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Wu Q, Zhang C, Xu F, Zang S, Wang D, Sun T, Su Y, Yang S, Ding Y, Que Y. Transcriptional Regulation of SugarCane Response to Sporisorium scitamineum: Insights from Time-Course Gene Coexpression and Ca 2+ Signaling. J Agric Food Chem 2024. [PMID: 38651833 DOI: 10.1021/acs.jafc.4c02123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Sugarcane response to Sporisorium scitamineum is determined by multiple major genes and numerous microeffector genes. Here, time-ordered gene coexpression networks were applied to explore the interaction between sugarcane and S. scitamineum. Totally, 2459 differentially expressed genes were identified and divided into 10 levels, and several stress-related subnetworks were established. Interestingly, the Ca2+ signaling pathway was activated to establish the response to sugarcane smut disease. Accordingly, two CAX genes (ScCAX2 and ScCAX3) were cloned and characterized from sugarcane. They were significantly upregulated under ABA stress but inhibited by MeJA treatment. Furthermore, overexpression of ScCAX2 and ScCAX3 enhanced the susceptibility of transgenic plants to the pathogen infection, suggesting its negative role in disease resistance. A regulatory model for ScCAX genes in disease response was thus depicted. This work helps to clarify the transcriptional regulation of sugarcane response to S. scitamineum stress and the function of the CAX gene in disease response.
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Affiliation(s)
- Qibin Wu
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chang Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongjiao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
| | - Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shaolin Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Yunnan Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan 661600, China
| | - Yinghong Ding
- College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youxiong Que
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Sanya 572024, Haikou 571101, Hainan, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Andersson E, Rothenberg EV, Peterson C, Olariu V. T-cell commitment inheritance-an agent-based multi-scale model. NPJ Syst Biol Appl 2024; 10:40. [PMID: 38632273 PMCID: PMC11024127 DOI: 10.1038/s41540-024-00368-y] [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: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
T-cell development provides an excellent model system for studying lineage commitment from a multipotent progenitor. The intrathymic development process has been thoroughly studied. The molecular circuitry controlling it has been dissected and the necessary steps like programmed shut off of progenitor genes and T-cell genes upregulation have been revealed. However, the exact timing between decision-making and commitment stage remains unexplored. To this end, we implemented an agent-based multi-scale model to investigate inheritance in early T-cell development. Treating each cell as an agent provides a powerful tool as it tracks each individual cell of a simulated T-cell colony, enabling the construction of lineage trees. Based on the lineage trees, we introduce the concept of the last common ancestors (LCA) of committed cells and analyse their relations, both at single-cell level and population level. In addition to simulating wild-type development, we also conduct knockdown analysis. Our simulations predicted that the commitment is a three-step process that occurs on average over several cell generations once a cell is first prepared by a transcriptional switch. This is followed by the loss of the Bcl11b-opposing function approximately two to three generations later. This is when our LCA analysis indicates that the decision to commit is taken even though in general another one to two generations elapse before the cell actually becomes committed by transitioning to the DN2b state. Our results showed that there is decision inheritance in the commitment mechanism.
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Affiliation(s)
- Emil Andersson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, 156-29, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Carsten Peterson
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden
| | - Victor Olariu
- Computational Science for Health and Environment, Centre for Environmental and Climate Science, Lund University, Lund, Sweden.
