas and melanoma in mice. Tumours from mice that were fed a short-term palm-oil-rich diet (PA), or tumour cells that were briefly exposed to PA in vitro, remained highly metastatic even after being serially transplanted (without further exposure to high levels of PA). This PA-induced prometastatic memory requires the fatty acid transporter CD36 and is associated with the stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A (as part of the COMPASS complex (Set1A/COMPASS)). Bulk, single-cell and positional RNA-sequencing analyses indicate that genes with this prometastatic memory predominantly relate to a neural signature that stimulates intratumoural Schwann cells and innervation, two parameters that are strongly correlated with metastasis but are aetiologically poorly understood3,4. Mechanistically, tumour-associated Schwann cells secrete a specialized proregenerative extracellular matrix, the ablation of which inhibits metastasis initiation. Both the PA-induced memory of this proneural signature and its long-term boost in metastasis require the transcription factor EGR2 and the glial-cell-stimulating peptide galanin. In summary, we provide evidence that a dietary metabolite induces stable transcriptional and chromatin changes that lead to a long-term stimulation of metastasis, and that this is related to a proregenerative state of tumour-activated Schwann cells.
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Affiliation(s)
- Gloria Pascual
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Diana Domínguez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Elosúa-Bayes
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carmelo Laudanna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Claudia Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Delphine Douillet
- Department of Biochemistry and Molecular Genetics and Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carolina Greco
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Aikaterini Symeonidi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Inmaculada Hernández
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sara Ruiz Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Coro Bescós
- Department of Oral and Maxillofacial Surgery, Vall D'Hebron Hospital, Barcelona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Moran Amit
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics and Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain.
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16
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Mandal K, Sarmah R, Bhattacharyya DK. POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:2659-2670. [PMID: 32175872 DOI: 10.1109/tcbb.2020.2980816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To understand the underlying biological mechanisms of gene expression data, it is important to discover the groups of genes that have similar expression patterns under certain subsets of conditions. Biclustering algorithms have been effective in analyzing large-scale gene expression data. Recently, traditional biclustering has been improved by introducing biological knowledge along with the expression data during the biclustering process. In this paper, we propose the Pathway-based Order Preserving Biclustering (POPBic) algorithm by incorporating Kyoto Encyclopedia of Genes and Genomes (KEGG) based on the hypothesis that two genes sharing similar pathways are likely to be similar. The basic principle of the POPBic approach is to apply the concept of Longest Common Subsequence between a pair of genes which have a high number of common pathways. The algorithm identifies the expression patterns from data using two major steps: (i) selection of significant seed genes and (ii) extraction of biclusters. We performe exhaustive experimentation with the POPBic algorithm using synthetic dataset to evaluate the bicluster model, finding its robustness in the presence of noise and identifying overlapping biclusters. We demonstrate that POPBic is able to discover biologically significant biclusters for four cancer microarray gene expression datasets. POPBic has been found to perform consistently well in comparison to its closest competitors.
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17
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Payra AK, Saha B, Ghosh A. Ortho_Sim_Loc: Essential protein prediction using orthology and priority-based similarity approach. Comput Biol Chem 2021; 92:107503. [PMID: 33962168 DOI: 10.1016/j.compbiolchem.2021.107503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 04/02/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Proteins are the essential macro-molecules of living organism. But all proteins cannot be considered as essential in different relevant studies. Essentiality of a protein is thus computed by computation methods rather than biological experiments which in turn save both time and effort. Different computational approaches are already predicted to select essential proteins successfully with different biological significances by researchers. Most of the experimental approaches return higher false negative outcomes with respect to others. In order to retain the prediction accuracy level, a novel methodology "Ortho_Sim_Loc"has been proposed which is a combined approach of Orthology, Similarity (using clustering and priority based GO-Annotation) and Subcellular localization. Ortho_Sim_Loc can predict enriched functional set essential proteins. The predicted results are validated with other existing methods like different centrality measures, LIDC. The validation results exhibits better performance of Ortho_Sim_Loc in compare to other existing computational approaches.
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Affiliation(s)
- Anjan Kumar Payra
- Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata, 700074, India.
| | - Banani Saha
- Department of Computer Science & Engineering, University of Calcutta, Saltlake City, Kolkata, 700073, India.
| | - Anupam Ghosh
- Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata, 700152, India.
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18
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Gueugneau M, Coudy-Gandilhon C, Chambon C, Verney J, Taillandier D, Combaret L, Polge C, Walrand S, Roche F, Barthélémy JC, Féasson L, Béchet D. Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men. Int J Mol Sci 2021; 22:4205. [PMID: 33921590 PMCID: PMC8074053 DOI: 10.3390/ijms22084205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
(1) Background: Aging is associated with a progressive decline in muscle mass and function. Aging is also a primary risk factor for metabolic syndrome, which further alters muscle metabolism. However, the molecular mechanisms involved remain to be clarified. Herein we performed omic profiling to decipher in muscle which dominating processes are associated with healthy aging and metabolic syndrome in old men. (2) Methods: This study included 15 healthy young, 15 healthy old, and 9 old men with metabolic syndrome. Old men were selected from a well-characterized cohort, and each vastus lateralis biopsy was used to combine global transcriptomic and proteomic analyses. (3) Results: Over-representation analysis of differentially expressed genes (ORA) and functional class scoring of pathways (FCS) indicated that healthy aging was mainly associated with upregulations of apoptosis and immune function and downregulations of glycolysis and protein catabolism. ORA and FCS indicated that with metabolic syndrome the dominating biological processes were upregulation of proteolysis and downregulation of oxidative phosphorylation. Proteomic profiling matched 586 muscle proteins between individuals. The proteome of healthy aging revealed modifications consistent with a fast-to-slow transition and downregulation of glycolysis. These transitions were reduced with metabolic syndrome, which was more associated with alterations in NADH/NAD+ shuttle and β-oxidation. Proteomic profiling further showed that all old muscles overexpressed protein chaperones to preserve proteostasis and myofiber integrity. There was also evidence of aging-related increases in reactive oxygen species but better detoxifications of cytotoxic aldehydes and membrane protection in healthy than in metabolic syndrome muscles. (4) Conclusions: Most candidate proteins and mRNAs identified herein constitute putative muscle biomarkers of healthy aging and metabolic syndrome in old men.
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Affiliation(s)
- Marine Gueugneau
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Coudy-Gandilhon
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Christophe Chambon
- Metabolomic and Proteomic Exploration Facility, Université Clermont Auvergne, INRAE, 63000 Clermont-Ferrand, France;
| | - Julien Verney
- Laboratoire AME2P, Université Clermont Auvergne, 3533 Clermont-Ferrand, France;
| | - Daniel Taillandier
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Lydie Combaret
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Cécile Polge
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Stéphane Walrand
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
| | - Frédéric Roche
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Jean-Claude Barthélémy
- Service de Physiologie Clinique et de l’Exercice, CHU Saint Etienne, 42055 Saint Etienne, France; (F.R.); (J.-C.B.)
