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Ru B, Sun J, Kang Q, Tong Y, Zhang J. A framework for identifying dysregulated chromatin regulators as master regulators in human cancer. Bioinformatics 2019; 35:1805-1812. [PMID: 30358822 DOI: 10.1093/bioinformatics/bty836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/22/2018] [Accepted: 10/24/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Chromatin regulators (CRs) are frequently dysregulated to reprogram the epigenetic landscape of the cancer genome. However, the underpinnings of the dysregulation of CRs and their downstream effectors remain to be elucidated. RESULTS Here, we designed an integrated framework based on multi-omics data to identify candidate master regulatory CRs affected by genomic alterations across eight cancer types in The Cancer Genome Atlas. Most of them showed consistent activated or repressed (i.e. oncogenic or tumor-suppressive) roles in cancer initiation and progression. In order to further explore the insight mechanism of the dysregulated CRs, we developed an R package ModReg based on differential connectivity to identify CRs as modulators of transcription factors (TFs) involved in tumorigenesis. Our analysis revealed that the connectivity between TFs and their target genes (TGs) tended to be disrupted in the patients who had a high expression of oncogenic CRs or low-expression of tumor-suppressive CRs. As a proof-of-principle study, 14 (82.4%) of the top-ranked 17 driver CRs in liver cancer were able to be validated by literature mining or experiments including shRNA knockdown and dCas9-based epigenetic editing. Moreover, we confirmed that CR SIRT7 physically interacted with TF NFE2L2, and positively modulated the transcriptional program of NFE2L2 by affecting ∼64% of its TGs. AVAILABILITY AND IMPLEMENTATION ModReg is freely accessible at http://cis.hku.hk/software/ModReg.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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202
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Mallm JP, Iskar M, Ishaque N, Klett LC, Kugler SJ, Muino JM, Teif VB, Poos AM, Großmann S, Erdel F, Tavernari D, Koser SD, Schumacher S, Brors B, König R, Remondini D, Vingron M, Stilgenbauer S, Lichter P, Zapatka M, Mertens D, Rippe K. Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. Mol Syst Biol 2019; 15:e8339. [PMID: 31118277 PMCID: PMC6529931 DOI: 10.15252/msb.20188339] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/02/2019] [Accepted: 04/17/2019] [Indexed: 12/22/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), a diverse set of genetic mutations is embedded in a deregulated epigenetic landscape that drives cancerogenesis. To elucidate the role of aberrant chromatin features, we mapped DNA methylation, seven histone modifications, nucleosome positions, chromatin accessibility, binding of EBF1 and CTCF, as well as the transcriptome of B cells from CLL patients and healthy donors. A globally increased histone deacetylase activity was detected and half of the genome comprised transcriptionally downregulated partially DNA methylated domains demarcated by CTCF CLL samples displayed a H3K4me3 redistribution and nucleosome gain at promoters as well as changes of enhancer activity and enhancer linkage to target genes. A DNA binding motif analysis identified transcription factors that gained or lost binding in CLL at sites with aberrant chromatin features. These findings were integrated into a gene regulatory enhancer containing network enriched for B-cell receptor signaling pathway components. Our study predicts novel molecular links to targets of CLL therapies and provides a valuable resource for further studies on the epigenetic contribution to the disease.
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Affiliation(s)
- Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Naveed Ishaque
- Division of Theoretical Bioinformatics and Heidelberg Center for Personalized Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lara C Klett
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sabrina J Kugler
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Jose M Muino
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Vladimir B Teif
- School of Biological Sciences, University of Essex, Colchester, UK
| | - Alexandra M Poos
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Sebastian Großmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
- Centre de Biologie Intégrative (CBI), CNRS, UPS, Toulouse, France
| | - Daniele Tavernari
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Sandra D Koser
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabrina Schumacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
- Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute Jena, Jena, Germany
| | - Daniel Remondini
- Department of Physics and Astronomy, Bologna University, Bologna, Italy
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Mertens
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
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203
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Holding AN, Giorgi FM, Donnelly A, Cullen AE, Nagarajan S, Selth LA, Markowetz F. VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer. Genome Biol 2019; 20:91. [PMID: 31084623 PMCID: PMC6515683 DOI: 10.1186/s13059-019-1698-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We apply our method to dissect the regulation of estrogen receptor-alpha activation in breast cancer to identify potential co-regulators of the estrogen receptor's transcriptional response. RESULTS VULCAN analysis of estrogen receptor activation in breast cancer highlights the key components of the estrogen receptor complex alongside a novel interaction with GRHL2. We demonstrate that GRHL2 is recruited to a subset of estrogen receptor binding sites and regulates transcriptional output, as evidenced by changes in estrogen receptor-associated eRNA expression and stronger estrogen receptor binding at active enhancers after GRHL2 knockdown. CONCLUSIONS Our findings provide new insight into the role of GRHL2 in regulating eRNA transcription as part of estrogen receptor signaling. These results demonstrate VULCAN, available from Bioconductor, as a powerful predictive tool.