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3
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Katebi A, Chen X, Ramirez D, Li S, Lu M. Data-driven modeling of core gene regulatory network underlying leukemogenesis in IDH mutant AML. NPJ Syst Biol Appl 2024; 10:38. [PMID: 38594351 PMCID: PMC11003984 DOI: 10.1038/s41540-024-00366-0] [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: 10/16/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Acute myeloid leukemia (AML) is characterized by uncontrolled proliferation of poorly differentiated myeloid cells, with a heterogenous mutational landscape. Mutations in IDH1 and IDH2 are found in 20% of the AML cases. Although much effort has been made to identify genes associated with leukemogenesis, the regulatory mechanism of AML state transition is still not fully understood. To alleviate this issue, here we develop a new computational approach that integrates genomic data from diverse sources, including gene expression and ATAC-seq datasets, curated gene regulatory interaction databases, and mathematical modeling to establish models of context-specific core gene regulatory networks (GRNs) for a mechanistic understanding of tumorigenesis of AML with IDH mutations. The approach adopts a new optimization procedure to identify the top network according to its accuracy in capturing gene expression states and its flexibility to allow sufficient control of state transitions. From GRN modeling, we identify key regulators associated with the function of IDH mutations, such as DNA methyltransferase DNMT1, and network destabilizers, such as E2F1. The constructed core regulatory network and outcomes of in-silico network perturbations are supported by survival data from AML patients. We expect that the combined bioinformatics and systems-biology modeling approach will be generally applicable to elucidate the gene regulation of disease progression.
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Affiliation(s)
- Ataur Katebi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Xiaowen Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Daniel Ramirez
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA
| | - Sheng Li
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA.
- The Jackson Laboratory Cancer Center, Bar Harbor, ME, USA.
| | - Mingyang Lu
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA, USA.
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Aci MM, Tsalgatidou PC, Boutsika A, Dalianis A, Michaliou M, Delis C, Tsitsigiannis DI, Paplomatas E, Malacrinò A, Schena L, Zambounis A. Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated with pear petal defense responses against Monilinia laxa infection. Front Plant Sci 2024; 15:1377937. [PMID: 38516670 PMCID: PMC10954844 DOI: 10.3389/fpls.2024.1377937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024]
Abstract
Pear brown rot and blossom blight caused by Monilinia laxa seriously affect pear production worldwide. Here, we compared the transcriptomic profiles of petals after inoculation with M. laxa using two pear cultivars with different levels of sensitivity to disease (Sissy, a relatively tolerant cultivar, and Kristalli, a highly susceptible cultivar). Physiological indexes were also monitored in the petals of both cultivars at 2 h and 48 h after infection (2 HAI and 48 HAI). RNA-seq data and weighted gene co-expression network analysis (WGCNA) allowed the identification of key genes and pathways involved in immune- and defense-related responses that were specific for each cultivar in a time-dependent manner. In particular, in the Kristalli cultivar, a significant transcriptome reprogramming occurred early at 2 HAI and was accompanied either by suppression of key differentially expressed genes (DEGs) involved in the modulation of any defense responses or by activation of DEGs acting as sensitivity factors promoting susceptibility. In contrast to the considerably high number of DEGs induced early in the Kristalli cultivar, upregulation of specific DEGs involved in pathogen perception and signal transduction, biosynthesis of secondary and primary metabolism, and other defense-related responses was delayed in the Sissy cultivar, occurring at 48 HAI. The WGCNA highlighted one module that was significantly and highly correlated to the relatively tolerant cultivar. Six hub genes were identified within this module, including three WRKY transcription factor-encoding genes: WRKY 65 (pycom05g27470), WRKY 71 (pycom10g22220), and WRKY28 (pycom17g13130), which may play a crucial role in enhancing the tolerance of pear petals to M. laxa. Our results will provide insights into the interplay of the molecular mechanisms underlying immune responses of petals at the pear-M. laxa pathosystem.
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Affiliation(s)
- Meriem Miyassa Aci
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | | | - Anastasia Boutsika
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, Thessaloniki, Greece
| | - Andreas Dalianis
- Laboratory of Vegetable Crops, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization Dimitra, Heraklion, Greece
| | - Maria Michaliou
- Laboratory of Vegetable Crops, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization Dimitra, Heraklion, Greece
| | - Costas Delis
- Department of Agriculture, University of the Peloponnese, Kalamata, Greece
| | - Dimitrios I. Tsitsigiannis
- Laboratory of Plant Pathology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Epaminondas Paplomatas
- Laboratory of Plant Pathology, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Antonino Malacrinò
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Leonardo Schena
- Department of Agriculture, Università degli Studi Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Antonios Zambounis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Dimitra, