1
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Li N, Gao Y, Zhang Y, Yu D, Lin J, Feng J, Li J, Xu Z, Zhang Y, Dang S, Zhou K, Liu Y, Li XD, Tye BK, Li Q, Gao N, Zhai Y. Parental histone transfer caught at the replication fork. Nature 2024; 627:890-897. [PMID: 38448592 DOI: 10.1038/s41586-024-07152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
In eukaryotes, DNA compacts into chromatin through nucleosomes1,2. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin3,4. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A-H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3-H4 tetramer, while the vacant H2A-H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3-H4 dimer and extends across the tetramerization interface of the H3-H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3-H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yuan Gao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yujie Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Daqi Yu
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jianwei Lin
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jian Li
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Zhichun Xu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Yingyi Zhang
- Biological Cryo-EM Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Keda Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Yang Liu
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Bik Kwoon Tye
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - Yuanliang Zhai
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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2
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Otto RM, Turska-Nowak A, Brown PM, Reynolds KA. A continuous epistasis model for predicting growth rate given combinatorial variation in gene expression and environment. Cell Syst 2024; 15:134-148.e7. [PMID: 38340730 PMCID: PMC10885703 DOI: 10.1016/j.cels.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/13/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Quantifying and predicting growth rate phenotype given variation in gene expression and environment is complicated by epistatic interactions and the vast combinatorial space of possible perturbations. We developed an approach for mapping expression-growth rate landscapes that integrates sparsely sampled experimental measurements with an interpretable machine learning model. We used mismatch CRISPRi across pairs and triples of genes to create over 8,000 titrated changes in E. coli gene expression under varied environmental contexts, exploring epistasis in up to 22 distinct environments. Our results show that a pairwise model previously used to describe drug interactions well-described these data. The model yielded interpretable parameters related to pathway architecture and generalized to predict the combined effect of up to four perturbations when trained solely on pairwise perturbation data. We anticipate this approach will be broadly applicable in optimizing bacterial growth conditions, generating pharmacogenomic models, and understanding the fundamental constraints on bacterial gene expression. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Ryan M Otto
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Agata Turska-Nowak
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Philip M Brown
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA
| | - Kimberly A Reynolds
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA; Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75230, USA.
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3
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Li J, Chen D, Liu H, Xi Y, Luo H, Wei Y, Liu J, Liang H, Zhang Q. Identifying potential genetic epistasis implicated in Alzheimer's disease via detection of SNP-SNP interaction on quantitative trait CSF Aβ 42. Neurobiol Aging 2024; 134:84-93. [PMID: 38039940 DOI: 10.1016/j.neurobiolaging.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 12/03/2023]
Abstract
Although genome-wide association studies have identified multiple Alzheimer's disease (AD)-associated loci by selecting the main effects of individual single-nucleotide polymorphisms (SNPs), the interpretation of genetic variance in AD is limited. Based on the linear regression method, we performed genome-wide SNP-SNP interaction on cerebrospinal fluid Aβ42 to identify potential genetic epistasis implicated in AD, with age, gender, and diagnosis as covariates. A GPU-based method was used to address the computational challenges posed by the analysis of epistasis. We found 368 SNP pairs to be statistically significant, and highly significant SNP-SNP interactions were identified between the marginal main effects of SNP pairs, which explained a relatively high variance at the Aβ42 level. Our results replicated 100 previously reported AD-related genes and 5 gene-gene interaction pairs of the protein-protein interaction network. Our bioinformatics analyses provided preliminary evidence that the 5-overlapping gene-gene interaction pairs play critical roles in inducing synaptic loss and dysfunction, thereby leading to memory decline and cognitive impairment in AD-affected brains.
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Affiliation(s)
- Jin Li
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Dandan Chen
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China; School of Automation Engineering, Northeast Electric Power University, Jilin, China
| | - Hongwei Liu
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Yang Xi
- School of Computer Science, Northeast Electric Power University, Jilin, China
| | - Haoran Luo
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Yiming Wei
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Junfeng Liu
- School of Computer Science, Northeast Electric Power University, Jilin, China
| | - Hong Liang
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China.
| | - Qiushi Zhang
- School of Computer Science, Northeast Electric Power University, Jilin, China.
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4
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de Vienne D, Coton C, Dillmann C. The genotype-phenotype relationship and evolutionary genetics in the light of the Metabolic Control Analysis. Biosystems 2023; 232:105000. [PMID: 37586656 DOI: 10.1016/j.biosystems.2023.105000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Metabolic control analysis has long been used as a systemic model of the genotype-phenotype (GP) relationship. By considering kinetic parameters and enzyme concentrations as reflecting the genotype level and metabolic fluxes or pools as phenotypes related to fitness, MCA has given a biological basis to the relationship between these two levels. The non-linear and concave relationship between enzymes and fluxes can account for common genetic effects that reductionist approaches have been powerless to explain, such as the dominance of active alleles over less active alleles, the various types of epistasis and heterosis, and reveals the structural links between these genetic effects. The summation property of the flux control coefficients accounts for the L-shaped distribution of Quantitative Trait Locus (QTL) effects, irrespective of other possible causes. Metabolic models of response to selection results in evolutionary scenarios that are markedly different from those derived from the classical infinitesimal model of quantitative genetics. In particular, evolution towards selective neutrality appears to be a consequence of the diminishing return of the flux-enzyme relationship. In this paper, we survey the historical and recent achievements of MCA in genetics, quantitative genetics and evolution, focusing on epistasis and the evolution of flux in relation to enzyme concentrations.
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Affiliation(s)
- D de Vienne
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
| | - C Coton
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
| | - C Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech. GQE-Le Moulon, IDEEV, 12, route 128, Gif-sur-Yvette, 91190, France.
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5
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Singhal P, Verma SS, Ritchie MD. Gene Interactions in Human Disease Studies-Evidence Is Mounting. Annu Rev Biomed Data Sci 2023; 6:377-395. [PMID: 37196359 DOI: 10.1146/annurev-biodatasci-102022-120818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Despite monumental advances in molecular technology to generate genome sequence data at scale, there is still a considerable proportion of heritability in most complex diseases that remains unexplained. Because many of the discoveries have been single-nucleotide variants with small to moderate effects on disease, the functional implication of many of the variants is still unknown and, thus, we have limited new drug targets and therapeutics. We, and many others, posit that one primary factor that has limited our ability to identify novel drug targets from genome-wide association studies may be due to gene interactions (epistasis), gene-environment interactions, network/pathway effects, or multiomic relationships. We propose that many of these complex models explain much of the underlying genetic architecture of complex disease. In this review, we discuss the evidence from multiple research avenues, ranging from pairs of alleles to multiomic integration studies and pharmacogenomics, that supports the need for further investigation of gene interactions (or epistasis) in genetic and genomic studies of human disease. Our goal is to catalog the mounting evidence for epistasis in genetic studies and the connections between genetic interactions and human health and disease that could enable precision medicine of the future.
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Affiliation(s)
- Pankhuri Singhal
- Genetics and Epigenetics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shefali Setia Verma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
- Penn Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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6
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Nielsen BF, Saad-Roy CM, Li Y, Sneppen K, Simonsen L, Viboud C, Levin SA, Grenfell BT. Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2. PLoS Comput Biol 2023; 19:e1010896. [PMID: 36791146 PMCID: PMC9974118 DOI: 10.1371/journal.pcbi.1010896] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/28/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines.
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Affiliation(s)
- Bjarke Frost Nielsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Chadi M. Saad-Roy
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Miller Institute for Basic Research in Science, University of California, Berkeley, California, United States of America
| | - Yimei Li
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Kim Sneppen
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lone Simonsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
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7
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Yang CH, Huang HC, Hou MF, Chuang LY, Lin YD. Fuzzy-Based Multiobjective Multifactor Dimensionality Reduction for Epistasis Analysis. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:378-387. [PMID: 35061588 DOI: 10.1109/tcbb.2022.3144303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epistasis detection is vital for understanding disease susceptibility in genetics. Multiobjective multifactor dimensionality reduction (MOMDR) was previously proposed to detect epistasis. MOMDR was performed using binary classification to distinguish the high-risk (H) and low-risk (L) groups to reduce multifactor dimensionality. However, the binary classification does not reflect the uncertainty of the H and L classification. In this study, we proposed an empirical fuzzy MOMDR (EFMOMDR) to address the limitations of binary classification using the degree of membership through an empirical fuzzy approach. The EFMOMDR can simultaneously consider two incorporated fuzzy-based measures, including correct classification rate and likelihood rate, and does not require parameter tuning. Simulation studies revealed that EFMOMDR has higher 7.14% detection success rates than MOMDR, indicating that the limitations of binary classification of MOMDR have been successfully improved by empirical fuzzy. Moreover, EFMOMDR was used to analyze coronary artery disease in the Wellcome Trust Case Control Consortium dataset.
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8
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Alemrajabi M, Macias Calix K, Assis R. Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure. J Mol Evol 2022; 90:429-437. [PMID: 36178491 PMCID: PMC9523185 DOI: 10.1007/s00239-022-10073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022]
Abstract
Epistasis is an evolutionary phenomenon whereby the fitness effect of a mutation depends on the genetic background in which it arises. A key source of epistasis in an RNA molecule is its secondary structure, which contains functionally important topological motifs held together by hydrogen bonds between Watson–Crick (WC) base pairs. Here we study epistasis in the secondary structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by examining properties of derived alleles arising from substitution mutations at ancestral WC base-paired and unpaired (UP) sites in 15 conserved topological motifs across the genome. We uncover fewer derived alleles and lower derived allele frequencies at WC than at UP sites, supporting the hypothesis that modifications to the secondary structure are often deleterious. At WC sites, we also find lower derived allele frequencies for mutations that abolish base pairing than for those that yield G·U “wobbles,” illustrating that weak base pairing can partially preserve the integrity of the secondary structure. Last, we show that WC sites under the strongest epistatic constraint reside in a three-stemmed pseudoknot motif that plays an essential role in programmed ribosomal frameshifting, whereas those under the weakest epistatic constraint are located in 3’ UTR motifs that regulate viral replication and pathogenicity. Our findings demonstrate the importance of epistasis in the evolution of the SARS-CoV-2 secondary structure, as well as highlight putative structural and functional targets of different forms of natural selection.
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Affiliation(s)
- Mahsa Alemrajabi
- Department of Physics, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Ksenia Macias Calix
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Raquel Assis
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, 33431, USA.
- Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL, 33431, USA.