- INSERM, SAINBIOSE, U1059, Dysfonction Vasculaire et Hémostase, Université Jean-Monnet, 42055 Saint-Etienne, France
| | - Léonard Féasson
- Unité de Myologie, Service de Physiologie Clinique et de l’Exercice, Centre Référent Maladies Neuromusculaires Euro-NmD, 42000 CHU de Saint-Etienne, France;
- Laboratoire Interuniversitaire de Biologie de la Motricité, Université de Lyon, Université Jean Monnet Saint-Etienne, 69000 Lyon, France
| | - Daniel Béchet
- Université Clermont Auvergne, INRAE, UNH, Unité de Nutrition Humaine, CRNH Auvergne, 63000 Clermont-Ferrand, France; (M.G.); (C.C.-G.); (D.T.); (L.C.); (C.P.); (S.W.)
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19
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Mandal K, Sarmah R, Bhattacharyya DK, Kalita JK, Borah B. Rank-preserving biclustering algorithm: a case study on miRNA breast cancer. Med Biol Eng Comput 2021; 59:989-1004. [PMID: 33840048 DOI: 10.1007/s11517-020-02271-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 09/15/2020] [Indexed: 10/21/2022]
Abstract
Effective biomarkers aid in the early diagnosis and monitoring of breast cancer and thus play an important role in the treatment of patients suffering from the disease. Growing evidence indicates that alteration of expression levels of miRNA is one of the principal causes of cancer. We analyze breast cancer miRNA data to discover a list of biclusters as well as breast cancer miRNA biomarkers which can help to understand better this critical disease and take important clinical decisions for treatment and diagnosis. In this paper, we propose a pattern-based parallel biclustering algorithm termed Rank-Preserving Biclustering (RPBic). The key strategy is to identify rank-preserved rows under a subset of columns based on a modified version of all substrings common subsequence (ALCS) framework. To illustrate the effectiveness of the RPBic algorithm, we consider synthetic datasets and show that RPBic outperforms relevant biclustering algorithms in terms of relevance and recovery. For breast cancer data, we identify 68 biclusters and establish that they have strong clinical characteristics among the samples. The differentially co-expressed miRNAs are found to be involved in KEGG cancer related pathways. Moreover, we identify frequency-based biomarkers (hsa-miR-410, hsa-miR-483-5p) and network-based biomarkers (hsa-miR-454, hsa-miR-137) which we validate to have strong connectivity with breast cancer. The source code and the datasets used can be found at http://agnigarh.tezu.ernet.in/~rosy8/Bioinformatics_RPBic_Data.rar . Graphical Abstract.
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Affiliation(s)
- Koyel Mandal
- Department of Computer Science and Engineering, Tezpur University, Assam, India.
| | - Rosy Sarmah
- Department of Computer Science and Engineering, Tezpur University, Assam, India
| | | | - Jugal Kumar Kalita
- Department of Computer Science, University of Colorado, Colorado Springs, CO, USA
| | - Bhogeswar Borah
- Department of Computer Science and Engineering, Tezpur University, Assam, India
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20
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Mehta AR, Gregory JM, Dando O, Carter RN, Burr K, Nanda J, Story D, McDade K, Smith C, Morton NM, Mahad DJ, Hardingham GE, Chandran S, Selvaraj BT. Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis. Acta Neuropathol 2021; 141:257-279. [PMID: 33398403 PMCID: PMC7847443 DOI: 10.1007/s00401-020-02252-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/30/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022]
Abstract
Axonal dysfunction is a common phenotype in neurodegenerative disorders, including in amyotrophic lateral sclerosis (ALS), where the key pathological cell-type, the motor neuron (MN), has an axon extending up to a metre long. The maintenance of axonal function is a highly energy-demanding process, raising the question of whether MN cellular energetics is perturbed in ALS, and whether its recovery promotes axonal rescue. To address this, we undertook cellular and molecular interrogation of multiple patient-derived induced pluripotent stem cell lines and patient autopsy samples harbouring the most common ALS causing mutation, C9orf72. Using paired mutant and isogenic expansion-corrected controls, we show that C9orf72 MNs have shorter axons, impaired fast axonal transport of mitochondrial cargo, and altered mitochondrial bioenergetic function. RNAseq revealed reduced gene expression of mitochondrially encoded electron transport chain transcripts, with neuropathological analysis of C9orf72-ALS post-mortem tissue importantly confirming selective dysregulation of the mitochondrially encoded transcripts in ventral horn spinal MNs, but not in corresponding dorsal horn sensory neurons, with findings reflected at the protein level. Mitochondrial DNA copy number was unaltered, both in vitro and in human post-mortem tissue. Genetic manipulation of mitochondrial biogenesis in C9orf72 MNs corrected the bioenergetic deficit and also rescued the axonal length and transport phenotypes. Collectively, our data show that loss of mitochondrial function is a key mediator of axonal dysfunction in C9orf72-ALS, and that boosting MN bioenergetics is sufficient to restore axonal homeostasis, opening new potential therapeutic strategies for ALS that target mitochondrial function.
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Affiliation(s)
- Arpan R Mehta
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jenna M Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Owen Dando
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Roderick N Carter
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Karen Burr
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Jyoti Nanda
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - David Story
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Karina McDade
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Nicholas M Morton
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Don J Mahad
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Giles E Hardingham
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
- Centre for Brain Development and Repair, inStem, Bangalore, India.
| | - Bhuvaneish T Selvaraj
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
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21
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2020; 80:1104-1122.e9. [PMID: 33259812 PMCID: PMC7674017 DOI: 10.1016/j.molcel.2020.11.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.
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Affiliation(s)
- Ryan M Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ellen L Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Indranil Paul
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Ahmed Youssef
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Dmitry Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Mamta Verma
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, Miami, FL, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Anne Hinds
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Tilston-Lunel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Benjamin L Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA; Department of Biology, University of Miami, Miami, FL, USA; Miami Institute of Data Science and Computing, Miami, FL, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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22
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Sharma P, Pandey AK, Bhattacharyya DK. Determining crucial genes associated with COVID-19 based on COPD Findings ✶,✶✶. Comput Biol Med 2020; 128:104126. [PMID: 33260035 PMCID: PMC7680043 DOI: 10.1016/j.compbiomed.2020.104126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/15/2020] [Accepted: 11/15/2020] [Indexed: 01/25/2023]
Abstract
Genes act in groups known as gene modules, which accomplish different cellular functions in the body. The modular nature of gene networks was used in this study to detect functionally enriched modules in samples obtained from COPD patients. We analyzed modules extracted from COPD samples and identified crucial genes associated with the disease COVID-19. We also extracted modules from a COVID-19 dataset and analyzed a suspected set of genes that may be associated with this deadly disease. We used information available for two other viruses that cause SARS and MERS because their physiology is similar to that of the COVID-19 virus. We report several crucial genes associated with COVID-19: RPA2, POLD4, MAPK8, IRF7, JUN, NFKB1, NFKBIA, CD40LG, FASLG, ICAM1, LIFR, STAT2 and CCR1. Most of these genes are related to the immune system and respiratory organs, which emphasizes the fact that COPD weakens this system and makes patients more susceptible to developing severe COVID-19. Association of respiratory disease COPD (Chronic Obstructive Pulmonary Disease) with COVID-19. Discuss the resemblance between SARS, MERS and COVID-19 causal agents. Uses gene module analysis and pathway information to determine the role of genes which may be associated with COVID-19. Few interesting genes were found which might be potentially useful in designing drugs targeting COVID-19.