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Affiliation(s)
- Andrew N Holding
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
- The Alan Turing Institute, 96 Euston Road, Kings Cross, London, NW1 2DB, UK.
| | - Federico M Giorgi
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, Bologna, Italy
| | - Amanda Donnelly
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy E Cullen
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories and Freemasons Foundation Centre for Men's Health, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Florian Markowetz
- CRUK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
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204
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Arnes L, Liu Z, Wang J, Maurer HC, Sagalovskiy I, Sanchez-Martin M, Bommakanti N, Garofalo DC, Balderes DA, Sussel L, Olive KP, Rabadan R. Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Gut 2019; 68:499-511. [PMID: 29440233 PMCID: PMC6086768 DOI: 10.1136/gutjnl-2017-314353] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 12/22/2017] [Accepted: 01/01/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease with limited therapeutic options. Genome and transcriptome analyses have identified signalling pathways and cancer driver genes with implications in patient stratification and targeted therapy. However, these analyses were performed in bulk samples and focused on coding genes, which represent a small fraction of the genome. DESIGN We developed a computational framework to reconstruct the non-coding transcriptome from cross-sectional RNA-Seq, integrating somatic copy number alterations (SCNA), common germline variants associated to PDA risk and clinical outcome. We validated the results in an independent cohort of paired epithelial and stromal RNA-Seq derived from laser capture microdissected human pancreatic tumours, allowing us to annotate the compartment specificity of their expression. We employed systems and experimental biology approaches to interrogate the function of epithelial long non-coding RNAs (lncRNAs) associated with genetic traits and clinical outcome in PDA. RESULTS We generated a catalogue of PDA-associated lncRNAs. We showed that lncRNAs define molecular subtypes with biological and clinical significance. We identified lncRNAs in genomic regions with SCNA and single nucleotide polymorphisms associated with lifetime risk of PDA and associated with clinical outcome using genomic and clinical data in PDA. Systems biology and experimental functional analysis of two epithelial lncRNAs (LINC00673 and FAM83H-AS1) suggest they regulate the transcriptional profile of pancreatic tumour samples and PDA cell lines. CONCLUSIONS Our findings indicate that lncRNAs are associated with genetic marks of pancreatic cancer risk, contribute to the transcriptional regulation of neoplastic cells and provide an important resource to design functional studies of lncRNAs in PDA.
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Affiliation(s)
- Luis Arnes
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Zhaoqi Liu
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Jiguang Wang
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Division of Life Science and Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - H. Carlo Maurer
- Columbia University Medical Center, New York, United States
- Department of Medicine, Division of Digestive and Liver Diseases, University of Colorado, Denver, United States
| | - Irina Sagalovskiy
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Marta Sanchez-Martin
- Columbia University Medical Center, New York, United States
- Institute for Cancer Genetics, University of Colorado, Denver, United States
| | - Nikhil Bommakanti
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
| | - Diana C. Garofalo
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
| | - Dina A. Balderes
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
| | - Lori Sussel
- Columbia University Medical Center, New York, United States
- Department of Genetics & Development, University of Colorado, Denver, United States
- Barbara Davis Center, University of Colorado, Denver, United States
| | - Kenneth P. Olive
- Columbia University Medical Center, New York, United States
- Department of Medicine, Division of Digestive and Liver Diseases, University of Colorado, Denver, United States
- Department of Pathology and Cell Biology
- Herbert Irving Comprehensive Cancer Center
| | - Raul Rabadan
- Columbia University Medical Center, New York, United States
- Department of Biomedical Informatics, Hong Kong University of Science and Technology, Hong Kong
- Department of Systems Biology, Hong Kong University of Science and Technology, Hong Kong
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205
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Ru B, Tong Y, Zhang J. MR4Cancer: a web server prioritizing master regulators for cancer. Bioinformatics 2019; 35:636-642. [PMID: 30052770 DOI: 10.1093/bioinformatics/bty658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 01/10/2023] Open
Abstract
MOTIVATION During cancer stage transition, a master regulator (MR) refers to the key gene controlling cancer initiation and progression by orchestrating the associated target genes (termed as its regulon). Due to their inherent importance, MRs can serve as critical biomarkers for cancer diagnosis and prognosis, and therapeutic targets. However, it is challenging to infer key MRs that might explain gene expression profile changes between two groups due to lack of context-specific regulons, whose expression level can collectively reflect the activity of likely MRs. There is also a need to design an easy-to-use tool of MR identification for research community. RESULTS First, we generated cancer-specific regulons for 26 cancer types by analyzing high-throughput omics data from TCGA, and extracted noncancer-specific regulons from public databases. We subsequently developed a web server MR4Cancer, integrating the regulons with statistical inference to identify and prioritize MRs driving a phenotypic divergence of interest. Based on the input gene list (e.g. differentially expressed genes) or expression profile with two groups, MR4Cancer outputs ranked MRs by enrichment testing against the predefined regulons. Gene Ontology and canonical pathway analyses are also conducted to elucidate the function of likely MRs. Moreover, MR4Cancer provides dynamic network visualization for MR-target relations, and users can interactively interrogate the network to produce new hypotheses and high-quality figures for publication. Finally, the presented case studies highlighted the performance of MR4Cancer. We expect this user-friendly and powerful web tool will provide researchers novel insights into tumorigenesis and therapeutic intervention. AVAILABILITY AND IMPLEMENTATION http://cis.hku.hk/MR4Cancer. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
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206
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Shi M, Shen W, Chong Y, Wang HQ. Improving GRN re-construction by mining hidden regulatory signals. IET Syst Biol 2019; 11:174-181. [PMID: 29125126 PMCID: PMC8687237 DOI: 10.1049/iet-syb.2017.0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Inferring gene regulatory networks (GRNs) from gene expression data is an important but challenging issue in systems biology. Here, the authors propose a dictionary learning-based approach that aims to infer GRNs by globally mining regulatory signals, known or latent. Gene expression is often regulated by various regulatory factors, some of which are observed and some of which are latent. The authors assume that all regulators are unknown for a target gene and the expression of the target gene can be mapped into a regulatory space spanned by all the regulators. Specifically, the authors modify the dictionary learning model, k-SVD, according to the sparse property of GRNs for mining the regulatory signals. The recovered regulatory signals are then used as a pool of regulatory factors to calculate a confidence score for a given transcription factor regulating a target gene. The capability of recovering hidden regulatory signals was verified on simulated data. Comparative experiments for GRN inference between the proposed algorithm (OURM) and some state-of-the-art algorithms, e.g. GENIE3 and ARACNE, on real-world data sets show the superior performance of OURM in inferring GRNs: higher area under the receiver operating characteristic curves and area under the precision-recall curves.