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9
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Abstract
The mapping from genotype to phenotype to fitness typically involves multiple nonlinearities that can transform the effects of mutations. For example, mutations may contribute additively to a phenotype, but their effects on fitness may combine non-additively because selection favors a low or intermediate value of that phenotype. This can cause incongruence between the topographical properties of a fitness landscape and its underlying genotype-phenotype landscape. Yet, genotype-phenotype landscapes are often used as a proxy for fitness landscapes to study the dynamics and predictability of evolution. Here, we use theoretical models and empirical data on transcription factor-DNA interactions to systematically study the incongruence of genotype-phenotype and fitness landscapes when selection favors a low or intermediate phenotypic value. Using the theoretical models, we prove a number of fundamental results. For example, selection for low or intermediate phenotypic values does not change simple sign epistasis into reciprocal sign epistasis, implying that genotype-phenotype landscapes with only simple sign epistasis motifs will always give rise to single-peaked fitness landscapes under such selection. More broadly, we show that such selection tends to create fitness landscapes that are more rugged than the underlying genotype-phenotype landscape, but this increased ruggedness typically does not frustrate adaptive evolution because the local adaptive peaks in the fitness landscape tend to be nearly as tall as the global peak. Many of these results carry forward to the empirical genotype-phenotype landscapes, which may help to explain why low- and intermediate-affinity transcription factor-DNA interactions are so prevalent in eukaryotic gene regulation. How do mutations change phenotypic traits and organismal fitness? This question is often addressed in the context of a classic metaphor of evolutionary theory—the fitness landscape. A fitness landscape is akin to a physical landscape, in which genotypes define spatial coordinates, and fitness defines the elevation of each coordinate. Evolution then acts like a hill-climbing process, in which populations ascend fitness peaks as a consequence of mutation and selection. It is becoming increasingly common to construct such landscapes using experimental data from high-throughput sequencing technologies and phenotypic assays, in systems such as macromolecules and gene regulatory circuits. Although these landscapes are typically defined by molecular phenotypes, and are therefore more appropriately referred to as genotype-phenotype landscapes, they are often used to study evolutionary dynamics. This requires the assumption that the molecular phenotype is a reasonable proxy for fitness, which need not be the case. For example, selection may favor a low or intermediate phenotypic value, causing incongruence between a fitness landscape and its underlying genotype-phenotype landscape. Here, we study such incongruence using a diversity of theoretical models and experimental data from gene regulatory systems. We regularly find incongruence, in that fitness landscapes tend to comprise more peaks than their underlying genotype-phenotype landscapes. However, using evolutionary simulations, we show that this increased ruggedness need not impede adaptation.
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Affiliation(s)
- Malvika Srivastava
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L. Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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10
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Yang X, Yang C, Lei J, Liu J. An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:2654-2671. [PMID: 34181547 DOI: 10.1109/tcbb.2021.3092719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Proposing a more effective and accurate epistatic loci detection method in large-scale genomic data has important research significance for improving crop quality, disease treatment, etc. Due to the characteristics of high accuracy and processing non-linear relationship, Bayesian network (BN) has been widely used in constructing the network of SNPs and phenotype traits and thus to mine epistatic loci. However, the shortcoming of BN is that it is easy to fall into local optimum and unable to process large-scale of SNPs. In this work, we transform the problem of learning Bayesian network into the optimization of integer linear programming (ILP). We use the algorithms of branch-and-bound and cutting planes to get the global optimal Bayesian network (ILPBN), and thus to get epistatic loci influencing specific phenotype traits. In order to handle large-scale of SNP loci and further to improve efficiency, we use the method of optimizing Markov blanket to reduce the number of candidate parent nodes for each node. In addition, we use α-BIC that is suitable for processing the epistatis mining to calculate the BN score. We use four properties of BN decomposable scoring functions to further reduce the number of candidate parent sets for each node. Experiment results show that ILPBN can not only process 2-locus and 3-locus epistasis mining, but also realize multi-locus epistasis detection. Finally, we compare ILPBN with several popular epistasis mining algorithms by using simulated and real Age-related macular disease (AMD) dataset. Experiment results show that ILPBN has better epistasis detection accuracy, F1-score and false positive rate in premise of ensuring the efficiency compared with other methods. Availability: Codes and dataset are available at: http://122.205.95.139/ILPBN/.
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11
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Zuanetti DA, Milan LA. Bayesian Modeling for Epistasis Analysis Using Data-Driven Reversible Jump. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:1495-1506. [PMID: 33301408 DOI: 10.1109/tcbb.2020.3043857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We propose a procedure for modeling a phenotype using QTLs which estimate the additive and dominance effects of genotypes and epistasis. The estimation of the model is implemented through a Bayesian approach which uses the data-driven reversible jump (DDRJ) for multiple QTL mapping and model selection. We compare the DDRJ's performance with the usual reversible jump (RJ), QTLBim, multiple interval mapping (MIM) and LASSO using real and simulated data sets. The DDRJ outperforms the available methods to estimate the number of QTLs in epistatic models and it identifies their locations in the genome, without increasing the number of false-positive QTLs in the considered data. Since QTL mapping is a regression model involving complex non-observable variables and their interactions, the model selection procedure proposed here is also useful in other areas of research. The application for identifying main and epistatic relevant QTLs to systolic blood pressure after salt intervention is our main motivation.
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12
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Ponte-Fernandez C, Gonzalez-Dominguez J, Carvajal-Rodriguez A, Martin MJ. Evaluation of Existing Methods for High-Order Epistasis Detection. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:912-926. [PMID: 33055017 DOI: 10.1109/tcbb.2020.3030312] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Finding epistatic interactions among loci when expressing a phenotype is a widely employed strategy to understand the genetic architecture of complex traits in GWAS. The abundance of methods dedicated to the same purpose, however, makes it increasingly difficult for scientists to decide which method is more suitable for their studies. This work compares the different epistasis detection methods published during the last decade in terms of runtime, detection power and type I error rate, with a special emphasis on high-order interactions. Results show that in terms of detection power, the only methods that perform well across all experiments are the exhaustive methods, although their computational cost may be prohibitive in large-scale studies. Regarding non-exhaustive methods, not one could consistently find epistasis interactions when marginal effects are absent. If marginal effects are present, there are methods that perform well for high-order interactions, such as BADTrees, FDHE-IW, SingleMI or SNPHarvester. As for false-positive control, only SNPHarvester, FDHE-IW and DCHE show good results. The study concludes that there is no single epistasis detection method to recommend in all scenarios. Authors should prioritize exhaustive methods when sufficient computational resources are available considering the data set size, and resort to non-exhaustive methods when the analysis time is prohibitive.
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13
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Sun S, Roth C, Floyd Averette A, Magwene PM, Heitman J. Epistatic genetic interactions govern morphogenesis during sexual reproduction and infection in a global human fungal pathogen. Proc Natl Acad Sci U S A 2022; 119:e2122293119. [PMID: 35169080 PMCID: PMC8872808 DOI: 10.1073/pnas.2122293119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Cellular development is orchestrated by evolutionarily conserved signaling pathways, which are often pleiotropic and involve intra- and interpathway epistatic interactions that form intricate, complex regulatory networks. Cryptococcus species are a group of closely related human fungal pathogens that grow as yeasts yet transition to hyphae during sexual reproduction. Additionally, during infection they can form large, polyploid titan cells that evade immunity and develop drug resistance. Multiple known signaling pathways regulate cellular development, yet how these are coordinated and interact with genetic variation is less well understood. Here, we conducted quantitative trait locus (QTL) analyses of a mapping population generated by sexual reproduction of two parents, only one of which is unisexually fertile. We observed transgressive segregation of the unisexual phenotype among progeny, as well as a large-cell phenotype under mating-inducing conditions. These large-cell progeny were found to produce titan cells both in vitro and in infected animals. Two major QTLs and corresponding quantitative trait genes (QTGs) were identified: RIC8 (encoding a guanine-exchange factor) and CNC06490 (encoding a putative Rho-GTPase activator), both involved in G protein signaling. The two QTGs interact epistatically with each other and with the mating-type locus in phenotypic determination. These findings provide insights into the complex genetics of morphogenesis during unisexual reproduction and pathogenic titan cell formation and illustrate how QTL analysis can be applied to identify epistasis between genes. This study shows that phenotypic outcomes are influenced by the genetic background upon which mutations arise, implicating dynamic, complex genotype-to-phenotype landscapes in fungal pathogens and beyond.
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Affiliation(s)
- Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Cullen Roth
- Department of Biology, Duke University, Durham, NC 27708
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710
| | - Paul M Magwene
- Department of Biology, Duke University, Durham, NC 27708
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710;
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Wang J, Zhang H, Ren W, Guo M, Yu G. EpiMC: Detecting Epistatic Interactions Using Multiple Clusterings. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:243-254. [PMID: 33989157 DOI: 10.1109/tcbb.2021.3080462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Detecting single nucleotide polymorphisms (SNPs) interactions is crucial to identify susceptibility genes associated with complex human diseases in genome-wide association studies. Clustering-based approaches are widely used in reducing search space and exploring potential relationships between SNPs in epistasis analysis. However, these approaches all only use a single measure to filter out nonsignificant SNP combinations, which may be significant ones from another perspective. In this paper, we propose a two-stage approach named EpiMC (Epistatic Interactions detection based on Multiple Clusterings) that employs multiple clusterings to obtain more precise candidate sets and more comprehensively detect high-order interactions based on these sets. In the first stage, EpiMC proposes a matrix factorization based multiple clusterings algorithm to generate multiple diverse clusterings, each of which divide all SNPs into different clusters. This stage aims to reduce the chance of filtering out potential candidates overlooked by a single clustering and groups associated SNPs together from different clustering perspectives. In the next stage, EpiMC considers both the single-locus effects and interaction effects to select high-quality disease associated SNPs, and then uses Jaccard similarity to get candidate sets. Finally, EpiMC uses exhaustive search on the obtained small candidate sets to precisely detect epsitatic interactions. Extensive simulation experiments show that EpiMC has a better performance in detecting high-order interactions than state-of-the-art solutions. On the Wellcome Trust Case Control Consortium (WTCCC) dataset, EpiMC detects several significant epistatic interactions associated with breast cancer (BC) and age-related macular degeneration (AMD), which again corroborate the effectiveness of EpiMC.