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Affiliation(s)
- Pooja Sharma
- Department of IT, BIT Sindri, Dhanbad, Jharkhand, 828123, India.
| | - Anuj K Pandey
- Department of EE, BIT Sindri, Dhanbad, Jharkhand, 828123, India
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23
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Nepomuceno-Chamorro IA, Nepomuceno JA, Galván-Rojas JL, Vega-Márquez B, Rubio-Escudero C. Using prior knowledge in the inference of gene association networks. APPL INTELL 2020. [DOI: 10.1007/s10489-020-01705-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Payra AK, Ghosh A. Identifying essential proteins using modified-monkey algorithm (MMA). Comput Biol Chem 2020; 88:107324. [DOI: 10.1016/j.compbiolchem.2020.107324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/28/2020] [Accepted: 06/24/2020] [Indexed: 11/15/2022]
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25
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Chowdhury HA, Bhattacharyya DK, Kalita JK. (Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1154-1173. [PMID: 30668502 DOI: 10.1109/tcbb.2019.2893170] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Analysis of gene expression data is widely used in transcriptomic studies to understand functions of molecules inside a cell and interactions among molecules. Differential co-expression analysis studies diseases and phenotypic variations by finding modules of genes whose co-expression patterns vary across conditions. We review the best practices in gene expression data analysis in terms of analysis of (differential) co-expression, co-expression network, differential networking, and differential connectivity considering both microarray and RNA-seq data along with comparisons. We highlight hurdles in RNA-seq data analysis using methods developed for microarrays. We include discussion of necessary tools for gene expression analysis throughout the paper. In addition, we shed light on scRNA-seq data analysis by including preprocessing and scRNA-seq in co-expression analysis along with useful tools specific to scRNA-seq. To get insights, biological interpretation and functional profiling is included. Finally, we provide guidelines for the analyst, along with research issues and challenges which should be addressed.
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26
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Li ZY, Guo HT, Calderón-Mantilla G, He JJ, Wang JL, Bonev BB, Zhu XQ, Elsheikha HM. Immunostimulatory efficacy and protective potential of putative TgERK7 protein in mice experimentally infected by Toxoplasma gondii. Int J Med Microbiol 2020; 310:151432. [PMID: 32654774 DOI: 10.1016/j.ijmm.2020.151432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/10/2020] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
The extracellular signal-regulated kinases (ERKs) serve as important determinants of cellular signal transduction pathways, and hence may play important roles during infections. Previous work suggested that putative ERK7 of Toxoplasma gondii is required for efficient intracellular replication of the parasite. However, the antigenic and immunostimulatory properties of TgERK7 protein remain unknown. The objective of this study was to produce a recombinant TgERK7 protein in vitro and to evaluate its effect on the induction of humoral and T cell-mediated immune responses against T. gondii infection in BALB/c mice. Immunization using TgERK7 mixed with Freund's adjuvants significantly increased the ratio of CD3e+CD4+ T/CD3e+CD8a+ T lymphocytes in spleen and elevated serum cytokines (IFN-γ, IL-2, IL-4, IL-10, IL-12p70, IL-23, MCP-1, and TNF-α) in immunized mice compared to control mice. On the contrary, immunization did not induce high levels of serum IgG antibodies. Five predicted peptides of TgERK7 were synthesized and conjugated with KLH and used to analyze the antibody specificity in the sera of immunized mice. We detected a progressive increase in the antibody level only against TgERK7 peptide A (DEVDKHVLRKYD). Antibody raised against this peptide significantly decreased intracellular proliferation of T. gondii in vitro, suggesting that peptide A can potentially induce a protective antibody response. We also showed that immunization improved the survival rate of mice challenged with a virulent strain and significantly reduced the parasite cyst burden within the brains of chronically infected mice. Our data show that TgERK7-based immunization induced TgERK7 peptide A-specific immune responses that can impart protective immunity against T. gondii infection. The therapeutic potential of targeting ERK7 signaling pathway for future toxoplasmosis treatment is warranted.
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Affiliation(s)
- Zhong-Yuan Li
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, College of Basic Medicine, Guilin Medical University, Guilin, Guangxi, 541199, China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China; College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Hai-Ting Guo
- Guangxi Key Laboratory of Brain and Cognitive Neuroscience, College of Basic Medicine, Guilin Medical University, Guilin, Guangxi, 541199, China
| | - Guillermo Calderón-Mantilla
- Universidad de La Sabana, Campus del Puente del Común, Km. 7, Autopista Norte de Bogotá. Chía, Cundinamarca, Colombia
| | - Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Jin-Lei Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China
| | - Boyan B Bonev
- School of life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 730046, China.
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
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27
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Vardarajan B, Kalia V, Manly J, Brickman A, Reyes‐Dumeyer D, Lantigua R, Ionita‐Laza I, Jones DP, Miller GW, Mayeux R. Differences in plasma metabolites related to Alzheimer's disease, APOE ε4 status, and ethnicity. Alzheimers Dement (N Y) 2020; 6:e12025. [PMID: 32377558 PMCID: PMC7201178 DOI: 10.1002/trc2.12025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/31/2020] [Indexed: 11/24/2022]
Abstract
INTRODUCTION We investigated metabolites in plasma to capture systemic biochemical changes associated with Alzheimer's disease (AD). METHODS Metabolites in plasma were measured in 59 AD cases and 60 healthy participants of African American (AA), Caribbean Hispanic (CH), and non-Hispanic white (NHW) ancestry using untargeted liquid-chromatography-based ultra-high-resolution mass spectrometry. Metabolite differences between AD and healthy, ethnic groups and apolipoprotein E gene (APOE) ε4 status were analyzed. Untargeted network analysis identified pathways enriched in AD-associated metabolites. RESULTS A total of 5929 annotated metabolites were measured. Partial least squares discriminant analysis (PLS-DA) inferred that AD clustered separately from healthy controls (area under the curve [AUC] = 0.9816); discriminating pathways included glycerophospholipid, sphingolipid, and non-essential amino acid (alanine, aspartate, glutamate) metabolism. Metabolic features in AA clustered differently from CH and NHW (AUC = 0.9275), and differed between APOE ε4 carriers and non-carriers (AUC = 0.9972). DISCUSSION Metabolites, specifically lipids, were associated with AD, APOE ε4, and ethnic group. Metabolite profiling can identify perturbed AD pathways, but genetic and ancestral background need to be considered.