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Affiliation(s)
- Ming Shi
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Weiming Shen
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Yanwen Chong
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, 129 Luoyu Road, Wuhan 430079, People's Republic of China
| | - Hong-Qiang Wang
- Machine Intelligence and Computational Biology Laboratory, Institute of Intelligent Machines, Chinese Academy of Science, PO Box 1130, Hefei 230031, People's Republic of China.
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207
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Heyduk K, Hwang M, Albert V, Silvera K, Lan T, Farr K, Chang TH, Chan MT, Winter K, Leebens-Mack J. Altered Gene Regulatory Networks Are Associated With the Transition From C 3 to Crassulacean Acid Metabolism in Erycina (Oncidiinae: Orchidaceae). FRONTIERS IN PLANT SCIENCE 2019; 9:2000. [PMID: 30745906 PMCID: PMC6360190 DOI: 10.3389/fpls.2018.02000] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/24/2018] [Indexed: 05/21/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis is a modification of the core C3 photosynthetic pathway that improves the ability of plants to assimilate carbon in water-limited environments. CAM plants fix CO2 mostly at night, when transpiration rates are low. All of the CAM pathway genes exist in ancestral C3 species, but the timing and magnitude of expression are greatly altered between C3 and CAM species. Understanding these regulatory changes is key to elucidating the mechanism by which CAM evolved from C3. Here, we use two closely related species in the Orchidaceae, Erycina pusilla (CAM) and Erycina crista-galli (C3), to conduct comparative transcriptomic analyses across multiple time points. Clustering of genes with expression variation across the diel cycle revealed some canonical CAM pathway genes similarly expressed in both species, regardless of photosynthetic pathway. However, gene network construction indicated that 149 gene families had significant differences in network connectivity and were further explored for these functional enrichments. Genes involved in light sensing and ABA signaling were some of the most differently connected genes between the C3 and CAM Erycina species, in agreement with the contrasting diel patterns of stomatal conductance in C3 and CAM plants. Our results suggest changes to transcriptional cascades are important for the transition from C3 to CAM photosynthesis in Erycina.
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Affiliation(s)
- Karolina Heyduk
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Michelle Hwang
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Victor Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Katia Silvera
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Kimberly Farr
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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208
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Manners HN, Roy S, Kalita JK. Intrinsic-overlapping co-expression module detection with application to Alzheimer's Disease. Comput Biol Chem 2018; 77:373-389. [PMID: 30466046 DOI: 10.1016/j.compbiolchem.2018.10.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022]
Abstract
Genes interact with each other and may cause perturbation in the molecular pathways leading to complex diseases. Often, instead of any single gene, a subset of genes interact, forming a network, to share common biological functions. Such a subnetwork is called a functional module or motif. Identifying such modules and central key genes in them, that may be responsible for a disease, may help design patient-specific drugs. In this study, we consider the neurodegenerative Alzheimer's Disease (AD) and identify potentially responsible genes from functional motif analysis. We start from the hypothesis that central genes in genetic modules are more relevant to a disease that is under investigation and identify hub genes from the modules as potential marker genes. Motifs or modules are often non-exclusive or overlapping in nature. Moreover, they sometimes show intrinsic or hierarchical distributions with overlapping functional roles. To the best of our knowledge, no prior work handles both the situations in an integrated way. We propose a non-exclusive clustering approach, CluViaN (Clustering Via Network) that can detect intrinsic as well as overlapping modules from gene co-expression networks constructed using microarray expression profiles. We compare our method with existing methods to evaluate the quality of modules extracted. CluViaN reports the presence of intrinsic and overlapping motifs in different species not reported by any other research. We further apply our method to extract significant AD specific modules using CluViaN and rank them based the number of genes from a module involved in the disease pathways. Finally, top central genes are identified by topological analysis of the modules. We use two different AD phenotype data for experimentation. We observe that central genes, namely PSEN1, APP, NDUFB2, NDUFA1, UQCR10, PPP3R1 and a few more, play significant roles in the AD. Interestingly, our experiments also find a hub gene, PML, which has recently been reported to play a role in plasticity, circadian rhythms and the response to proteins which can cause neurodegenerative disorders. MUC4, another hub gene that we find experimentally is yet to be investigated for its potential role in AD. A software implementation of CluViaN in Java is available for download at https://sites.google.com/site/swarupnehu/publications/resources/CluViaN Software.rar.
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Affiliation(s)
- Hazel Nicolette Manners
- Department of Information Technology, North Eastern Hill University, Shillong, Meghalaya, India.
| | - Swarup Roy
- Department of Computer Applications, Sikkim University, Gangtok, Sikkim, India; Department of Information Technology, North Eastern Hill University, Shillong, Meghalaya, India.
| | - Jugal K Kalita
- Department of Computer Science, University of Colorado, Colorado Springs, USA.