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15
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John E, Jacques S, Phan HTT, Liu L, Pereira D, Croll D, Singh KB, Oliver RP, Tan KC. Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat. PLoS Pathog 2022; 18:e1010149. [PMID: 34990464 PMCID: PMC8735624 DOI: 10.1371/journal.ppat.1010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022] Open
Abstract
The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in representative P. nodorum isolates from Australia and South Africa. The presence of PE401 removed the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both 'selfish' and 'altruistic' characteristics. This offers an insight into a complex NE-NE interaction that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Huyen T. T. Phan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Lifang Liu
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Karam B. Singh
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
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16
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Kuo T, Du W, Miyachi Y, Dadi PK, Jacobson DA, Segrè D, Accili D. Antagonistic epistasis of Hnf4α and FoxO1 metabolic networks through enhancer interactions in β-cell function. Mol Metab 2021; 53:101256. [PMID: 34048961 PMCID: PMC8225970 DOI: 10.1016/j.molmet.2021.101256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Genetic and acquired abnormalities contribute to pancreatic β-cell failure in diabetes. Transcription factors Hnf4α (MODY1) and FoxO1 are respective examples of these two components and act through β-cell-specific enhancers. However, their relationship is unclear. METHODS In this report, we show by genome-wide interrogation of chromatin modifications that ablation of FoxO1 in mature β-cells enriches active Hnf4α enhancers according to a HOMER analysis. RESULTS To model the functional significance of this predicted unusual enhancer utilization, we generated single and compound knockouts of FoxO1 and Hnf4α in β-cells. Single knockout of either gene impaired insulin secretion in mechanistically distinct fashions as indicated by their responses to sulfonylurea and calcium fluxes. Surprisingly, the defective β-cell secretory function of either single mutant in hyperglycemic clamps and isolated islets treated with various secretagogues was completely reversed in double mutants lacking FoxO1 and Hnf4α. Gene expression analyses revealed distinct epistatic modalities by which the two transcription factors regulate networks associated with reversal of β-cell dysfunction. An antagonistic network regulating glycolysis, including β-cell "disallowed" genes, and a synergistic network regulating protocadherins emerged as likely mediators of the functional restoration of insulin secretion. CONCLUSIONS The findings provide evidence of antagonistic epistasis as a model of gene/environment interactions in the pathogenesis of β-cell dysfunction.
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Affiliation(s)
- Taiyi Kuo
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Wen Du
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Yasutaka Miyachi
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Prasanna K Dadi
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - David A Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Daniel Segrè
- Department of Biology, Department of Biomedical Engineering, Department of Physics, Boston University, Boston, MA, USA
| | - Domenico Accili
- Department of Medicine and Berrie Diabetes Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
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17
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Bocharova A, Vagaitseva K, Marusin A, Zhukova N, Zhukova I, Minaycheva L, Makeeva O, Stepanov V. Association and Gene-Gene Interactions Study of Late-Onset Alzheimer's Disease in the Russian Population. Genes (Basel) 2021; 12:genes12101647. [PMID: 34681041 PMCID: PMC8535278 DOI: 10.3390/genes12101647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 12/29/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, and represents the most common cause of dementia. In this study, we performed several different analyses to detect loci involved in development of the late onset AD in the Russian population. DNA samples from 472 unrelated subjects were genotyped for 63 SNPs using iPLEX Assay and real-time PCR. We identified five genetic loci that were significantly associated with LOAD risk for the Russian population (TOMM40 rs2075650, APOE rs429358 and rs769449, NECTIN rs6857, APOE ε4). The results of the analysis based on comparison of the haplotype frequencies showed two risk haplotypes and one protective haplotype. The GMDR analysis demonstrated three significant models as a result: a one-factor, a two-factor and a three-factor model. A protein-protein interaction network with three subnetworks was formed for the 24 proteins. Eight proteins with a large number of interactions are identified: APOE, SORL1, APOC1, CD33, CLU, TOMM40, CNTNAP2 and CACNA1C. The present study confirms the importance of the APOE-TOMM40 locus as the main risk locus of development and progress of LOAD in the Russian population. Association analysis and bioinformatics approaches detected interactions both at the association level of single SNPs and at the level of genes and proteins.
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Affiliation(s)
- Anna Bocharova
- Tomsk National Research Medical Center, Research Institute of Medical Genetics, 634050 Tomsk, Russia; (K.V.); (A.M.); (L.M.); (V.S.)
- Correspondence:
| | - Kseniya Vagaitseva
- Tomsk National Research Medical Center, Research Institute of Medical Genetics, 634050 Tomsk, Russia; (K.V.); (A.M.); (L.M.); (V.S.)
| | - Andrey Marusin
- Tomsk National Research Medical Center, Research Institute of Medical Genetics, 634050 Tomsk, Russia; (K.V.); (A.M.); (L.M.); (V.S.)
| | - Natalia Zhukova
- Department of Neurology and Neurosurgery, Faculty of General Medicine, Siberian State Medical University, 634050 Tomsk, Russia; (N.Z.); (I.Z.)
- Nebbiolo Center for Clinical Trials, 634009 Tomsk, Russia;
| | - Irina Zhukova
- Department of Neurology and Neurosurgery, Faculty of General Medicine, Siberian State Medical University, 634050 Tomsk, Russia; (N.Z.); (I.Z.)
- Nebbiolo Center for Clinical Trials, 634009 Tomsk, Russia;
| | - Larisa Minaycheva
- Tomsk National Research Medical Center, Research Institute of Medical Genetics, 634050 Tomsk, Russia; (K.V.); (A.M.); (L.M.); (V.S.)
| | - Oksana Makeeva
- Nebbiolo Center for Clinical Trials, 634009 Tomsk, Russia;
| | - Vadim Stepanov
- Tomsk National Research Medical Center, Research Institute of Medical Genetics, 634050 Tomsk, Russia; (K.V.); (A.M.); (L.M.); (V.S.)
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Wang X, Liu J, Dai Z, Sui Y. Andrographolide improves PCP-induced schizophrenia-like behaviors through blocking interaction between NRF2 and KEAP1. J Pharmacol Sci 2021; 147:9-17. [PMID: 34294378 DOI: 10.1016/j.jphs.2021.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/02/2021] [Accepted: 05/17/2021] [Indexed: 12/15/2022] Open
Abstract
Schizophrenia is one of the foremost psychological illness around the world, and recent evidence shows that inflammation and oxidative stress may play a critical role in the etiology of schizophrenia. Andrographolide is a diterpenoid lactone from Andrographis paniculate, which has shown anti-inflammation and anti-oxidative effects. In this study, we explored whether andrographolide can improve schizophrenia-like behaviors through its inhibition of inflammation and oxidative stress in Phencyclidine (PCP)-induced mouse model of schizophrenia. We found that abnormal behavioral including locomotor activity, forced swimming and novel object recognition were ameliorated following andrographolide administration (5 mg/kg and 10 mg/kg). Andrographolide inhibited PCP-induced production of inflammatory cytokines, decreased p-p65, p-IκBα, p-p38 and p-ERK1/2 in the prefrontal cortex. Andrographolide significantly declined the level of MDA and GSH, as well as elevated the activity of SOD, CAT and GCH-px. In addition, andrographolide increased expression of NRF-2, HO-1 and NQO-1, promoted nuclear translocation of NRF-2 through blocking the interaction between NRF-2 and KEAP1, which may be associated with directly binding to NRF-2. Furthermore, antioxidative effects and anti-schizophrenia-like behaviors of andrographolide were compromised by the application of NRF-2 inhibitor ML385. In conclusion, these results suggested that andrographolide improved oxidative stress and schizophrenia-like behaviors induced by PCP through increasing NRF-2 pathway.
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Affiliation(s)
- Xiying Wang
- Department of Psychiatry, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, China.
| | - Jia Liu
- Department of Clinical Pharmacy, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiping Dai
- Department of Psychiatry, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Yuxiu Sui
- Department of Psychiatry, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing, China
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Elmes K, Schmich F, Szczurek E, Jenkins J, Beerenwinkel N, Gavryushkin A. Learning epistatic gene interactions from perturbation screens. PLoS One 2021; 16:e0254491. [PMID: 34255784 PMCID: PMC8277066 DOI: 10.1371/journal.pone.0254491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
The treatment of complex diseases often relies on combinatorial therapy, a strategy where drugs are used to target multiple genes simultaneously. Promising candidate genes for combinatorial perturbation often constitute epistatic genes, i.e., genes which contribute to a phenotype in a non-linear fashion. Experimental identification of the full landscape of genetic interactions by perturbing all gene combinations is prohibitive due to the exponential growth of testable hypotheses. Here we present a model for the inference of pairwise epistatic, including synthetic lethal, gene interactions from siRNA-based perturbation screens. The model exploits the combinatorial nature of siRNA-based screens resulting from the high numbers of sequence-dependent off-target effects, where each siRNA apart from its intended target knocks down hundreds of additional genes. We show that conditional and marginal epistasis can be estimated as interaction coefficients of regression models on perturbation data. We compare two methods, namely glinternet and xyz, for selecting non-zero effects in high dimensions as components of the model, and make recommendations for the appropriate use of each. For data simulated from real RNAi screening libraries, we show that glinternet successfully identifies epistatic gene pairs with high accuracy across a wide range of relevant parameters for the signal-to-noise ratio of observed phenotypes, the effect size of epistasis and the number of observations per double knockdown. xyz is also able to identify interactions from lower dimensional data sets (fewer genes), but is less accurate for many dimensions. Higher accuracy of glinternet, however, comes at the cost of longer running time compared to xyz. The general model is widely applicable and allows mining the wealth of publicly available RNAi screening data for the estimation of epistatic interactions between genes. As a proof of concept, we apply the model to search for interactions, and potential targets for treatment, among previously published sets of siRNA perturbation screens on various pathogens. The identified interactions include both known epistatic interactions as well as novel findings.
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Affiliation(s)
- Kieran Elmes
- Department of Computer Science, University of Otago, Dunedin, New Zealand
| | - Fabian Schmich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ewa Szczurek
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail: (NB); (AG)
| | - Alex Gavryushkin
- Department of Computer Science, University of Otago, Dunedin, New Zealand
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NB); (AG)
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20
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Wang L, Wang Y, Fu Y, Gao Y, Du J, Yang C, Liu J. AFSBN: A Method of Artificial Fish Swarm Optimizing Bayesian Network for Epistasis Detection. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:1369-1383. [PMID: 31670676 DOI: 10.1109/tcbb.2019.2949780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
How to mine the interaction between SNPs (namely epistasis) efficiently and accurately must be considered when to tackle the complexity of underlying biological mechanisms. In order to overcome the defect of low learning efficiency and local optimal, this work proposes an epistasis mining method using artificial fish swarm optimizing Bayesian network (AFSBN). This method uses the characteristics of global optimization, good robustness and fast convergence about the artificial fish swarm algorithm, and uses the algorithm into the heuristic search strategy of Bayesian network. The initial network structure can be evolved through the manipulations of foraging behavior, clustering behavior, tail-chasing behavior and random behavior. This algorithm chooses different behaviors to modify the network state according to the changing of surrounding environment and the states of partners. It realizes the interaction between each artificial fish and its neighboring environment, and finally finds the optimal network in the population. We compared AFSBN with other existing algorithms on both simulated and real datasets. The experimental results demonstrate that our method outperforms others in epistasis detection accuracy in the case of not affecting the efficiency basically for different datasets.