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Affiliation(s)
- Badri Vardarajan
- College of Physicians and SurgeonsTaub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew York
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew York
| | - Vrinda Kalia
- Department of Environmental Health SciencesMailman School of Public HealthColumbia UniversityNew YorkNew York
| | - Jennifer Manly
- College of Physicians and SurgeonsTaub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew York
| | - Adam Brickman
- College of Physicians and SurgeonsTaub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew York
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew York
| | - Dolly Reyes‐Dumeyer
- College of Physicians and SurgeonsTaub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew York
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
| | - Rafael Lantigua
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew York
| | - Iuliana Ionita‐Laza
- Department of BiostatisticsMailman School of Public HealthColumbia UniversityNew YorkNew York
| | - Dean P. Jones
- Clinical Biomarkers LaboratoryDepartment of MedicineEmory UniversityAtlantaGeorgia
- Department of Pathology and Cell BiologyCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
| | - Gary W. Miller
- Department of Environmental Health SciencesMailman School of Public HealthColumbia UniversityNew YorkNew York
| | - Richard Mayeux
- College of Physicians and SurgeonsTaub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew York
- The Gertrude H. Sergievsky CenterCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
- Department of NeurologyCollege of Physicians and SurgeonsColumbia University and the New York Presbyterian HospitalNew YorkNew York
- Department of EpidemiologyMailman School of Public HealthColumbia UniversityNew YorkNew York
- Department of PsychiatryCollege of Physicians and SurgeonsColumbia UniversityNew YorkNew York
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28
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Das S, McClain CJ, Rai SN. Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges. Entropy (Basel) 2020; 22:E427. [PMID: 33286201 DOI: 10.3390/e22040427] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/18/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022]
Abstract
Over the last decade, gene set analysis has become the first choice for gaining insights into underlying complex biology of diseases through gene expression and gene association studies. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Although gene set analysis approaches are extensively used in gene expression and genome wide association data analysis, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. In this article, we provide a comprehensive overview, statistical structure and steps of gene set analysis approaches used for microarrays, RNA-sequencing and genome wide association data analysis. Further, we also classify the gene set analysis approaches and tools by the type of genomic study, null hypothesis, sampling model and nature of the test statistic, etc. Rather than reviewing the gene set analysis approaches individually, we provide the generation-wise evolution of such approaches for microarrays, RNA-sequencing and genome wide association studies and discuss their relative merits and limitations. Here, we identify the key biological and statistical challenges in current gene set analysis, which will be addressed by statisticians and biologists collectively in order to develop the next generation of gene set analysis approaches. Further, this study will serve as a catalog and provide guidelines to genome researchers and experimental biologists for choosing the proper gene set analysis approach based on several factors.
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29
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Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform. Nat Biotechnol 2020; 38:638-648. [PMID: 32249828 DOI: 10.1038/s41587-020-0437-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Systematic mapping of genetic interactions (GIs) and interrogation of the functions of sizable genomic segments in mammalian cells represent important goals of biomedical research. To advance these goals, we present a CRISPR (clustered regularly interspaced short palindromic repeats)-based screening system for combinatorial genetic manipulation that employs coexpression of CRISPR-associated nucleases 9 and 12a (Cas9 and Cas12a) and machine-learning-optimized libraries of hybrid Cas9-Cas12a guide RNAs. This system, named Cas Hybrid for Multiplexed Editing and screening Applications (CHyMErA), outperforms genetic screens using Cas9 or Cas12a editing alone. Application of CHyMErA to the ablation of mammalian paralog gene pairs reveals extensive GIs and uncovers phenotypes normally masked by functional redundancy. Application of CHyMErA in a chemogenetic interaction screen identifies genes that impact cell growth in response to mTOR pathway inhibition. Moreover, by systematically targeting thousands of alternative splicing events, CHyMErA identifies exons underlying human cell line fitness. CHyMErA thus represents an effective screening approach for GI mapping and the functional analysis of sizable genomic regions, such as alternative exons.
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Affiliation(s)
| | - Michael Aregger
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kevin R Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alexander Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Tanja Durbic
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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30
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Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun 2019; 10:5137. [PMID: 31723143 PMCID: PMC6853988 DOI: 10.1038/s41467-019-12970-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.
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Affiliation(s)
- Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - James C Lee
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Taeyoung Hwang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill M Goldstein
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
| | - Abigail F Groff
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nydia P Chang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Adam Williams
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Jorge Henao-Meija
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
| | - Richard A Flavell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University, School of Medicine, New Haven, CT, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
- Joslin Diabetes Center, Boston, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
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31
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Brito GC, Schormann W, Gidda SK, Mullen RT, Andrews DW. Genome-wide analysis of Homo sapiens, Arabidopsis thaliana, and Saccharomyces cerevisiae reveals novel attributes of tail-anchored membrane proteins. BMC Genomics 2019; 20:835. [PMID: 31711414 PMCID: PMC6849228 DOI: 10.1186/s12864-019-6232-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/28/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Tail-anchored membrane proteins (TAMPs) differ from other integral membrane proteins, because they contain a single transmembrane domain at the extreme carboxyl-terminus and are therefore obliged to target to membranes post-translationally. Although 3-5% of all transmembrane proteins are predicted to be TAMPs only a small number are well characterized. RESULTS To identify novel putative TAMPs across different species, we used TAMPfinder software to identify 859, 657 and 119 putative TAMPs in human (Homo sapiens), plant (Arabidopsis thaliana), and yeast (Saccharomyces cerevisiae), respectively. Bioinformatics analyses of these putative TAMP sequences suggest that the list is highly enriched for authentic TAMPs. To experimentally validate the software predictions several human and plant proteins identified by TAMPfinder that were previously uncharacterized were expressed in cells and visualized at subcellular membranes by fluorescence microscopy and further analyzed by carbonate extraction or by bimolecular fluorescence complementation. With the exception of the pro-apoptotic protein harakiri, which is, peripherally bound to the membrane this subset of novel proteins behave like genuine TAMPs. Comprehensive bioinformatics analysis of the generated TAMP datasets revealed previously unappreciated common and species-specific features such as the unusual size distribution of and the propensity of TAMP proteins to be part of larger complexes. Additionally, novel features of the amino acid sequences that anchor TAMPs to membranes were also revealed. CONCLUSIONS The findings in this study more than double the number of predicted annotated TAMPs and provide new insights into the common and species-specific features of TAMPs. Furthermore, the list of TAMPs and annotations provide a resource for further investigation.