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209
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Durón C, Pan Y, Gutmann DH, Hardin J, Radunskaya A. Variability of Betweenness Centrality and Its Effect on Identifying Essential Genes. Bull Math Biol 2018; 81:3655-3673. [PMID: 30350013 DOI: 10.1007/s11538-018-0526-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/11/2018] [Indexed: 11/27/2022]
Abstract
This paper begins to build a theoretical framework that would enable the pharmaceutical industry to use network complexity measures as a way to identify drug targets. The variability of a betweenness measure for a network node is examined through different methods of network perturbation. Our results indicate a robustness of betweenness centrality in the identification of target genes.
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Affiliation(s)
- Christina Durón
- Math Department, Claremont Graduate University, Claremont, CA, 91711, USA
| | - Yuan Pan
- Neurology and Neurological Sciences, Stanford University Medical Center, Palo Alto, CA, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Johanna Hardin
- Math Department, Pomona College, Claremont, CA, 91711, USA
| | - Ami Radunskaya
- Math Department, Pomona College, Claremont, CA, 91711, USA.
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210
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Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang F, Zhao XY, Qiao J. Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. Cell Stem Cell 2018; 23:599-614.e4. [PMID: 30174296 DOI: 10.1016/j.stem.2018.08.007] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/08/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022]
Abstract
Spermatogenesis generates mature male gametes and is critical for the proper transmission of genetic information between generations. However, the developmental landscapes of human spermatogenesis remain unknown. Here, we performed single-cell RNA sequencing (scRNA-seq) analysis for 2,854 testicular cells from donors with normal spermatogenesis and 174 testicular cells from one nonobstructive azoospermia (NOA) donor. A hierarchical model was established, which was characterized by the sequential and stepwise development of three spermatogonia subtypes, seven spermatocyte subtypes, and four spermatid subtypes. Further analysis identified several stage-specific marker genes of human germ cells, such as HMGA1, PIWIL4, TEX29, SCML1, and CCDC112. Moreover, we identified altered gene expression patterns in the testicular somatic cells of one NOA patient via scRNA-seq analysis, paving the way for further diagnosis of male infertility. Our work allows for the reconstruction of transcriptional programs inherent to sequential cell fate transition during human spermatogenesis and has implications for deciphering male-related reproductive disorders.
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Affiliation(s)
- Mei Wang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Xixi Liu
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Gang Chang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, PRC
| | - Yidong Chen
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PRC
| | - Geng An
- Reproductive Medicine Center of The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, PRC
| | - Liying Yan
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Shuai Gao
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yanwen Xu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Yueli Cui
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Ji Dong
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yuhan Chen
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Xiaoying Fan
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yuqiong Hu
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PRC
| | - Ke Song
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Xiaohui Zhu
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yun Gao
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Zhaokai Yao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Shuhui Bian
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PRC
| | - Yu Hou
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Jiahao Lu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Rui Wang
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yong Fan
- Reproductive Medicine Center of The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, PRC
| | - Ying Lian
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Wenhao Tang
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yapeng Wang
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Jianqiao Liu
- Reproductive Medicine Center of The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, PRC
| | - Lianming Zhao
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Luyu Wang
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Zhaoting Liu
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Renpei Yuan
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Yujia Shi
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC
| | - Boqiang Hu
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Xiulian Ren
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC
| | - Fuchou Tang
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100191, PRC; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PRC.
| | - Xiao-Yang Zhao
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, PRC; Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangdong 510515, PRC.
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, PRC; Biomedical Pioneering Innovation Center and Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, PRC; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, PRC.
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211
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Veras PST, Ramos PIP, de Menezes JPB. In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages. Front Cell Infect Microbiol 2018; 8:326. [PMID: 30283744 PMCID: PMC6157484 DOI: 10.3389/fcimb.2018.00326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/27/2018] [Indexed: 12/12/2022] Open
Abstract
Leishmaniasis is a vector-borne, neglected tropical disease with a worldwide distribution that can present in a variety of clinical forms, depending on the parasite species and host genetic background. The pathogenesis of this disease remains far from being elucidated because the involvement of a complex immune response orchestrated by host cells significantly affects the clinical outcome. Among these cells, macrophages are the main host cells, produce cytokines and chemokines, thereby triggering events that contribute to the mediation of the host immune response and, subsequently, to the establishment of infection or, alternatively, disease control. There has been relatively limited commercial interest in developing new pharmaceutical compounds to treat leishmaniasis. Moreover, advances in the understanding of the underlying biology of Leishmania spp. have not translated into the development of effective new chemotherapeutic compounds. As a result, biomarkers as surrogate disease endpoints present several potential advantages to be used in the identification of targets capable of facilitating therapeutic interventions considered to ameliorate disease outcome. More recently, large-scale genomic and proteomic analyses have allowed the identification and characterization of the pathways involved in the infection process in both parasites and the host, and these analyses have been shown to be more effective than studying individual molecules to elucidate disease pathogenesis. RNA-seq and proteomics are large-scale approaches that characterize genes or proteins in a given cell line, tissue, or organism to provide a global and more integrated view of the myriad biological processes that occur within a cell than focusing on an individual gene or protein. Bioinformatics provides us with the means to computationally analyze and integrate the large volumes of data generated by high-throughput sequencing approaches. The integration of genomic expression and proteomic data offers a rich multi-dimensional analysis, despite the inherent technical and statistical challenges. We propose that these types of global analyses facilitate the identification, among a large number of genes and proteins, those that hold potential as biomarkers. The present review focuses on large-scale studies that have identified and evaluated relevant biomarkers in macrophages in response to Leishmania infection.