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21
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Yashin AI, Wu D, Arbeev K, Bagley O, Akushevich I, Duan M, Yashkin A, Ukraintseva S. Interplay between stress-related genes may influence Alzheimer's disease development: The results of genetic interaction analyses of human data. Mech Ageing Dev 2021; 196:111477. [PMID: 33798591 PMCID: PMC8173104 DOI: 10.1016/j.mad.2021.111477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 01/05/2023]
Abstract
Emerging evidence from experimental and clinical research suggests that stress-related genes may play key roles in AD development. The fact that genome-wide association studies were not able to detect a contribution of such genes to AD indicates the possibility that these genes may influence AD non-linearly, through interactions of their products. In this paper, we selected two stress-related genes (GCN2/EIF2AK4 and APP) based on recent findings from experimental studies which suggest that the interplay between these genes might influence AD in humans. To test this hypothesis, we evaluated the effects of interactions between SNPs in these two genes on AD occurrence, using the Health and Retirement Study data on white indidividuals. We found several interacting SNP-pairs whose associations with AD remained statistically significant after correction for multiple testing. These findings emphasize the importance of nonlinear mechanisms of polygenic AD regulation that cannot be detected in traditional association studies. To estimate collective effects of multiple interacting SNP-pairs on AD, we constructed a new composite index, called Interaction Polygenic Risk Score, and showed that its association with AD is highly statistically significant. These results open a new avenue in the analyses of mechanisms of complex multigenic AD regulation.
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Affiliation(s)
| | - Deqing Wu
- Biodemography of Aging Research Unit, Duke University SSRI, USA
| | | | - Olivia Bagley
- Biodemography of Aging Research Unit, Duke University SSRI, USA
| | - Igor Akushevich
- Biodemography of Aging Research Unit, Duke University SSRI, USA
| | - Matt Duan
- Biodemography of Aging Research Unit, Duke University SSRI, USA
| | - Arseniy Yashkin
- Biodemography of Aging Research Unit, Duke University SSRI, USA
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22
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Liao Y, Cao W, Zhang K, Zhou Y, Xu X, Zhao X, Yang X, Wang J, Zhao S, Zhang S, Yang L, Liu D, Tian Y, Wu W. Bioinformatic and integrated analysis identifies an lncRNA-miRNA-mRNA interaction mechanism in gastric adenocarcinoma. Genes Genomics 2021; 43:613-622. [PMID: 33779949 DOI: 10.1007/s13258-021-01086-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND lncRNAs-miRNAs-mRNAs networks play an important role in Gastric adenocarcinoma (GA). Identification of these networks provide new insight into the role of these RNAs in gastric cancer. OBJECTIVES Biological information databases were screened to characterize and examine the regulatory networks and to further investigate the potential prognostic relationship this regulation has in GA. METHODS By mining The Cancer Genome Atlas (TCGA) database, we gathered information on GA-related lncRNAs, miRNAs, and mRNAs. We identified differentially expressed (DE) lncRNAs, miRNAs, and mRNAs using R software. The lncRNA-miRNA-mRNA interaction network was constructed and subsequent survival examination was performed. Representative genes were selected out using The Biological Networks Gene Ontology plug-in tool on Cytoscape. Additional analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms were used to screen representative genes for functional enrichment. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) were used to identify the expression of five candidate differential expressed RNAs. RESULTS Information of samples from 375 cases of gastric cancer and 32 healthy cases (normal tissues) were downloaded from the TCGA database. A total of 1632 DE-mRNAs, 1008 DE-lncRNAs and 104 DE-miRNAs were identified and screened. Among them, 65 DE-lncRNAs, 10 DE-miRNAs, and 10 DE-mRNAs form lncRNAs-miRNAs-mRNAs regulatory network. Additionally, 10 lncRNAs and 2 mRNAs were associated with the prognosis of GA. Multivariable COX analysis revealed that AC018781.1 and VCAN-AS1 were independent risk factors for GA. GO functional enrichment analysis found DE-mRNA was significantly enriched TERM (P < 0.05). The KEGG signal regulatory network analysis found 11 significantly enrichment networks, the most prevailing was for the AGE-RAGE signaling pathway associated with Diabetic complications. Results of RT-qPCR was consistent with the in silico results. CONCLUSIONS The results of the present study represent a view of GA from a analysis of lncRNA, miRNA and mRNA. The network of lncRNA-miRNA-mRNA interactions revealed here may potentially further experimental studies and may help biomarker development for GA.
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Affiliation(s)
- Yong Liao
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Wen Cao
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Kunpeng Zhang
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Yang Zhou
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Xin Xu
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Xiaoling Zhao
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Xu Yang
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Jitao Wang
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Shouwen Zhao
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Shiyu Zhang
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Longfei Yang
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Dengxiang Liu
- Department of Hepatobiliary Surgery, Xingtai People's Hospital of Hebei Medical University, Xingtai, 054001, Hebei, People's Republic of China
| | - Yanpeng Tian
- Department of Obstetrics and Gynecology, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Shijiazhuang, 050000, Hebei, People's Republic of China.
| | - Weizhong Wu
- Department of General Surgery, The First Hospital of Hebei Medical University, No. 89 Donggang Road, Shijiazhuang, 050000, Hebei, People's Republic of China.
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23
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Pizzo L, Lasser M, Yusuff T, Jensen M, Ingraham P, Huber E, Singh MD, Monahan C, Iyer J, Desai I, Karthikeyan S, Gould DJ, Yennawar S, Weiner AT, Pounraja VK, Krishnan A, Rolls MM, Lowery LA, Girirajan S. Functional assessment of the "two-hit" model for neurodevelopmental defects in Drosophila and X. laevis. PLoS Genet 2021; 17:e1009112. [PMID: 33819264 PMCID: PMC8049494 DOI: 10.1371/journal.pgen.1009112] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/15/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
We previously identified a deletion on chromosome 16p12.1 that is mostly inherited and associated with multiple neurodevelopmental outcomes, where severely affected probands carried an excess of rare pathogenic variants compared to mildly affected carrier parents. We hypothesized that the 16p12.1 deletion sensitizes the genome for disease, while "second-hits" in the genetic background modulate the phenotypic trajectory. To test this model, we examined how neurodevelopmental defects conferred by knockdown of individual 16p12.1 homologs are modulated by simultaneous knockdown of homologs of "second-hit" genes in Drosophila melanogaster and Xenopus laevis. We observed that knockdown of 16p12.1 homologs affect multiple phenotypic domains, leading to delayed developmental timing, seizure susceptibility, brain alterations, abnormal dendrite and axonal morphology, and cellular proliferation defects. Compared to genes within the 16p11.2 deletion, which has higher de novo occurrence, 16p12.1 homologs were less likely to interact with each other in Drosophila models or a human brain-specific interaction network, suggesting that interactions with "second-hit" genes may confer higher impact towards neurodevelopmental phenotypes. Assessment of 212 pairwise interactions in Drosophila between 16p12.1 homologs and 76 homologs of patient-specific "second-hit" genes (such as ARID1B and CACNA1A), genes within neurodevelopmental pathways (such as PTEN and UBE3A), and transcriptomic targets (such as DSCAM and TRRAP) identified genetic interactions in 63% of the tested pairs. In 11 out of 15 families, patient-specific "second-hits" enhanced or suppressed the phenotypic effects of one or many 16p12.1 homologs in 32/96 pairwise combinations tested. In fact, homologs of SETD5 synergistically interacted with homologs of MOSMO in both Drosophila and X. laevis, leading to modified cellular and brain phenotypes, as well as axon outgrowth defects that were not observed with knockdown of either individual homolog. Our results suggest that several 16p12.1 genes sensitize the genome towards neurodevelopmental defects, and complex interactions with "second-hit" genes determine the ultimate phenotypic manifestation.
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Affiliation(s)
- Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Micaela Lasser
- Department of Biology, Boston College, Chestnut Hill, MA, United States of America
| | - Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Phoebe Ingraham
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Mayanglambam Dhruba Singh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Connor Monahan
- Department of Biology, Boston College, Chestnut Hill, MA, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Inshya Desai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Siddharth Karthikeyan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Dagny J. Gould
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Alexis T. Weiner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Vijay Kumar Pounraja
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Arjun Krishnan
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Melissa M. Rolls
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
| | - Laura Anne Lowery
- Department of Medicine, Boston University Medical Center, Boston, MA, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States of America
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States of America
- * E-mail:
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Gutiérrez-Díez PJ, Gomez-Pilar J, Hornero R, Martínez-Rodríguez J, López-Marcos MA, Russo J. The role of gene to gene interaction in the breast's genomic signature of pregnancy. Sci Rep 2021; 11:2643. [PMID: 33514799 PMCID: PMC7846553 DOI: 10.1038/s41598-021-81704-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
Full-term pregnancy at an early age confers long-term protection against breast cancer. Published data shows a specific transcriptomic profile controlling chromatin remodeling that could play a relevant role in the pregnancy-induced protection. This process of chromatin remodeling, induced by the breast differentiation caused by the first full-term pregnancy, has mainly been measured by the expression level of genes individually considered. However, genes equally expressed during the process of chromatin remodeling may behave differently in their interaction with other genes. These changes at the gene cluster level could constitute an additional dimension of chromatin remodeling and therefore of the pregnancy-induced protection. In this research, we apply Information and Graph Theories, Differential Co-expression Network Analysis, and Multiple Regression Analysis, specially designed to examine structural and informational aspects of data sets, to analyze this question. Our findings demonstrate that, independently of the changes in the gene expression at the individual level, there are significant changes in gene-gene interactions and gene cluster behaviors. These changes indicate that the parous breast, through the process of early full-term pregnancy, generates more modules in the networks, with higher density, and a genomic structure performing additional and more complex functions than those found in the nulliparous breast.
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Affiliation(s)
- Pedro J Gutiérrez-Díez
- IMUVA Mathematical Institute, University of Valladolid, Valladolid, Spain
- Faculty of Economics, University of Valladolid, Valladolid, Spain
| | - Javier Gomez-Pilar
- Biomedical Engineering Group, University of Valladolid, Paseo de Belén, 15, 47011, Valladolid, Spain.
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales Y Nanomedicina (CIBER-BBN), Valladolid, Spain.
| | - Roberto Hornero
- IMUVA Mathematical Institute, University of Valladolid, Valladolid, Spain
- Biomedical Engineering Group, University of Valladolid, Paseo de Belén, 15, 47011, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales Y Nanomedicina (CIBER-BBN), Valladolid, Spain
| | - Julia Martínez-Rodríguez
- IMUVA Mathematical Institute, University of Valladolid, Valladolid, Spain
- Faculty of Economics, University of Valladolid, Valladolid, Spain
| | - Miguel A López-Marcos
- IMUVA Mathematical Institute, University of Valladolid, Valladolid, Spain
- Faculty of Science, University of Valladolid, Valladolid, Spain
| | - Jose Russo
- The Irma H. Russo, MD Breast Cancer Research Laboratory, Fox Chase Cancer Center - Temple University Health System, Philadelphia, USA
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Roth C, Murray D, Scott A, Fu C, Averette AF, Sun S, Heitman J, Magwene PM. Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PLoS Genet 2021; 17:e1009313. [PMID: 33493169 PMCID: PMC7861560 DOI: 10.1371/journal.pgen.1009313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 12/17/2020] [Indexed: 01/11/2023] Open
Abstract
Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of Cryptococcus deneoformans, which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent C. deneoformans strains. Using a "function-valued" QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes, RIC8, which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes SSK1 and SSK2, which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of Cryptococcus, and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.