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Affiliation(s)
- Glauber Costa Brito
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Wiebke Schormann
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - David W Andrews
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada. .,Departments of Biochemistry and Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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Abstract
BACKGROUND Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the importance of this type of analysis, more than 70 pathway analysis methods have been proposed so far. These can be categorized into two main categories: non-topology-based (non-TB) and topology-based (TB). Although some review papers discuss this topic from different aspects, there is no systematic, large-scale assessment of such methods. Furthermore, the majority of the pathway analysis approaches rely on the assumption of uniformity of p values under the null hypothesis, which is often not true. RESULTS This article presents the most comprehensive comparative study on pathway analysis methods available to date. We compare the actual performance of 13 widely used pathway analysis methods in over 1085 analyses. These comparisons were performed using 2601 samples from 75 human disease data sets and 121 samples from 11 knockout mouse data sets. In addition, we investigate the extent to which each method is biased under the null hypothesis. Together, these data and results constitute a reliable benchmark against which future pathway analysis methods could and should be tested. CONCLUSION Overall, the result shows that no method is perfect. In general, TB methods appear to perform better than non-TB methods. This is somewhat expected since the TB methods take into consideration the structure of the pathway which is meant to describe the underlying phenomena. We also discover that most, if not all, listed approaches are biased and can produce skewed results under the null.
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Affiliation(s)
- Tuan-Minh Nguyen
- Department of Computer Science, Wayne State University, Detroit, 48202 USA
| | - Adib Shafi
- Department of Computer Science, Wayne State University, Detroit, 48202 USA
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, 89557 USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, 48202 USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, 48202 USA
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33
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Brunette GJ, Jamalruddin MA, Baldock RA, Clark NL, Bernstein KA. Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes. Proc Natl Acad Sci U S A 2019; 116:19593-9. [PMID: 31501324 DOI: 10.1073/pnas.1906559116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
DNA repair is critical for genome stability and is maintained through conserved pathways. Traditional genome-wide mammalian screens are both expensive and laborious. However, computational approaches circumvent these limitations and are a powerful tool to identify new DNA repair factors. By analyzing the evolutionary relationships between genes in the major DNA repair pathways, we uncovered functional relationships between individual genes and identified partners. Here we ranked 17,487 mammalian genes for coevolution with 6 distinct DNA repair pathways. Direct comparison to genetic screens for homologous recombination or Fanconi anemia factors indicates that our evolution-based screen is comparable, if not superior, to traditional screening approaches. Demonstrating the utility of our strategy, we identify a role for the DNA damage-induced apoptosis suppressor (DDIAS) gene in double-strand break repair based on its coevolution with homologous recombination. DDIAS knockdown results in DNA double-strand breaks, indicated by ATM kinase activation and 53BP1 foci induction. Additionally, DDIAS-depleted cells are deficient for homologous recombination. Our results reveal that evolutionary analysis is a powerful tool to uncover novel factors and functional relationships in DNA repair.
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34
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Zimmerman SJ, Aldridge CL, Oh KP, Cornman RS, Oyler‐McCance SJ. Signatures of adaptive divergence among populations of an avian species of conservation concern. Evol Appl 2019; 12:1661-1677. [PMID: 31462921 PMCID: PMC6708427 DOI: 10.1111/eva.12825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the genetic underpinning of adaptive divergence among populations is a key goal of evolutionary biology and conservation. Gunnison sage-grouse (Centrocercus minimus) is a sagebrush obligate species with a constricted range consisting of seven discrete populations, each with distinctly different habitat and climatic conditions. Though geographically close, populations have low levels of natural gene flow resulting in relatively high levels of differentiation. Here, we use 15,033 SNP loci in genomic outlier analyses, genotype-environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation in an avian species of conservation concern. We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. The identified gene set was enriched for cytochrome P450 gene family members (CYP4V2, CYP2R1, CYP2C23B, CYP4B1) and could impact metabolism of plant secondary metabolites, a critical challenge for sagebrush obligates. Additionally, the gene set was also enriched with members potentially involved in antiviral response (DEAD box helicase gene family and SETX). Our results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring. This information can be useful in managing this species of conservation concern, for example, to identify unique populations to conserve, avoid translocation or release of individuals that may swamp locally adapted genetic diversity, or guide habitat restoration efforts.
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Affiliation(s)
- Shawna J. Zimmerman
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Cameron L. Aldridge
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Kevin P. Oh
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
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35
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Morenikeji OB, Hawkes ME, Hudson AO, Thomas BN. Computational Network Analysis Identifies Evolutionarily Conserved miRNA Gene Interactions Potentially Regulating Immune Response in Bovine Trypanosomosis. Front Microbiol 2019; 10:2010. [PMID: 31555241 PMCID: PMC6722470 DOI: 10.3389/fmicb.2019.02010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022] Open
Abstract
Bovine trypanosomosis is a devastating disease that causes huge economic loss to the global cattle industry on a yearly basis. Selection of accurate biomarkers are important in early disease diagnosis and treatment. Of late, micro-RNAs (miRNAs) are becoming the most useful biomarkers for both infectious and non-infectious diseases in humans, but this is not the case in animals. miRNAs are non-coding RNAs that regulate gene expression through binding to the 3'-, 5'-untranslated regions (UTR) or coding sequence (CDS) region of one or more target genes. The molecular identification of miRNAs that regulates the expression of immune genes responding to bovine trypanosomosis is poorly defined, as is the possibility that these miRNAs could serve as potential biomarkers for disease diagnosis and treatment currently unknown. To this end, we utilized in silico tools to elucidate conserved miRNAs regulating immune response genes during infection, in addition to cataloging significant genes. Based on the p value of 1.77E-32, we selected 25 significantly expressed immune genes. Using prediction analysis, we identified a total of 4,251 bovine miRNAs targeting these selected genes across the 3'UTR, 5'UTR and CDS regions. Thereafter, we identified candidate miRNAs based on the number of gene targets and their abundance at the three regions. In all, we found the top 13 miRNAs that are significantly conserved targeting 7 innate immune response genes, including bta-mir-2460, bta-mir-193a, bta-mir-2316, and bta-mir-2456. Our gene ontology analysis suggests that these miRNAs are involved in gene silencing, cellular protein modification process, RNA-induced silencing complex, regulation of humoral immune response mediated by circulating immunoglobulin and negative regulation of chronic inflammatory response, among others. In conclusion, this study identifies specific miRNAs that may be involved in the regulation of gene expression during bovine trypanosomosis. These miRNAs have the potential to be used as biomarkers in the animal and veterinary research community to facilitate the development of tools for early disease diagnosis/detection, drug targeting, and the rational design of drugs to facilitate disease treatment.
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Affiliation(s)
- Olanrewaju B. Morenikeji
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Megan E. Hawkes
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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Blanco-Míguez A, Blanco G, Gutierrez-Jácome A, Fdez-Riverola F, Sánchez B, Lourenço A. Computational prediction of the bioactivity potential of proteomes based on expert knowledge. J Biomed Inform 2019; 91:103121. [PMID: 30738947 DOI: 10.1016/j.jbi.2019.103121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Advances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico screening of proteomes and metaproteomes is key to uncover bioactivities of translational, clinical and biotechnological interest, and to help assign functions to certain proteins, such as those predicted as hypothetical. This work introduces a new method for the prediction of the bioactivity potential of proteomes/metaproteomes, supporting the discovery of functionally relevant proteins based on prior knowledge. This methodology complements functional annotation enrichment methods by allowing the assignment of functions to proteins annotated as hypothetical/putative/uncharacterised, as well as and enabling the detection of specific bioactivities and the recovery of proteins from defined taxa. This work shows how the new method can be applied to screen proteome and metaproteome sets to obtain predictions of clinical or biotechnological interest based on reference datasets. Notably, with this methodology, the large information files obtained after DNA sequencing or protein identification experiments can be associated for translational purposes that, in cases such as antibiotic-resistance pathogens or foodborne diseases, may represent changes in how these important and global health burdens are approached in the clinical practice. Finally, the Sequence-based Expert-driven pRoteome bioactivity Prediction EnvironmENT, a public Web service implemented in Scala functional programming style, is introduced as means to ensure broad access to the method as well as to discuss main implementation issues, such as modularity, extensibility and interoperability.