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Affiliation(s)
- Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil.,National Institute of Tropical Disease, Brasilia, Brazil
| | - Pablo Ivan Pereira Ramos
- Center for Data and Knowledge Integration for Health, Gonçalo Moniz Institute, Fiocruz-Bahia, Salvador, Brazil
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212
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Smith BA, Balanis NG, Nanjundiah A, Sheu KM, Tsai BL, Zhang Q, Park JW, Thompson M, Huang J, Witte ON, Graeber TG. A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. Cell Rep 2018; 24:3353-3366.e5. [PMID: 30232014 PMCID: PMC6382070 DOI: 10.1016/j.celrep.2018.08.062] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/12/2018] [Accepted: 08/21/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer progression to an aggressive phenotype often co-opts aspects of stem cell biology. Here, we developed gene signatures for normal human stem cell populations to understand the relationship between epithelial cancers and stem cell transcriptional programs. Using a pan-cancer approach, we reveal that aggressive epithelial cancers are enriched for a transcriptional signature shared by epithelial adult stem cells. The adult stem cell signature selected for epithelial cancers with worse overall survival and alterations of oncogenic drivers. Lethal small cell neuroendocrine lung, prostate, and bladder cancers transcriptionally converged onto the adult stem cell signature and not other stem cell signatures tested. We found that DNA methyltransferase expression correlated with adult stem cell signature status and was enriched in small cell neuroendocrine cancers. DNA methylation analysis uncovered a shared epigenomic profile between small cell neuroendocrine cancers. These pan-cancer findings establish a molecular link between human adult stem cells and aggressive epithelial cancers.
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Affiliation(s)
- Bryan A Smith
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Nikolas G Balanis
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Avinash Nanjundiah
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Katherine M Sheu
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Brandon L Tsai
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Qingfu Zhang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Pathology, The First Affiliated Hospital of China Medical University, 110001 Shenyang, China
| | - Jung Wook Park
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Michael Thompson
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA 90095, USA.
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213
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Lavarenne J, Guyomarc'h S, Sallaud C, Gantet P, Lucas M. The Spring of Systems Biology-Driven Breeding. TRENDS IN PLANT SCIENCE 2018; 23:706-720. [PMID: 29764727 DOI: 10.1016/j.tplants.2018.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 05/08/2023]
Abstract
Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies.
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Affiliation(s)
- Jérémy Lavarenne
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Biogemma, Centre de Recherches de Chappes, Route d'Ennezat, 63720 Chappes, France
| | - Soazig Guyomarc'h
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Christophe Sallaud
- Biogemma, Centre de Recherches de Chappes, Route d'Ennezat, 63720 Chappes, France
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France.
| | - Mikaël Lucas
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
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214
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Villaverde AF, Becker K, Banga JR. PREMER: A Tool to Infer Biological Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1193-1202. [PMID: 28981423 DOI: 10.1109/tcbb.2017.2758786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features-such as distinguishing between direct and indirect interactions or determining the direction of a causal link-requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end, we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux, and OSX (https://sites.google.com/site/premertoolbox/).
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215
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Structure Optimization for Large Gene Networks Based on Greedy Strategy. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018; 2018:9674108. [PMID: 30013615 PMCID: PMC6022335 DOI: 10.1155/2018/9674108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023]
Abstract
In the last few years, gene networks have become one of most important tools to model biological processes. Among other utilities, these networks visually show biological relationships between genes. However, due to the large amount of the currently generated genetic data, their size has grown to the point of being unmanageable. To solve this problem, it is possible to use computational approaches, such as heuristics-based methods, to analyze and optimize gene network's structure by pruning irrelevant relationships. In this paper we present a new method, called GeSOp, to optimize large gene network structures. The method is able to perform a considerably prune of the irrelevant relationships comprising the input network. To do so, the method is based on a greedy heuristic to obtain the most relevant subnetwork. The performance of our method was tested by means of two experiments on gene networks obtained from different organisms. The first experiment shows how GeSOp is able not only to carry out a significant reduction in the size of the network, but also to maintain the biological information ratio. In the second experiment, the ability to improve the biological indicators of the network is checked. Hence, the results presented show that GeSOp is a reliable method to optimize and improve the structure of large gene networks.
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216
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Tong Y, Sun J, Wong CF, Kang Q, Ru B, Wong CN, Chan AS, Leung SY, Zhang J. MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. Genome Biol 2018; 19:73. [PMID: 29871649 PMCID: PMC5989391 DOI: 10.1186/s13059-018-1442-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/03/2018] [Indexed: 12/11/2022] Open
Abstract
Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumorigenesis called MICMIC. Many predictions are directly validated by dCas9-based epigenetic editing to support the accuracy and efficiency of our tool. Oncogenic and lineage-specific transcription factors are shown to aberrantly shape the methylation landscape by modifying tumor-subtype core regulatory circuitry. Notably, the gene regulatory networks orchestrated by enhancer methylation across different cancer types are seen to converge on a common architecture. MICMIC is available on https://github.com/ZhangJlab/MICMIC .
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Affiliation(s)
- Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chi Fat Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Qingzheng Kang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - April Sheila Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong.