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Affiliation(s)
- Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alexandria Scott
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna F. Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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Zeng HL, Dichio V, Rodríguez Horta E, Thorell K, Aurell E. Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes. Proc Natl Acad Sci U S A 2020; 117:31519-31526. [PMID: 33203681 PMCID: PMC7733830 DOI: 10.1073/pnas.2012331117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to deeper understanding of microbial pathogenesis. We have considered all complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes deposited in the Global Initiative on Sharing All Influenza Data (GISAID) repository until four different cutoff dates, and used direct coupling analysis together with an assumption of quasi-linkage equilibrium to infer epistatic contributions to fitness from polymorphic loci. We find eight interactions, of which three are between pairs where one locus lies in gene ORF3a, both loci holding nonsynonymous mutations. We also find interactions between two loci in gene nsp13, both holding nonsynonymous mutations, and four interactions involving one locus holding a synonymous mutation. Altogether, we infer interactions between loci in viral genes ORF3a and nsp2, nsp12, and nsp6, between ORF8 and nsp4, and between loci in genes nsp2, nsp13, and nsp14. The paper opens the prospect to use prominent epistatically linked pairs as a starting point to search for combinatorial weaknesses of recombinant viral pathogens.
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Affiliation(s)
- Hong-Li Zeng
- New Energy Technology Engineering Laboratory of Jiangsu Province, School of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
- Nordic Institute for Theoretical Physics, Royal Institute of Technology and Stockholm University, 10691 Stockholm, Sweden
| | - Vito Dichio
- Nordic Institute for Theoretical Physics, Royal Institute of Technology and Stockholm University, 10691 Stockholm, Sweden
- Department of Physics, University of Trieste, 34151 Trieste, Italy
- Department of Computational Science and Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Edwin Rodríguez Horta
- Group of Complex Systems and Statistical Physics, Department of Theoretical Physics, Physics Faculty, University of Havana, 10400 Havana, Cuba
| | - Kaisa Thorell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Center for Translational Microbiome Research, Department of Microbiology, Cell and Tumor Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Erik Aurell
- Department of Computational Science and Technology, AlbaNova University Center, 10691 Stockholm, Sweden;
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Abstract
Genome-wide association studies (GWAS) explain a fraction of the underlying heritability of genetic diseases. Investigating epistatic interactions between two or more loci help to close this gap. Unfortunately, the sheer number of loci combinations to process and hypotheses prohibit the process both computationally and statistically. Epistasis test prioritization algorithms rank likely epistatic single nucleotide polymorphism (SNP) pairs to limit the number of tests. However, they still suffer from very low precision. It was shown in the literature that selecting SNPs that are individually correlated with the phenotype and also diverse with respect to genomic location leads to better phenotype prediction due to genetic complementation. Here, we propose that an algorithm that pairs SNPs from such diverse regions and ranks them can improve prediction power. We propose an epistasis test prioritization algorithm that optimizes a submodular set function to select a diverse and complementary set of genomic regions that span the underlying genome. The SNP pairs from these regions are then further ranked w.r.t. their co-coverage of the case cohort. We compare our algorithm with the state of the art on three GWAS and show that (1) we substantially improve precision (from 0.003 to 0.652) while maintaining the significance of selected pairs, (2) decrease the number of tests by 25-fold, and (3) decrease the runtime by 4-fold. We also show that promoting SNPs from regulatory/coding regions improves the performance (up to 0.8). Potpourri is available at http:/ciceklab.cs.bilkent.edu.tr/potpourri.
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Affiliation(s)
- Gizem Caylak
- Computer Engineering Department, Bilkent University, Ankara, Turkey
| | - Oznur Tastan
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - A Ercument Cicek
- Computer Engineering Department, Bilkent University, Ankara, Turkey
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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28
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Abstract
More and more genome-wide association studies are being designed to uncover the full genetic basis of common diseases. Nonetheless, the resulting loci are often insufficient to fully recover the observed heritability. Epistasis, or gene-gene interaction, is one of many hypotheses put forward to explain this missing heritability. In the present work, we propose epiGWAS, a new approach for epistasis detection that identifies interactions between a target SNP and the rest of the genome. This contrasts with the classical strategy of epistasis detection through exhaustive pairwise SNP testing. We draw inspiration from causal inference in randomized clinical trials, which allows us to take into account linkage disequilibrium. EpiGWAS encompasses several methods, which we compare to state-of-the-art techniques for epistasis detection on simulated and real data. The promising results demonstrate empirically the benefits of EpiGWAS to identify pairwise interactions.
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Affiliation(s)
- Lotfi Slim
- CBIO—Centre for Computational Biology, Mines ParisTech, Paris, France
- Translational Sciences, SANOFI R&D, Chilly-Mazarin, France
- * E-mail:
| | | | - Chloé-Agathe Azencott
- CBIO—Centre for Computational Biology, Mines ParisTech, Paris, France
- Institut Curie, PSL Research University, INSERM, U900, Paris, France
| | - Jean-Philippe Vert
- CBIO—Centre for Computational Biology, Mines ParisTech, Paris, France
- Google Brain, Paris, France
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Szilágyi A, Kovács VP, Szathmáry E, Santos M. Evolution of linkage and genome expansion in protocells: The origin of chromosomes. PLoS Genet 2020; 16:e1009155. [PMID: 33119583 PMCID: PMC7665907 DOI: 10.1371/journal.pgen.1009155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/13/2020] [Accepted: 09/24/2020] [Indexed: 11/18/2022] Open
Abstract
Chromosomes are likely to have assembled from unlinked genes in early evolution. Genetic linkage reduces the assortment load and intragenomic conflict in reproducing protocell models to the extent that chromosomes can go to fixation even if chromosomes suffer from a replicative disadvantage, relative to unlinked genes, proportional to their length. Here we numerically show that chromosomes spread within protocells even if recurrent deleterious mutations affecting replicating genes (as ribozymes) are considered. Dosage effect selects for optimal genomic composition within protocells that carries over to the genic composition of emerging chromosomes. Lacking an accurate segregation mechanism, protocells continue to benefit from the stochastic corrector principle (group selection of early replicators), but now at the chromosome level. A remarkable feature of this process is the appearance of multigene families (in optimal genic proportions) on chromosomes. An added benefit of chromosome formation is an increase in the selectively maintainable genome size (number of different genes), primarily due to the marked reduction of the assortment load. The establishment of chromosomes is under strong positive selection in protocells harboring unlinked genes. The error threshold of replication is raised to higher genome size by linkage due to the fact that deleterious mutations affecting protocells metabolism (hence fitness) show antagonistic (diminishing return) epistasis. This result strengthens the established benefit conferred by chromosomes on protocells allowing for the fixation of highly specific and efficient enzymes. The emergence of chromosomes harboring several genes is a crucial ingredient of the major evolutionary transition from naked replicators to cells. Linkage of replicating genes reduces conflict between them and alleviates the problem of chance loss of genes upon stochastic protocell fission. The emerging organization of protocells maintaining several segregating chromosomes with balanced gene composition also allows for an increase in the number of gene types despite recurrent deleterious mutations. We suggest that this interim genomic organization enabled protocells to evolve specific and efficient enzymes and paved the way toward an accurate mechanism for chromosome segregation later in evolution.
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Affiliation(s)
- András Szilágyi
- Institute of Evolution, Centre for Ecological Research, Tihany, Hungary
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Pullach/Munich, Germany
| | | | - Eörs Szathmáry
- Institute of Evolution, Centre for Ecological Research, Tihany, Hungary
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Pullach/Munich, Germany
- * E-mail:
| | - Mauro Santos
- Institute of Evolution, Centre for Ecological Research, Tihany, Hungary
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
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Hind J, Lisboa P, Hussain AJ, Al-Jumeily D. A Novel Approach to Detecting Epistasis using Random Sampling Regularisation. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1535-1545. [PMID: 31634840 DOI: 10.1109/tcbb.2019.2948330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Epistasis is a progressive approach that complements the 'common disease, common variant' hypothesis that highlights the potential for connected networks of genetic variants collaborating to produce a phenotypic expression. Epistasis is commonly performed as a pairwise or limitless-arity capacity that considers variant networks as either variant vs variant or as high order interactions. This type of analysis extends the number of tests that were previously performed in a standard approach such as Genome-Wide Association Study (GWAS), in which False Discovery Rate (FDR) is already an issue, therefore by multiplying the number of tests up to a factorial rate also increases the issue of FDR. Further to this, epistasis introduces its own limitations of computational complexity and intensity that are generated based on the analysis performed; to consider the most intense approach, a multivariate analysis introduces a time complexity of O(n!). Proposed in this paper is a novel methodology for the detection of epistasis using interpretable methods and best practice to outline interactions through filtering processes. Using a process of Random Sampling Regularisation which randomly splits and produces sample sets to conduct a voting system to regularise the significance and reliability of biological markers, SNPs. Preliminary results are promising, outlining a concise detection of interactions. Results for the detection of epistasis, in the classification of breast cancer patients, indicated eight outlined risk candidate interactions from five variants and a singular candidate variant with high protective association.
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Yin Y, Guan B, Zhao Y, Li Y. SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease. Biomed Res Int 2020; 2020:5610658. [PMID: 32908899 PMCID: PMC7468611 DOI: 10.1155/2020/5610658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022]
Abstract
Detecting SNP-SNP interactions associated with disease is significant in genome-wide association study (GWAS). Owing to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power and long running time. To tackle these drawbacks, a fast self-adaptive memetic algorithm (SAMA) is proposed in this paper. In this method, the crossover, mutation, and selection of standard memetic algorithm are improved to make SAMA adapt to the detection of SNP-SNP interactions associated with disease. Furthermore, a self-adaptive local search algorithm is introduced to enhance the detecting power of the proposed method. SAMA is evaluated on a variety of simulated datasets and a real-world biological dataset, and a comparative study between it and the other four methods (FHSA-SED, AntEpiSeeker, IEACO, and DESeeker) that have been developed recently based on evolutionary algorithms is performed. The results of extensive experiments show that SAMA outperforms the other four compared methods in terms of detection power and running time.
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Affiliation(s)
- Ying Yin
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Boxin Guan
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yuhai Zhao
- Key Laboratory of Intelligent Computing in Medical Image, Minister of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yuan Li
- School of Information Science and Technology, North China University of Technology, Beijing 100144, China
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32
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Li H, Wang M, Li W, He L, Zhou Y, Zhu J, Che R, Warburton ML, Yang X, Yan J. Genetic variants and underlying mechanisms influencing variance heterogeneity in maize. Plant J 2020; 103:1089-1102. [PMID: 32344461 DOI: 10.1111/tpj.14786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 04/04/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance-heterogeneity genome-wide association study to examine the contribution of variance heterogeneity to oil-related quantitative traits. We identified 79 unique variance-controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance-heterogeneity genes for 21 oil-related traits using the Levene test (P < 1.0 × 10-5 ). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean-effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two-hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high-oil maize (Zea mays L.).