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Affiliation(s)
- Aitor Blanco-Míguez
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas, s/n, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares, S/N, 33300 Villaviciosa, Asturias, Spain
| | - Guillermo Blanco
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas, s/n, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares, S/N, 33300 Villaviciosa, Asturias, Spain
| | - Alberto Gutierrez-Jácome
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas, s/n, 32004 Ourense, Spain
| | - Florentino Fdez-Riverola
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas, s/n, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares, S/N, 33300 Villaviciosa, Asturias, Spain
| | - Anália Lourenço
- ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas, s/n, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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38
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Xu S, Ware KE, Ding Y, Kim SY, Sheth MU, Rao S, Chan W, Armstrong AJ, Eward WC, Jolly MK, Somarelli JA. An Integrative Systems Biology and Experimental Approach Identifies Convergence of Epithelial Plasticity, Metabolism, and Autophagy to Promote Chemoresistance. J Clin Med 2019; 8:jcm8020205. [PMID: 30736412 PMCID: PMC6406733 DOI: 10.3390/jcm8020205] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 01/09/2023] Open
Abstract
The evolution of therapeutic resistance is a major cause of death for cancer patients. The development of therapy resistance is shaped by the ecological dynamics within the tumor microenvironment and the selective pressure of the host immune system. These selective forces often lead to evolutionary convergence on pathways or hallmarks that drive progression. Thus, a deeper understanding of the evolutionary convergences that occur could reveal vulnerabilities to treat therapy-resistant cancer. To this end, we combined phylogenetic clustering, systems biology analyses, and molecular experimentation to identify convergences in gene expression data onto common signaling pathways. We applied these methods to derive new insights about the networks at play during transforming growth factor-β (TGF-β)-mediated epithelial–mesenchymal transition in lung cancer. Phylogenetic analyses of gene expression data from TGF-β-treated cells revealed convergence of cells toward amine metabolic pathways and autophagy during TGF-β treatment. Knockdown of the autophagy regulatory, ATG16L1, re-sensitized lung cancer cells to cancer therapies following TGF-β-induced resistance, implicating autophagy as a TGF-β-mediated chemoresistance mechanism. In addition, high ATG16L expression was found to be a poor prognostic marker in multiple cancer types. These analyses reveal the usefulness of combining evolutionary and systems biology methods with experimental validation to illuminate new therapeutic vulnerabilities for cancer.
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Affiliation(s)
- Shengnan Xu
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Kathryn E Ware
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Yuantong Ding
- Department of Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 2 7710, USA.
| | - Maya U Sheth
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Sneha Rao
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Wesley Chan
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Andrew J Armstrong
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
- Solid Tumor Program and the Duke Prostate and Urologic Cancer Center, Duke University Medical Center, Durham, NC 27710, USA.
| | - William C Eward
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.
- Current address: Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - Jason A Somarelli
- Duke Cancer Institute and the Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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Jiang LG, Li B, Liu SX, Wang HW, Li CP, Song SH, Beatty M, Zastrow-Hayes G, Yang XH, Qin F, He Y. Characterization of Proteome Variation During Modern Maize Breeding. Mol Cell Proteomics 2019; 18:263-276. [PMID: 30409858 PMCID: PMC6356080 DOI: 10.1074/mcp.ra118.001021] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/06/2018] [Indexed: 12/21/2022] Open
Abstract
The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.
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Affiliation(s)
- Lu-Guang Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Bo Li
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Sheng-Xue Liu
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hong-Wei Wang
- Agricultural College, Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Hubei 434000, China
| | - Cui-Ping Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Hui Song
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | - Xiao-Hong Yang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Feng Qin
- College of Biological Sciences, China Agricultural University, Beijing 100094, China;.
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China;.
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Haque M, Sarmah R, Bhattacharyya DK. A common neighbor based technique to detect protein complexes in PPI networks. J Genet Eng Biotechnol 2019; 16:227-238. [PMID: 30647726 PMCID: PMC6296598 DOI: 10.1016/j.jgeb.2017.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/26/2017] [Accepted: 10/05/2017] [Indexed: 01/15/2023]
Abstract
Detection of protein complexes by analyzing and understanding PPI networks is an important task and critical to all aspects of cell biology. We present a technique called PROtein COmplex DEtection based on common neighborhood (PROCODE) that considers the inherent organization of protein complexes as well as the regions with heavy interactions in PPI networks to detect protein complexes. Initially, the core of the protein complexes is detected based on the neighborhood of PPI network. Then a merging strategy based on density is used to attach proteins and protein complexes to the core-protein complexes to form biologically meaningful structures. The predicted protein complexes of PROCODE was evaluated and analyzed using four PPI network datasets out of which three were from budding yeast and one from human. Our proposed technique is compared with some of the existing techniques using standard benchmark complexes and PROCODE was found to match very well with actual protein complexes in the benchmark data. The detected complexes were at par with existing biological evidence and knowledge.
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Mahfouz MA, Nepomuceno JA. Graph coloring for extracting discriminative genes in cancer data. Ann Hum Genet 2019; 83:141-159. [PMID: 30644085 DOI: 10.1111/ahg.12297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 10/12/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND OBJECTIVE The major difficulty of the analysis of the input gene expression data in a microarray-based approach for an automated diagnosis of cancer is the large number of genes (high dimensionality) with many irrelevant genes (noise) compared to the very small number of samples. This research study tackles the dimensionality reduction challenge in this area. METHODS This research study introduces a dimension-reduction technique termed graph coloring approach (GCA) for microarray data-based cancer classification based on analyzing the absolute correlation between gene-gene pairs and partitioning genes into several hubs using graph coloring. GCA starts by a gene-selection step in which top relevant genes are selected using a biserial correlation. Each time, a gene from an ordered list of top relevant genes is selected as the hub gene (representative) and redundant genes are added to its group; the process is repeated recursively for the remaining genes. A gene is considered redundant if its absolute correlation with the hub gene is greater than a controlling threshold. A suitable range for the threshold is estimated by computing a percentage graph for the absolute correlation between gene-gene pairs. Each value in the estimated range for the threshold can efficiently produce a new feature subset. RESULTS GCA achieved significant improvement over several existing techniques in terms of higher accuracy and a smaller number of features. Also, genes selected by this method are relevant genes according to the information stored in scientific repositories. CONCLUSIONS The proposed dimension-reduction technique can help biologists accurately predict cancer in several areas of the body.