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217
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Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H, Qiao J, Tang F. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat Cell Biol 2018; 20:721-734. [DOI: 10.1038/s41556-018-0105-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/17/2018] [Indexed: 12/11/2022]
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218
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Pan Y, Duron C, Bush EC, Ma Y, Sims PA, Gutmann DH, Radunskaya A, Hardin J. Graph complexity analysis identifies an ETV5 tumor-specific network in human and murine low-grade glioma. PLoS One 2018; 13:e0190001. [PMID: 29787563 PMCID: PMC5963759 DOI: 10.1371/journal.pone.0190001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 12/06/2017] [Indexed: 01/10/2023] Open
Abstract
Conventional differential expression analyses have been successfully employed to identify genes whose levels change across experimental conditions. One limitation of this approach is the inability to discover central regulators that control gene expression networks. In addition, while methods for identifying central nodes in a network are widely implemented, the bioinformatics validation process and the theoretical error estimates that reflect the uncertainty in each step of the analysis are rarely considered. Using the betweenness centrality measure, we identified Etv5 as a potential tissue-level regulator in murine neurofibromatosis type 1 (Nf1) low-grade brain tumors (optic gliomas). As such, the expression of Etv5 and Etv5 target genes were increased in multiple independently-generated mouse optic glioma models relative to non-neoplastic (normal healthy) optic nerves, as well as in the cognate human tumors (pilocytic astrocytoma) relative to normal human brain. Importantly, differential Etv5 and Etv5 network expression was not directly the result of Nf1 gene dysfunction in specific cell types, but rather reflects a property of the tumor as an aggregate tissue. Moreover, this differential Etv5 expression was independently validated at the RNA and protein levels. Taken together, the combined use of network analysis, differential RNA expression findings, and experimental validation highlights the potential of the computational network approach to provide new insights into tumor biology.
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Affiliation(s)
- Yuan Pan
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Christina Duron
- Department of Mathematics, Claremont Graduate University, Claremont, California, United Strates of America
| | - Erin C. Bush
- Departments of Systems Biology and of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Yu Ma
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter A. Sims
- Departments of Systems Biology and of Biochemistry & Molecular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - David H. Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ami Radunskaya
- Department of Mathematics, Pomona College, Claremont, California, United States of America
| | - Johanna Hardin
- Department of Mathematics, Pomona College, Claremont, California, United States of America
- * E-mail:
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219
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Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer Discov 2018; 8:582-599. [PMID: 29510988 PMCID: PMC5967627 DOI: 10.1158/2159-8290.cd-16-0861] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/06/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023]
Abstract
High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator proteins that were conserved across independent cohorts. A 10-protein transcriptional module-centered around a TEAD4-MYCN positive feedback loop-emerged as the regulatory driver of the high-risk subtype associated with MYCN amplification. Silencing of either gene collapsed MYCN-amplified (MYCNAmp) neuroblastoma transcriptional hallmarks and abrogated viability in vitro and in vivo Consistently, TEAD4 emerged as a robust prognostic marker of poor survival, with activity independent of the canonical Hippo pathway transcriptional coactivators YAP and TAZ. These results suggest novel therapeutic strategies for the large subset of MYCN-deregulated neuroblastomas.Significance: Despite progress in understanding of neuroblastoma genetics, little progress has been made toward personalized treatment. Here, we present a framework to determine the downstream effectors of the genetic alterations sustaining neuroblastoma subtypes, which can be easily extended to other tumor types. We show the critical effect of disrupting a 10-protein module centered around a YAP/TAZ-independent TEAD4-MYCN positive feedback loop in MYCNAmp neuroblastomas, nominating TEAD4 as a novel candidate for therapeutic intervention. Cancer Discov; 8(5); 582-99. ©2018 AACR.This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Presha Rajbhandari
- Department of Systems Biology, Columbia University, New York, New York
- Department of Biological Sciences, Columbia University, New York, New York
| | - Gonzalo Lopez
- Department of Systems Biology, Columbia University, New York, New York
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Claudia Capdevila
- Department of Systems Biology, Columbia University, New York, New York
| | | | - Jiyang Yu
- Department of Systems Biology, Columbia University, New York, New York
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ruth Rodriguez-Barrueco
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
- Departament de Patologia i Terapèutica Experimental, Facultat de Medicina i Ciències de la Salut, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Daniel Martinez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, New York
| | - Archana Iyer
- Department of Systems Biology, Columbia University, New York, New York
| | - Jo Lynne Harenza
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Derek Oldridge
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Katleen De Preter
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - Shahab Asgharzadeh
- Division of Hematology/Oncology, Saban Research Institute, The Children's Hospital Los Angeles, Los Angeles, California
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Robert C Seeger
- Division of Hematology/Oncology, Saban Research Institute, The Children's Hospital Los Angeles, Los Angeles, California
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jun S Wei
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Jo Vandesompele
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics & Cancer Research Institute Ghent (CRIG), Ghent University, Gent, Belgium
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, the Netherlands
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Antonio Iavarone
- Department of Neurology and Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, New York
| | - Anna Lasorella
- Department of Pediatrics and Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University, New York, New York
| | - Jose M Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, New York.