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Min Wang
- Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, Beijing, 100083, China
| | - Weijun Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Linlin He
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Yuanyuan Zhou
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Marilyn L Warburton
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, 39759, USA
| | - Xiaohong Yang
- Key Laboratory of Crop Genomics and Genetic Improvement, National Maize Improvement Center of China, China Agricultural University, Beijing, 100083, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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33
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Sun Y, Wang X, Shang J, Liu JX, Zheng CH, Lei X. Introducing Heuristic Information Into Ant Colony Optimization Algorithm for Identifying Epistasis. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:1253-1261. [PMID: 30403637 DOI: 10.1109/tcbb.2018.2879673] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Epistasis learning, which is aimed at detecting associations between multiple Single Nucleotide Polymorphisms (SNPs) and complex diseases, has gained increasing attention in genome wide association studies. Although much work has been done on mapping the SNPs underlying complex diseases, there is still difficulty in detecting epistatic interactions due to the lack of heuristic information to expedite the search process. In this study, a method EACO is proposed to detect epistatic interactions based on the ant colony optimization (ACO) algorithm, the highlights of which are the introduced heuristic information, fitness function, and a candidate solutions filtration strategy. The heuristic information multi-SURF* is introduced into EACO for identifying epistasis, which is incorporated into ant-decision rules to guide the search with linear time. Two functionally complementary fitness functions, mutual information and the Gini index, are combined to effectively evaluate the associations between SNP combinations and the phenotype. Furthermore, a strategy for candidate solutions filtration is provided to adaptively retain all optimal solutions which yields a more accurate way for epistasis searching. Experiments of EACO, as well as three ACO based methods (AntEpiSeeker, MACOED, and epiACO) and four commonly used methods (BOOST, SNPRuler, TEAM, and epiMODE) are performed on both simulation data sets and a real data set of age-related macular degeneration. Results indicate that EACO is promising in identifying epistasis.
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Shaw LM, Li C, Woods DP, Alvarez MA, Lin H, Lau MY, Chen A, Dubcovsky J. Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat. PLoS Genet 2020; 16:e1008812. [PMID: 32658893 PMCID: PMC7394450 DOI: 10.1371/journal.pgen.1008812] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/31/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
In Arabidopsis, CONSTANS (CO) integrates light and circadian clock signals to promote flowering under long days (LD). In the grasses, a duplication generated two paralogs designated as CONSTANS1 (CO1) and CONSTANS2 (CO2). Here we show that in tetraploid wheat plants grown under LD, combined loss-of-function mutations in the A and B-genome homeologs of CO1 and CO2 (co1 co2) result in a small (3 d) but significant (P<0.0001) acceleration of heading time both in PHOTOPERIOD1 (PPD1) sensitive (Ppd-A1b, functional ancestral allele) and insensitive (Ppd-A1a, functional dominant allele) backgrounds. Under short days (SD), co1 co2 mutants headed 13 d earlier than the wild type (P<0.0001) in the presence of Ppd-A1a. However, in the presence of Ppd-A1b, spikes from both genotypes failed to emerge by 180 d. These results indicate that CO1 and CO2 operate mainly as weak heading time repressors in both LD and SD. By contrast, in ppd1 mutants with loss-of-function mutations in both PPD1 homeologs, the wild type Co1 allele accelerated heading time >60 d relative to the co1 mutant allele under LD. We detected significant genetic interactions among CO1, CO2 and PPD1 genes on heading time, which were reflected in complex interactions at the transcriptional and protein levels. Loss-of-function mutations in PPD1 delayed heading more than combined co1 co2 mutations and, more importantly, PPD1 was able to perceive and respond to differences in photoperiod in the absence of functional CO1 and CO2 genes. Similarly, CO1 was able to accelerate heading time in response to LD in the absence of a functional PPD1. Taken together, these results indicate that PPD1 and CO1 are able to respond to photoperiod in the absence of each other, and that interactions between these two photoperiod pathways at the transcriptional and protein levels are important to fine-tune the flowering response in wheat.
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Affiliation(s)
- Lindsay M. Shaw
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Currently at Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Daniel P. Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Maria A. Alvarez
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Mei Y. Lau
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Andrew Chen
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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Sarkar D, Maranas CD. SNPeffect: identifying functional roles of SNPs using metabolic networks. Plant J 2020; 103:512-531. [PMID: 32167625 PMCID: PMC9328443 DOI: 10.1111/tpj.14746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/20/2020] [Indexed: 05/04/2023]
Abstract
Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.
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Affiliation(s)
- Debolina Sarkar
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Costas D. Maranas
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPAUSA
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Lord CJ, Quinn N, Ryan CJ. Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions. eLife 2020; 9:e58925. [PMID: 32463358 PMCID: PMC7289598 DOI: 10.7554/elife.58925] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Genetic interactions, including synthetic lethal effects, can now be systematically identified in cancer cell lines using high-throughput genetic perturbation screens. Despite this advance, few genetic interactions have been reproduced across multiple studies and many appear highly context-specific. Here, by developing a new computational approach, we identified 220 robust driver-gene associated genetic interactions that can be reproduced across independent experiments and across non-overlapping cell line panels. Analysis of these interactions demonstrated that: (i) oncogene addiction effects are more robust than oncogene-related synthetic lethal effects; and (ii) robust genetic interactions are enriched among gene pairs whose protein products physically interact. Exploiting the latter observation, we used a protein-protein interaction network to identify robust synthetic lethal effects associated with passenger gene alterations and validated two new synthetic lethal effects. Our results suggest that protein-protein interaction networks can be used to prioritise therapeutic targets that will be more robust to tumour heterogeneity.
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Affiliation(s)
- Christopher J Lord
- Breast Cancer Now Toby Robins Research Centre and Cancer Research UK Gene Function Laboratory, Institute of Cancer ResearchLondonUnited Kingdom
| | - Niall Quinn
- School of Computer Science and Systems Biology Ireland, University College DublinDublinIreland
| | - Colm J Ryan
- School of Computer Science and Systems Biology Ireland, University College DublinDublinIreland
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Yi X, Zhou Q, Zhang Y, Zhou J, Lin J. Variants in clopidogrel-relevant genes and early neurological deterioration in ischemic stroke patients receiving clopidogrel. BMC Neurol 2020; 20:159. [PMID: 32345264 PMCID: PMC7187527 DOI: 10.1186/s12883-020-01703-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Early neurological deterioration (END) is common in acute ischemic stroke (IS). However, the underlying mechanisms for END are unclear. The aim of this study was to evaluate the associations of 16 variants in clopidogrel-relevant genes and interactions among these variants with END in acute IS patients receiving clopidogrel treatment. METHODS We consecutively enrolled 375 acute IS patients between June 2014 and January 2015. Platelet aggregation was measured on admission and after the 7-10 days of clopidogrel treatment. The 16 variants in clopidogrel-relevant genes were examined using mass spectrometry. The primary outcome was END within the 10 days of admission. Gene-gene interactions were analyzed by generalized multifactor dimensionality reduction (GMDR) methods. RESULTS Among the 375 patients, 95 (25.3%) patients developed END within the first 10 days of admission. Among the 16 variants, only CYP2C19*2 (rs4244285) AA/AG was associated with END using single-locus analytical approach. GMDR analysis revealed that there was a synergistic effect of gene-gene interactions among CYP2C19*2 rs4244285, P2Y12 rs16863323, and GPIIIa rs2317676 on the risk for END. The high-risk interactions among the three variants were associated with the higher platelet aggregation and independent predictor for END after adjusting for the covariates (hazard ratio: 2.82; 95% confidence interval: 1.36-7.76; P = 0.003). CONCLUSIONS END is very common in patients with acute IS. The mechanisms leading to END are most likely multifactorial. Interactions among CYP2C19*2 rs4244285, P2Y12 rs16863323, and GPIIIa rs2317676 may confer a higher risk for END. It was very important to modify clopidogrel therapy for the patients carrying the high-risk interactive genotypes. CLINICAL TRIAL REGISTRATION INFORMATION The study described here is registered at http://www.chictr.org/ (unique Identifier: ChiCTR-OCH-14004724). The date of trial registration was May 30, 2014.
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Affiliation(s)
- Xingyang Yi
- Department of Neurology, the People’s Hospital of Deyang City, Deyang, 618000 Sichuan China
| | - Qiang Zhou
- Department of Neurology, the Third Affiliated Hospital of Wenzhou Medical University, 108 Wanson Road, Ruian City, Wenzhou, 325200 Zhejiang China
| | - Yongyin Zhang
- Department of Neurology, the Third Affiliated Hospital of Wenzhou Medical University, 108 Wanson Road, Ruian City, Wenzhou, 325200 Zhejiang China
| | - Ju Zhou
- Department of Neurology, the People’s Hospital of Deyang City, Deyang, 618000 Sichuan China
| | - Jing Lin
- Department of Neurology, the Third Affiliated Hospital of Wenzhou Medical University, 108 Wanson Road, Ruian City, Wenzhou, 325200 Zhejiang China
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Li H, Jiang S, Li C, Liu L, Lin Z, He H, Deng XW, Zhang Z, Wang X. The hybrid protein interactome contributes to rice heterosis as epistatic effects. Plant J 2020; 102:116-128. [PMID: 31736145 DOI: 10.1111/tpj.14616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
Heterosis is the phenomenon in which hybrid progeny exhibits superior traits in comparison with those of their parents. Genomic variations between the two parental genomes may generate epistasis interactions, which is one of the genetic hypotheses explaining heterosis. We postulate that protein-protein interactions specific to F1 hybrids (F1 -specific PPIs) may occur when two parental genomes combine, as the proteome of each parent may supply novel interacting partners. To test our assumption, an inter-subspecies hybrid interactome was simulated by in silico PPI prediction between rice japonica (cultivar Nipponbare) and indica (cultivar 9311). Four-thousand, six-hundred and twelve F1 -specific PPIs accounting for 20.5% of total PPIs in the hybrid interactome were found. Genes participating in F1 -specific PPIs tend to encode metabolic enzymes and are generally localized in genomic regions harboring metabolic gene clusters. To test the genetic effect of F1 -specific PPIs in heterosis, genomic selection analysis was performed for trait prediction with additive, dominant and epistatic effects separately considered in the model. We found that the removal of single nucleotide polymorphisms associated with F1 -specific PPIs reduced prediction accuracy when epistatic effects were considered in the model, but no significant changes were observed when additive or dominant effects were considered. In summary, genomic divergence widely dispersed between japonica and indica rice may generate F1 -specific PPIs, part of which may accumulatively contribute to heterosis according to our computational analysis. These candidate F1 -specific PPIs, especially for those involved in metabolic biosynthesis pathways, are worthy of experimental validation when large-scale protein interactome datasets are generated in hybrid rice in the future.