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Affiliation(s)
- Mohamed A Mahfouz
- Department of Computer and Systems Engineering, Faculty of Engineering, Alexandria University, Alexandria, Egypt
| | - Juan A Nepomuceno
- Departmento de Lenguajes y Sistemas Informáticos, Higher Technical School of Computer Engineering, University of Seville, Seville, Spain
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Abstract
Pathway analysis is a wide class of methods allowing to determine the alteration of functional processes in complex diseases. However, biological pathways are still partial, and knowledge coming from posttranscriptional regulators has started to be considered in a systematic way only recently. Here we will give a global and updated view of the main pathway and subpathway analysis methodologies, focusing on the improvements obtained through the recent introduction of microRNAs as regulatory elements in these frameworks.
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Affiliation(s)
- Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Micale
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.
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Larochelle M, Bergeron D, Arcand B, Bachand F. Proximity-dependent biotinylation by TurboID to identify protein-protein interaction networks in yeast. J Cell Sci 2019; 132:jcs.232249. [DOI: 10.1242/jcs.232249] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/29/2019] [Indexed: 01/27/2023] Open
Abstract
The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-MS) has changed the field of protein-protein interaction studies. Yet, despite the recurrent and successful use of BioID-based protein-protein interactions screening in mammalian cells, the implementation of PDB-MS in yeast has not been effective. Here we report a simple and rapid approach in yeast to effectively screen for proximal and interacting proteins in their natural cellular environment by using TurboID, a recently described version of the BirA biotin ligase. Using the protein arginine methyltransferase Rmt3 and the RNA exosome subunits, Rrp6 and Dis3, the application of PDB-MS in yeast by using TurboID was able to recover protein-protein interactions previously identified using other biochemical approaches and provided new complementary information for a given protein bait. The development of a rapid and effective PDB assay that can systematically analyze protein-protein interactions in living yeast cells opens the way for large-scale proteomics studies in this powerful model organism.
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Affiliation(s)
- Marc Larochelle
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Danny Bergeron
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - Bruno Arcand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
| | - François Bachand
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Qc, Canada
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Abstract
Background Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists’ capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter-gene sets association is rarely taken into consideration. Deep learning, an emerging machine learning technique in computational biology, can be used to generate an unbiased combination of gene set, and to determine the biological relevance and analysis consistency of these combining gene sets by leveraging large genomic data sets. Results In this study, we proposed a gene superset autoencoder (GSAE), a multi-layer autoencoder model with the incorporation of a priori defined gene sets that retain the crucial biological features in the latent layer. We introduced the concept of the gene superset, an unbiased combination of gene sets with weights trained by the autoencoder, where each node in the latent layer is a superset. Trained with genomic data from TCGA and evaluated with their accompanying clinical parameters, we showed gene supersets’ ability of discriminating tumor subtypes and their prognostic capability. We further demonstrated the biological relevance of the top component gene sets in the significant supersets. Conclusions Using autoencoder model and gene superset at its latent layer, we demonstrated that gene supersets retain sufficient biological information with respect to tumor subtypes and clinical prognostic significance. Superset also provides high reproducibility on survival analysis and accurate prediction for cancer subtypes. Electronic supplementary material The online version of this article (10.1186/s12918-018-0642-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hung-I Harry Chen
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.,Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Yu-Chiao Chiu
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Tinghe Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Songyao Zhang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.,Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA. .,Department of Epidemiology & Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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Tian AL, Lu M, Zhang FK, Calderón-Mantilla G, Petsalaki E, Tian X, Wang W, Huang SY, Li X, Elsheikha HM, Zhu XQ. The pervasive effects of recombinant Fasciola gigantica Ras-related protein Rab10 on the functions of goat peripheral blood mononuclear cells. Parasit Vectors 2018; 11:579. [PMID: 30400957 PMCID: PMC6219056 DOI: 10.1186/s13071-018-3148-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/14/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Fasciola gigantica-induced immunomodulation is a major hurdle faced by the host for controlling infection. Here, we elucidated the role of F. gigantica Ras-related protein Rab10 (FgRab10) in the modulation of key functions of peripheral blood mononuclear cells (PBMCs) of goats. METHODS We cloned and expressed recombinant FgRab10 (rFgRab10) protein and examined its effects on several functions of goat PBMCs. Protein interactors of rFgRab10 were predicted in silico by querying the databases Intact, String, BioPlex and BioGrid. In addition, a total energy analysis of each of the identified interactions was also conducted. Gene Ontology (GO) enrichment analysis was carried out using FuncAssociate 3.0. RESULTS The FgRab10 gene (618 bp), encodes 205-amino-acid residues with a molecular mass of ~23 kDa, had complete nucleotide sequence homology with F. hepatica Ras family protein gene (PIS87503.1). The rFgRab10 protein specifically cross-reacted with anti-Fasciola antibodies as shown by Western blot and immunofluorescence analysis. This protein exhibited multiple effects on goat PBMCs, including increased production of cytokines [interleukin-2 (IL-2), IL-4, IL-10, transforming growth factor beta (TGF-β) and interferon gamma (IFN-γ)] and total nitric oxide (NO), enhancing apoptosis and migration of PBMCs, and promoting the phagocytic ability of monocytes. However, it significantly inhibited cell proliferation. Homology modelling revealed 63% identity between rFgRab10 and human Rab10 protein (Uniprot ID: P61026). Protein interaction network analysis revealed more stabilizing interactions between Rab proteins geranylgeranyltransferase component A 1 (CHM) and Rab proteins geranylgeranyltransferase component A 2 (CHML) and rFgRab10 protein. Gene Ontology analysis identified RabGTPase mediated signaling as the most represented pathway. CONCLUSIONS rFgRab10 protein exerts profound influences on various functions of goat PBMCs. This finding may help explain why F. gigantica is capable of provoking recognition by host immune cells, less capable of destroying this successful parasite.
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Affiliation(s)
- Ai-Ling Tian
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046 People’s Republic of China
| | - MingMin Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Fu-Kai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046 People’s Republic of China
| | - Guillermo Calderón-Mantilla
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD UK
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD UK
| | - XiaoWei Tian
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - WenJuan Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Si-Yang Huang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province 225009 People’s Republic of China
- Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009 People’s Republic of China
| | - XiangRui Li
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046 People’s Republic of China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province 225009 People’s Republic of China
- Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009 People’s Republic of China
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Yue Z, Neylon MT, Nguyen T, Ratliff T, Chen JY. "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data. IEEE/ACM Trans Comput Biol Bioinform 2018; 15:1991-1998. [PMID: 30040650 PMCID: PMC6380687 DOI: 10.1109/tcbb.2018.2858755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this article, we present a computational framework to identify "causal relationships" among super gene sets. For "causal relationships," we refer to both stimulatory and inhibitory regulatory relationships, regardless of through direct or indirect mechanisms. For super gene sets, we refer to "pathways, annotated lists, and gene signatures," or PAGs. To identify causal relationships among PAGs, we extend the previous work on identifying PAG-to-PAG regulatory relationships by further requiring them to be significantly enriched with gene-to-gene co-expression pairs across the two PAGs involved. This is achieved by developing a quantitative metric based on PAG-to-PAG Co-expressions (PPC), which we use to infer the likelihood that PAG-to-PAG relationships under examination are causal-either stimulatory or inhibitory. Since true causal relationships are unknown, we approximate the overall performance of inferring causal relationships with the performance of recalling known r-type PAG-to-PAG relationships from causal PAG-to-PAG inference, using a functional genomics benchmark dataset from the GEO database. We report the area-under-curve (AUC) performance for both precision and recall being 0.81. By applying our framework to a myeloid-derived suppressor cells (MDSC) dataset, we further demonstrate that this framework is effective in helping build multi-scale biomolecular systems models with new insights on regulatory and causal links for downstream biological interpretations.