- Department of Biomedical Informatics, Columbia University, New York, New York
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York
- Herbert Irving Comprehensive Cancer Center and J.P. Sulzberger Columbia Genome Center, Columbia University, New York, New York
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220
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Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep 2018; 23:255-269.e4. [PMID: 29617665 PMCID: PMC5916795 DOI: 10.1016/j.celrep.2018.03.077] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/20/2018] [Accepted: 03/19/2018] [Indexed: 12/24/2022] Open
Abstract
Metabolic reprogramming provides critical information for clinical oncology. Using molecular data of 9,125 patient samples from The Cancer Genome Atlas, we identified tumor subtypes in 33 cancer types based on mRNA expression patterns of seven major metabolic processes and assessed their clinical relevance. Our metabolic expression subtypes correlated extensively with clinical outcome: subtypes with upregulated carbohydrate, nucleotide, and vitamin/cofactor metabolism most consistently correlated with worse prognosis, whereas subtypes with upregulated lipid metabolism showed the opposite. Metabolic subtypes correlated with diverse somatic drivers but exhibited effects convergent on cancer hallmark pathways and were modulated by highly recurrent master regulators across cancer types. As a proof-of-concept example, we demonstrated that knockdown of SNAI1 or RUNX1-master regulators of carbohydrate metabolic subtypes-modulates metabolic activity and drug sensitivity. Our study provides a system-level view of metabolic heterogeneity within and across cancer types and identifies pathway cross-talk, suggesting related prognostic, therapeutic, and predictive utility.
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Affiliation(s)
- Xinxin Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongyuan Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Farshad Farshidfar
- Departments of Surgery and Oncology, University of Calgary, Calgary, T2N 4N2 Alberta, Canada; Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, T2N 4N1 Alberta, Canada
| | - Xiaoyan Xu
- Department of Pathophysiology, College of Basic Medicine Science, China Medical University, Shenyang, Liaoning Province 110122, China; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Proteomics and Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yumeng Wang
- Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Feixiong Cheng
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Proteomics and Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kamalika Mojumdar
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Di Du
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhongqi Ge
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George V Thomas
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University Knight Cancer Institute, Portland, OR 97239, USA
| | - Kivanc Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Lingxiang Liu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Huiwen Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Calena Marchand
- Faculty of Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Oliver F Bathe
- Departments of Surgery and Oncology, University of Calgary, Calgary, T2N 4N2 Alberta, Canada.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
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221
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Izzi V, Lakkala J, Devarajan R, Savolainen ER, Koistinen P, Heljasvaara R, Pihlajaniemi T. Vanin 1 (VNN1) levels predict poor outcome in acute myeloid leukemia. Am J Hematol 2018; 93:E4-E7. [PMID: 28971505 DOI: 10.1002/ajh.24925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Valerio Izzi
- Centre of Excellence in Cell-Extracellular Matrix Research and Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu; Oulu Finland
| | - Juho Lakkala
- Centre of Excellence in Cell-Extracellular Matrix Research and Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu; Oulu Finland
| | - Raman Devarajan
- Centre of Excellence in Cell-Extracellular Matrix Research and Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu; Oulu Finland
| | - Eeva-Riitta Savolainen
- Nordlab Oulu and Institute of Diagnostics, Department of Clinical Chemistry; Oulu University Hospital, University of Oulu; Oulu Finland
- Medical Research Center Oulu, Institute of Clinical Medicine, Oulu University Hospital, University of Oulu; Oulu Finland
| | - Pirjo Koistinen
- Medical Research Center Oulu, Institute of Clinical Medicine, Oulu University Hospital, University of Oulu; Oulu Finland
| | - Ritva Heljasvaara
- Centre of Excellence in Cell-Extracellular Matrix Research and Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu; Oulu Finland
- Centre for Cancer Biomarkers (CCBIO), Department of Biomedicine; University of Bergen; Bergen N-5009 Norway
| | - Taina Pihlajaniemi
- Centre of Excellence in Cell-Extracellular Matrix Research and Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu; Oulu Finland
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222
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Chen Y, Widschwendter M, Teschendorff AE. Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development. Genome Biol 2017; 18:236. [PMID: 29262847 PMCID: PMC5738803 DOI: 10.1186/s13059-017-1366-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Background Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylation of the aryl hydrocarbon-receptor repressor (AHRR) locus, which is observed in blood and squamous epithelial cells of smokers, but not in lung cancer. Results Using a novel systems-epigenomics algorithm, called SEPIRA, which leverages the power of a large RNA-sequencing expression compendium to infer regulatory activity from messenger RNA expression or DNA methylation (DNAm) profiles, we infer the landscape of binding activity of lung-specific transcription factors (TFs) in lung carcinogenesis. We show that lung-specific TFs become preferentially inactivated in lung cancer and precursor lung cancer lesions and further demonstrate that these results can be derived using only DNAm data. We identify subsets of TFs which become inactivated in precursor cells. Among these regulatory factors, we identify AHR, the aryl hydrocarbon-receptor which controls a healthy immune response in the lung epithelium and whose repressor, AHRR, has recently been implicated in smoking-mediated lung cancer. In addition, we identify FOXJ1, a TF which promotes growth of airway cilia and effective clearance of the lung airway epithelium from carcinogens. Conclusions We identify TFs, such as AHR, which become inactivated in the earliest stages of lung cancer and which, unlike AHRR hypomethylation, are also inactivated in lung cancer itself. The novel systems-epigenomics algorithm SEPIRA will be useful to the wider epigenome-wide association study community as a means of inferring regulatory activity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1366-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuting Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK. .,UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.