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Affiliation(s)
- Hong Li
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shuqin Jiang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Lei Liu
- Beijing Key Laboratory of Plant Resources Research and Development, School of Sciences, Beijing Technology and Business University, Beijing, 100048, China
| | - Zechuan Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xing-Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Bravi B, Ravasio R, Brito C, Wyart M. Direct coupling analysis of epistasis in allosteric materials. PLoS Comput Biol 2020; 16:e1007630. [PMID: 32119660 PMCID: PMC7067494 DOI: 10.1371/journal.pcbi.1007630] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/12/2020] [Accepted: 01/03/2020] [Indexed: 11/22/2022] Open
Abstract
In allosteric proteins, the binding of a ligand modifies function at a distant active site. Such allosteric pathways can be used as target for drug design, generating considerable interest in inferring them from sequence alignment data. Currently, different methods lead to conflicting results, in particular on the existence of long-range evolutionary couplings between distant amino-acids mediating allostery. Here we propose a resolution of this conundrum, by studying epistasis and its inference in models where an allosteric material is evolved in silico to perform a mechanical task. We find in our model the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range and have a simple mechanical interpretation. We perform a Direct Coupling Analysis (DCA) and find that DCA predicts well the cost of point mutations but is a rather poor generative model. Strikingly, it can predict short-range epistasis but fails to capture long-range epistasis, in consistence with empirical findings. We propose that such failure is generic when function requires subparts to work in concert. We illustrate this idea with a simple model, which suggests that other methods may be better suited to capture long-range effects. Allostery in proteins is the property of highly specific responses to ligand binding at a distant site. To inform protocols of de novo drug design, it is fundamental to understand the impact of mutations on allosteric regulation and whether it can be predicted from evolutionary correlations. In this work we consider allosteric architectures artificially evolved to optimize the cooperativity of binding at allosteric and active site. We first characterize the emergent pattern of epistasis as well as the underlying mechanical phenomena, finding the four types of epistasis (Synergistic, Sign, Antagonistic, Saturation), which can be both short or long-range. The numerical evolution of these allosteric architectures allows us to benchmark Direct Coupling Analysis, a method which relies on co-evolution in sequence data to infer direct evolutionary couplings, in connection to allostery. We show that Direct Coupling Analysis predicts quantitatively point mutation costs but underestimates strong long-range epistasis. We provide an argument, based on a simplified model, illustrating the reasons for this discrepancy. Our analysis suggests neural networks as more promising tool to measure epistasis.
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Affiliation(s)
- Barbara Bravi
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (BB); (MW)
| | - Riccardo Ravasio
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Carolina Brito
- Instituto de Fìsica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Matthieu Wyart
- Institute of Physics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail: (BB); (MW)
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Rio S, Mary-Huard T, Moreau L, Bauland C, Palaffre C, Madur D, Combes V, Charcosset A. Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLoS Genet 2020; 16:e1008241. [PMID: 32130208 PMCID: PMC7075643 DOI: 10.1371/journal.pgen.1008241] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/16/2020] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.
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Affiliation(s)
- Simon Rio
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
- MIA, INRAE, AgroParisTech, Université Paris-Saclay, 75005, Paris, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l’INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
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Fergus P, Montanez CC, Abdulaimma B, Lisboa P, Chalmers C, Pineles B. Utilizing Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:668-678. [PMID: 30183645 DOI: 10.1109/tcbb.2018.2868667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Genome-Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. The main objective is to find single nucleotide polymorphisms (SNPs) that influence a particular phenotype (i.e., disease trait). GWAS typically use a p-value threshold of 5*10-8 to identify highly ranked SNPs. While this approach has proven useful for detecting disease-susceptible SNPs, evidence has shown that many of these are, in fact, false positives. Consequently, there is some ambiguity about the most suitable threshold for claiming genome-wide significance. Many believe that using lower p-values will allow us to investigate the joint epistatic interactions between SNPs and provide better insights into phenotype expression. One example that uses this approach is multifactor dimensionality reduction (MDR), which identifies combinations of SNPs that interact to influence a particular outcome. However, computational complexity is increased exponentially as a function of higher-order combinations making approaches like MDR difficult to implement. Even so, understanding epistatic interactions in complex diseases is a fundamental component for robust genotype-phenotype mapping. In this paper, we propose a novel framework that combines GWAS quality control and logistic regression with deep learning stacked autoencoders to abstract higher-order SNP interactions from large, complex genotyped data for case-control classification tasks in GWAS analysis. We focus on the challenging problem of classifying preterm births which has a strong genetic component with unexplained heritability reportedly between 20-40 percent. A GWAS data set, obtained from dbGap is utilised, which contains predominantly urban low-income African-American women who had normal and preterm deliveries. Epistatic interactions from original SNP sequences were extracted through a deep learning stacked autoencoder model and used to fine-tune a classifier for discriminating between term and preterm births observations. All models are evaluated using standard binary classifier performance metrics. The findings show that important information pertaining to SNPs and epistasis can be extracted from 4,666 raw SNPs generated using logistic regression (p-value = 5*10-3) and used to fit a highly accurate classifier model. The following results (Sen = 0.9562, Spec = 0.8780, Gini = 0.9490, Logloss = 0.5901, AUC = 0.9745, and MSE = 0.2010) were obtained using 50 hidden nodes and (Sen = 0.9289, Spec = 0.9591, Gini = 0.9651, Logloss = 0.3080, AUC = 0.9825, and MSE = 0.0942) using 500 hidden nodes. The results were compared with a Support Vector Machine (SVM), a Random Forest (RF), and a Fishers Linear Discriminant Analysis classifier, which all failed to improve on the deep learning approach.
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Hina A, Cao Y, Song S, Li S, Sharmin RA, Elattar MA, Bhat JA, Zhao T. High-Resolution Mapping in Two RIL Populations Refines Major "QTL Hotspot" Regions for Seed Size and Shape in Soybean ( Glycine max L.). Int J Mol Sci 2020; 21:E1040. [PMID: 32033213 PMCID: PMC7038151 DOI: 10.3390/ijms21031040] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 01/10/2023] Open
Abstract
Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in multiple environments to identify main and epistatic-effect quantitative trait loci (QTLs) for six seed size and shape traits in soybean. A total of 88 and 48 QTLs were detected through composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 15 QTLs were common among both methods; two of them were major (R2 > 10%) and novel QTLs (viz., qSW-1-1ZN and qSLT-20-1K3N). Additionally, 51 and 27 QTLs were identified for the first time through CIM and MCIM methods, respectively. Colocalization of QTLs occurred in four major QTL hotspots/clusters, viz., "QTL Hotspot A", "QTL Hotspot B", "QTL Hotspot C", and "QTL Hotspot D" located on Chr06, Chr10, Chr13, and Chr20, respectively. Based on gene annotation, gene ontology (GO) enrichment, and RNA-Seq analysis, 23 genes within four "QTL Hotspots" were predicted as possible candidates, regulating soybean seed size and shape. Network analyses demonstrated that 15 QTLs showed significant additive x environment (AE) effects, and 16 pairs of QTLs showing epistatic effects were also detected. However, except three epistatic QTLs, viz., qSL-13-3ZY, qSL-13-4ZY, and qSW-13-4ZY, all the remaining QTLs depicted no main effects. Hence, the present study is a detailed and comprehensive investigation uncovering the genetic basis of seed size and shape in soybeans. The use of a high-density map identified new genomic regions providing valuable information and could be the primary target for further fine mapping, candidate gene identification, and marker-assisted breeding (MAB).
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Affiliation(s)
- Aiman Hina
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Yongce Cao
- Shaanxi Key Laboratory of Chinese Jujube; College of Life Science, Yan’an University, Yan’an 716000, China;
| | - Shiyu Song
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Shuguang Li
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Ripa Akter Sharmin
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Mahmoud A. Elattar
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Javaid Akhter Bhat
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
| | - Tuanjie Zhao
- Ministry of Agriculture (MOA) Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory for Crop Genetics and Germplasm Enhancement, Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China; (A.H.); (S.S.); (S.L.); (R.A.S.); (M.A.E.)
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Li B, Tang M, Caseys C, Nelson A, Zhou M, Zhou X, Brady SM, Kliebenstein DJ. Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense. Genetics 2020; 214:529-541. [PMID: 31852726 PMCID: PMC7017016 DOI: 10.1534/genetics.119.302996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/17/2019] [Indexed: 11/18/2022] Open
Abstract
Plants integrate internal and external signals to finely coordinate growth and defense for maximal fitness within a complex environment. A common model suggests that growth and defense show a trade-offs relationship driven by energy costs. However, recent studies suggest that the coordination of growth and defense likely involves more conditional and intricate connections than implied by the trade-off model. To explore how a transcription factor (TF) network may coordinate growth and defense, we used a high-throughput phenotyping approach to measure growth and flowering in a set of single and pairwise mutants previously linked to the aliphatic glucosinolate (GLS) defense pathway. Supporting a link between growth and defense, 17 of the 20 tested defense-associated TFs significantly influenced plant growth and/or flowering time. The TFs' effects were conditional upon the environment and age of the plant, and more critically varied across the growth and defense phenotypes for a given genotype. In support of the coordination model of growth and defense, the TF mutant's effects on short-chain aliphatic GLS and growth did not display a simple correlation. We propose that large TF networks integrate internal and external signals and separately modulate growth and the accumulation of the defensive aliphatic GLS.
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Affiliation(s)
- Baohua Li
- Department of Plant Sciences, University of California, Davis, California 95616
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Michelle Tang
- Department of Plant Sciences, University of California, Davis, California 95616
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Céline Caseys
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Ayla Nelson
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Marium Zhou
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Xue Zhou
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, California 95616
- DynaMo Center of Excellence, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
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Molinaro A, Orlandi P, Niccolai F, Agretti P, De Marco G, Ferrarini E, Di Cosmo C, Vitti P, Piaggi P, Di Desidero T, Bocci G, Tonacchera M. Genetic interaction analysis of VEGF-A rs3025039 and VEGFR-2 rs2071559 identifies a genetic profile at higher risk to develop nodular goiter. J Endocrinol Invest 2020; 43:149-155. [PMID: 31376092 DOI: 10.1007/s40618-019-01092-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022]
Abstract
CONTEXT Nodular goiter in patients from areas of iodine deficiency is due to the growth of follicular and endothelial cells, involving different vascular-related growth factors in its pathogenesis. OBJECTIVE The aim of our study was to examine the association of known single polymorphisms of vascular endothelial growth factor-A [VEGF-A], VEGF receptor-2 [VEGFR-2] and hypoxia-inducible factor-1α [HIF-1α] genes or their genetic interactions with the risk of nodular goiter development. PATIENTS AND METHODS 116 normal subjects, without any thyroid disease, and 108 subjects with nodular goiter [subjects with goiter and at least one thyroid nodule of > 1 cm of maximum size and in absence of signs of autoimmunity] were selected from a homogeneous population living in a mild iodine deficiency geographic area. Analyses were performed on germline DNA obtained from blood samples and VEGF-A rs3025039, VEGFR-2 rs2071559, and HIF-1αrs11549465 SNPs were investigated by real-time PCR technique. The multifactor dimensionality reduction [MDR] methodology was applied to investigate the genetic interaction between SNPs. Hardy-Weinberg equilibrium was performed. RESULTS None of the studied polymorphisms were individually associated with a higher risk to develop nodular goiter [P > 0.05]. The combination of the VEGF-A rs3025039 and VEGFR-2 rs2071559 polymorphisms had the highest accuracy of 0.58 [P = 0.018] and the interaction of some genotypes was significantly associated with the risk of nodular goiter development. CONCLUSIONS Our results support a genetic interaction between the VEGF-A rs3025039 and VEGFR-2 rs2071559 polymorphisms as a predictor of the risk to develop nodular goiter in subjects coming from an area with mild iodine deficiency.