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Affiliation(s)
- Zongliang Yue
- Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35233, US.
| | - Michael T. Neylon
- School of Informatics and Computing, Indiana University, Indianapolis, IN 46202, US.
| | - Thanh Nguyen
- Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35233, US.
| | - Timothy Ratliff
- Purdue University Center for Cancer Research, West Lafayette, IN 47906, US.
| | - Jake Y. Chen
- Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35233, US.
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Liu J, Li M, Luo XJ, Su B. Systems-level analysis of risk genes reveals the modular nature of schizophrenia. Schizophr Res 2018; 201:261-269. [PMID: 29789256 DOI: 10.1016/j.schres.2018.05.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 12/31/2022]
Abstract
Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10-31). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10-11), closeness centrality (P = 7.56 × 10-11), betweeness centrality (P = 1.29 × 10-11), clustering coefficient (P = 2.22 × 10-2), and shorter average shortest path length (P = 7.56 × 10-11). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia.
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Affiliation(s)
- Jiewei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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Kim J, Shin M, Kim J, Park C, Lee S, Woo J, Kim H, Seo D, Yu S, Park S. CASS: A distributed network clustering algorithm based on structure similarity for large-scale network. PLoS One 2018; 13:e0203670. [PMID: 30303961 PMCID: PMC6179193 DOI: 10.1371/journal.pone.0203670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 08/24/2018] [Indexed: 12/21/2022] Open
Abstract
As the size of networks increases, it is becoming important to analyze large-scale network data. A network clustering algorithm is useful for analysis of network data. Conventional network clustering algorithms in a single machine environment rather than a parallel machine environment are actively being researched. However, these algorithms cannot analyze large-scale network data because of memory size issues. As a solution, we propose a network clustering algorithm for large-scale network data analysis using Apache Spark by changing the paradigm of the conventional clustering algorithm to improve its efficiency in the Apache Spark environment. We also apply optimization approaches such as Bloom filter and shuffle selection to reduce memory usage and execution time. By evaluating our proposed algorithm based on an average normalized cut, we confirmed that the algorithm can analyze diverse large-scale network datasets such as biological, co-authorship, internet topology and social networks. Experimental results show that the proposed algorithm can develop more accurate clusters than comparative algorithms with less memory usage. Furthermore, we confirm the proposed optimization approaches and the scalability of the proposed algorithm. In addition, we validate that clusters found from the proposed algorithm can represent biologically meaningful functions.
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Affiliation(s)
- Jungrim Kim
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Mincheol Shin
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Jeongwoo Kim
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Chihyun Park
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Sujin Lee
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Jaemin Woo
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Hyerim Kim
- Department of Computer Science, Yonsei University, Seoul, South Korea
| | - Dongmin Seo
- Korea Institute of Science and Technology Information, Daejeon, South Korea
| | - Seokjong Yu
- Korea Institute of Science and Technology Information, Daejeon, South Korea
| | - Sanghyun Park
- Department of Computer Science, Yonsei University, Seoul, South Korea
- * E-mail:
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Cesari G, Algaba E, Moretti S, Nepomuceno JA. An application of the Shapley value to the analysis of co-expression networks. Appl Netw Sci 2018; 3:35. [PMID: 30839839 PMCID: PMC6214322 DOI: 10.1007/s41109-018-0095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/14/2018] [Indexed: 06/09/2023]
Abstract
We study the problem of identifying relevant genes in a co-expression network using a (cooperative) game theoretic approach. The Shapley value of a cooperative game is used to asses the relevance of each gene in interaction with the others, and to stress the role of nodes in the periphery of a co-expression network for the regulation of complex biological pathways of interest. An application of the method to the analysis of gene expression data from microarrays is presented, as well as a comparison with classical centrality indices. Finally, making further assumptions about the a priori importance of genes, we combine the game theoretic model with other techniques from cluster analysis.
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Affiliation(s)
- Giulia Cesari
- Department of Mathematics, Politecnico di Milano, Milano, Italy
| | - Encarnación Algaba
- Department of Applied Mathematics and IMUS, University of Seville, Seville, Spain
| | - Stefano Moretti
- Université Paris-Dauphine, PSL Research University, CNRS, LAMSADE, Paris, 75016 France
| | - Juan A. Nepomuceno
- Department of Computer Languages and Systems, University of Seville, Seville, Spain
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50
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Hasenpusch-Theil K, West S, Kelman A, Kozic Z, Horrocks S, McMahon AP, Price DJ, Mason JO, Theil T. Gli3 controls the onset of cortical neurogenesis by regulating the radial glial cell cycle through Cdk6 expression. Development 2018; 145:dev.163147. [PMID: 30093555 PMCID: PMC6141774 DOI: 10.1242/dev.163147] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/13/2018] [Indexed: 01/03/2023]
Abstract
The cerebral cortex contains an enormous number of neurons, allowing it to perform highly complex neural tasks. Understanding how these neurons develop at the correct time and place and in accurate numbers constitutes a major challenge. Here, we demonstrate a novel role for Gli3, a key regulator of cortical development, in cortical neurogenesis. We show that the onset of neuron formation is delayed in Gli3 conditional mouse mutants. Gene expression profiling and cell cycle measurements indicate that shortening of the G1 and S phases in radial glial cells precedes this delay. Reduced G1 length correlates with an upregulation of the cyclin-dependent kinase gene Cdk6, which is directly regulated by Gli3. Moreover, pharmacological interference with Cdk6 function rescues the delayed neurogenesis in Gli3 mutant embryos. Overall, our data indicate that Gli3 controls the onset of cortical neurogenesis by determining the levels of Cdk6 expression, thereby regulating neuronal output and cortical size.
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Affiliation(s)
- Kerstin Hasenpusch-Theil
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Stephen West
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Alexandra Kelman
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Zrinko Kozic
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Sophie Horrocks
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad-CIRM Center for Regenerative Medicine and Stem Cell Research, W.M. Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - David J Price
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - John O Mason
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Thomas Theil
- Centre for Discovery Brain Sciences, Hugh Robson Building, University of Edinburgh, Edinburgh EH8 9XD, UK
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