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223
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He J, Zhou Z, Reed M, Califano A. Accelerated parallel algorithm for gene network reverse engineering. BMC SYSTEMS BIOLOGY 2017; 11:83. [PMID: 28950860 PMCID: PMC5615246 DOI: 10.1186/s12918-017-0458-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) represents one of the most effective tools to reconstruct gene regulatory networks from large-scale molecular profile datasets. However, previous implementations require intensive computing resources and, in some cases, restrict the number of samples that can be used. These issues can be addressed elegantly in a GPU computing framework, where repeated mathematical computation can be done efficiently, but requires extensive redesign to apply parallel computing techniques to the original serial algorithm, involving detailed optimization efforts based on a deep understanding of both hardware and software architecture. Result Here, we present an accelerated parallel implementation of ARACNE (GPU-ARACNE). By taking advantage of multi-level parallelism and the Compute Unified Device Architecture (CUDA) parallel kernel-call library, GPU-ARACNE successfully parallelizes a serial algorithm and simplifies the user experience from multi-step operations to one step. Using public datasets on comparable hardware configurations, we showed that GPU-ARACNE is faster than previous implementations and is able to reconstruct equally valid gene regulatory networks. Conclusion Given that previous versions of ARACNE are extremely resource demanding, either in computational time or in hardware investment, GPU-ARACNE is remarkably valuable for researchers who need to build complex regulatory networks from large expression datasets, but with limited budget on computational resources. In addition, our GPU-centered optimization of adaptive partitioning for Mutual Information (MI) estimation provides lessons that are applicable to other domains. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0458-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing He
- Department of Biomedical Informatics, Columbia University, 168th Street, New York, 10032, NY, USA.,Department of Systems Biology, 1130 St Nicholas Street, New York, 10032, NY, USA
| | - Zhou Zhou
- Department of Computer Science, New York, 10027, NY, USA
| | - Michael Reed
- Department of Computer Science, New York, 10027, NY, USA
| | - Andrea Califano
- Department of Systems Biology, 1130 St Nicholas Street, New York, 10032, NY, USA.
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224
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Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017; 20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
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225
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Moran B, Rahman A, Palonen K, Lanigan FT, Gallagher WM. Master Transcriptional Regulators in Cancer: Discovery via Reverse Engineering Approaches and Subsequent Validation. Cancer Res 2017; 77:2186-2190. [PMID: 28428271 DOI: 10.1158/0008-5472.can-16-1813] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/08/2016] [Accepted: 02/22/2017] [Indexed: 11/16/2022]
Abstract
Reverse engineering of transcriptional networks using gene expression data enables identification of genes that underpin the development and progression of different cancers. Methods to this end have been available for over a decade and, with a critical mass of transcriptomic data in the oncology arena having been reached, they are ever more applicable. Extensive and complex networks can be distilled into a small set of key master transcriptional regulators (MTR), genes that are very highly connected and have been shown to be involved in processes of known importance in disease. Interpreting and validating the results of standardized bioinformatic methods is of crucial importance in determining the inherent value of MTRs. In this review, we briefly describe how MTRs are identified and focus on providing an overview of how MTRs can and have been validated for use in clinical decision making in malignant diseases, along with serving as tractable therapeutic targets. Cancer Res; 77(9); 2186-90. ©2017 AACR.
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Affiliation(s)
- Bruce Moran
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Research, UCD Conway Institute, University College Dublin, Dublin, Ireland.,OncoMark Limited, NovaUCD, Belfield Innovation Park, Belfield, Dublin, Ireland
| | - Arman Rahman
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Research, UCD Conway Institute, University College Dublin, Dublin, Ireland.,OncoMark Limited, NovaUCD, Belfield Innovation Park, Belfield, Dublin, Ireland
| | - Katja Palonen
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Research, UCD Conway Institute, University College Dublin, Dublin, Ireland.,OncoMark Limited, NovaUCD, Belfield Innovation Park, Belfield, Dublin, Ireland
| | - Fiona T Lanigan
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Research, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Research, UCD Conway Institute, University College Dublin, Dublin, Ireland. .,OncoMark Limited, NovaUCD, Belfield Innovation Park, Belfield, Dublin, Ireland
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226
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Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R, Mochida K. Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2017; 8:2055. [PMID: 29234348 PMCID: PMC5712366 DOI: 10.3389/fpls.2017.02055] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/16/2017] [Indexed: 05/08/2023]
Abstract
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis. The expression data are feasible to infer network sparsity based on ARX models. We found that genes involved in biological processes such as transcriptional regulation, protein degradation, and post-transcriptional modification and photosynthesis are significantly enriched in the periodic genes, suggesting that these processes might be regulated by circadian rhythm in B. distachyon. On the basis of the time-series expression patterns of the periodic genes, we constructed a chronological gene co-expression network and identified putative transcription factors encoding genes that might be involved in the time-specific regulatory transcriptional network. Moreover, we inferred a transcriptional network composed of the periodic genes in B. distachyon, aiming to identify genes associated with other genes through variable selection by grouping time points for each gene. Based on the ARX model with the group SCAD regularization using our time-series expression datasets of the periodic genes, we constructed gene networks and found that the networks represent typical scale-free structure. Our findings demonstrate that the diurnal changes in the transcriptome in B. distachyon leaves have a sparse network structure, demonstrating the spatiotemporal gene regulatory network over the cyclic phase transitions in B. distachyon diurnal growth.
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Affiliation(s)
- Satoru Koda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | | | - Kotaro Takahagi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
| | - Yukiko Uehara-Yamaguchi
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Minami Shimizu
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Komaki Inoue
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, Kochi University, Kochi, Japan
| | - Hiroshi Honda
- Graduate School of Mathematics, Kyushu University, Fukuoka, Japan
| | - Shinto Eguchi
- The Institute of Statistical Mathematics, Tokyo, Japan
| | - Ryuei Nishii
- Institute of Mathematics for Industry, Kyushu University, Fukuoka, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa, Japan
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
- *Correspondence: Keiichi Mochida, Ryuei Nishii,
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