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Affiliation(s)
- A Molinaro
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy
| | - P Orlandi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - F Niccolai
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Agretti
- Laboratory of Chemistry and Endocrinology, University Hospital of Pisa, Pisa, Italy
| | - G De Marco
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy
| | - E Ferrarini
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy
| | - C Di Cosmo
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy
| | - P Vitti
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy
| | - P Piaggi
- Department of Energy and Systems Engineering, University of Pisa, Pisa, Italy
| | - T Di Desidero
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - G Bocci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - M Tonacchera
- Department of Clinical and Experimental Medicine, Endocrinology Section, University of Pisa, Via Paradisa 2, Cisanello, 56124, Pisa, Italy.
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Straub J, Gregor A, Sauerer T, Fliedner A, Distel L, Suchy C, Ekici AB, Ferrazzi F, Zweier C. Genetic interaction screen for severe neurodevelopmental disorders reveals a functional link between Ube3a and Mef2 in Drosophila melanogaster. Sci Rep 2020; 10:1204. [PMID: 31988313 PMCID: PMC6985129 DOI: 10.1038/s41598-020-58182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically extremely heterogeneous with shared phenotypes often associated with genes from the same networks. Mutations in TCF4, MEF2C, UBE3A, ZEB2 or ATRX cause phenotypically overlapping, syndromic forms of NDDs with severe intellectual disability, epilepsy and microcephaly. To characterize potential functional links between these genes/proteins, we screened for genetic interactions in Drosophila melanogaster. We induced ubiquitous or tissue specific knockdown or overexpression of each single orthologous gene (Da, Mef2, Ube3a, Zfh1, XNP) and in pairwise combinations. Subsequently, we assessed parameters such as lethality, wing and eye morphology, neuromuscular junction morphology, bang sensitivity and climbing behaviour in comparison between single and pairwise dosage manipulations. We found most stringent evidence for genetic interaction between Ube3a and Mef2 as simultaneous dosage manipulation in different tissues including glia, wing and eye resulted in multiple phenotype modifications. We subsequently found evidence for physical interaction between UBE3A and MEF2C also in human cells. Systematic pairwise assessment of the Drosophila orthologues of five genes implicated in clinically overlapping, severe NDDs and subsequent confirmation in a human cell line revealed interactions between UBE3A/Ube3a and MEF2C/Mef2, thus contributing to the characterization of the underlying molecular commonalities.
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Affiliation(s)
- Jonas Straub
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tatjana Sauerer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anna Fliedner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Laila Distel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christine Suchy
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.
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Yang CH, Lin YD, Chuang LY. Class Balanced Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:71-81. [PMID: 30040653 DOI: 10.1109/tcbb.2018.2858776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Detecting gene-gene interactions in single-nucleotide polymorphism data is vital for understanding disease susceptibility. However, existing approaches may be limited by the sample size in case-control studies. Herein, we propose a balance approach for the multifactor dimensionality reduction (BMDR) method to increase the accuracy of estimates of the prediction error rate in small samples. BMDR explicitly selects the best model by evaluating the average of prediction error rates over k-fold cross-validation without cross-validation consistency selection. In this study, we used several epistatic models with and without marginal effects under different parameter settings (heritability and minor allele frequencies) to evaluate the performance of existing approaches. Using simulated data sets, BMDR successfully detected gene-gene interactions, particularly for data sets with small sample sizes. A large data set was obtained from the Wellcome Trust Case Control Consortium, and results indicated that BMDR could effectively detect significant gene-gene interactions.
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Li X, Zhang S, Wong KC. Nature-Inspired Multiobjective Epistasis Elucidation from Genome-Wide Association Studies. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:226-237. [PMID: 29994485 DOI: 10.1109/tcbb.2018.2849759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In recent years, the detection of epistatic interactions of multiple genetic variants on the causes of complex diseases brings a significant challenge in genome-wide association studies (GWAS). However, most of the existing methods still suffer from algorithmic limitations such as single-objective optimization, intensive computational requirement, and premature convergence. In this paper, we propose and formulate an epistatic interaction multi-objective artificial bee colony algorithm based on decomposition (EIMOABC/D) to address those problems for genetic interaction detection in genome-wide association studies. First, to direct the genetic interaction detection, two objective functions are formulated to characterize various epistatic models; rank probability model is proposed to sort each population into different nondomination levels based on the fast nondominated sorting approach. After that, the mutual information based local search algorithm is proposed to guide the population search for disease model evaluations in an unbiased manner. To validate the effectiveness of EIMOABC/D, we compare EIMOABC/D against seven state-of-the-art methods on 77 epistatic models including eight small-scale epistatic models with marginal effects, eight large-scale epistatic models with marginal effects, 60 large-scale epistatic models without any marginal effect, and one case study. The experimental results indicate that our proposed algorithm EIMOABC/D outperforms seven state-of-the-art methods on those epistatic models. Furthermore, time complexity analysis and parameter analysis are conducted to demonstrate various properties of our proposed algorithm.
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Gao T, Qian J. EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions. PLoS Comput Biol 2019; 15:e1007436. [PMID: 31665135 PMCID: PMC6821050 DOI: 10.1371/journal.pcbi.1007436] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/24/2019] [Indexed: 12/20/2022] Open
Abstract
Long-range regulation by distal enhancers is crucial for many biological processes. The existing methods for enhancer-target gene prediction often require many genomic features. This makes them difficult to be applied to many cell types, in which the relevant datasets are not always available. Here, we design a tool EAGLE, an enhancer and gene learning ensemble method for identification of Enhancer-Gene (EG) interactions. Unlike existing tools, EAGLE used only six features derived from the genomic features of enhancers and gene expression datasets. Cross-validation revealed that EAGLE outperformed other existing methods. Enrichment analyses on special transcriptional factors, epigenetic modifications, and eQTLs demonstrated that EAGLE could distinguish the interacting pairs from non- interacting ones. Finally, EAGLE was applied to mouse and human genomes and identified 7,680,203 and 7,437,255 EG interactions involving 31,375 and 43,724 genes, 138,547 and 177,062 enhancers across 89 and 110 tissue/cell types in mouse and human, respectively. The obtained interactions are accessible through an interactive database enhanceratlas.org. The EAGLE method is available at https://github.com/EvansGao/EAGLE and the predicted datasets are available in http://www.enhanceratlas.org/. Enhancers are DNA sequences that interact with promoters and activate target genes. Since enhancers often located far from the target genes and the nearest genes are not always the targets of the enhancers, the prediction of enhancer-target gene relationships is a big challenge. Although a few computational tools are designed for the prediction of enhancer-target genes, it’s difficult to apply them in most tissue/cell types due to a lack of enough genomic datasets. Here we proposed a new method, EAGLE, which utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions. Comparing with other existing tools, EAGLE displayed a better performance in the 10-fold cross-validation and cross-sample test. Moreover, the predictions by EAGLE were validated by other independent evidence such as the enrichment of relevant transcriptional factors, epigenetic modifications, and eQTLs. Finally, we integrated the enhancer-target relationships obtained from human and mouse genomes into an interactive database EnhancerAtlas, http://www.enhanceratlas.org/.
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Affiliation(s)
- Tianshun Gao
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
| | - Jiang Qian
- The Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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He T, Hill CB, Angessa TT, Zhang XQ, Chen K, Moody D, Telfer P, Westcott S, Li C. Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection. J Exp Bot 2019; 70:5603-5616. [PMID: 31504706 PMCID: PMC6812734 DOI: 10.1093/jxb/erz332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 05/10/2023]
Abstract
Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.
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Affiliation(s)
- Tianhua He
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Kefei Chen
- SAGI-WEST, Faculty of Science and Engineering, Curtin University, Bentley, WA, Australia
| | | | - Paul Telfer
- Australian Grain Technologies Pty Ltd (AGT), SA, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Hubei Jingzhou, China
- Correspondence:
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Rohde PD, Jensen IR, Sarup PM, Ørsted M, Demontis D, Sørensen P, Kristensen TN. Genetic Signatures of Drug Response Variability in Drosophila melanogaster. Genetics 2019; 213:633-650. [PMID: 31455722 PMCID: PMC6781897 DOI: 10.1534/genetics.119.302381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/26/2019] [Indexed: 12/27/2022] Open
Abstract
Knowledge of the genetic basis underlying variation in response to environmental exposures or treatments is important in many research areas. For example, knowing the set of causal genetic variants for drug responses could revolutionize personalized medicine. We used Drosophila melanogaster to investigate the genetic signature underlying behavioral variability in response to methylphenidate (MPH), a drug used in the treatment of attention-deficit/hyperactivity disorder. We exposed a wild-type D. melanogaster population to MPH and a control treatment, and observed an increase in locomotor activity in MPH-exposed individuals. Whole-genome transcriptomic analyses revealed that the behavioral response to MPH was associated with abundant gene expression alterations. To confirm these patterns in a different genetic background and to further advance knowledge on the genetic signature of drug response variability, we used a system of inbred lines, the Drosophila Genetic Reference Panel (DGRP). Based on the DGRP, we showed that the behavioral response to MPH was strongly genotype-dependent. Using an integrative genomic approach, we incorporated known gene interactions into the genomic analyses of the DGRP, and identified putative candidate genes for variability in drug response. We successfully validated 71% of the investigated candidate genes by gene expression knockdown. Furthermore, we showed that MPH has cross-generational behavioral and transcriptomic effects. Our findings establish a foundation for understanding the genetic mechanisms driving genotype-specific responses to medical treatment, and highlight the opportunities that integrative genomic approaches have in optimizing medical treatment of complex diseases.
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Affiliation(s)
- Palle Duun Rohde
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
| | - Iben Ravnborg Jensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Pernille Merete Sarup
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Michael Ørsted
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
| | - Ditte Demontis
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus C, Denmark
- Center for Integrative Sequencing, Aarhus University, 8000, Denmark
- Department of Biomedicine, Aarhus University, 8000, Denmark
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Torsten Nygaard Kristensen
- Section for Biology and Environmental Science, Department of Chemistry and Bioscience, Aalborg University, 9220, Denmark
- Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University, 8000, Denmark
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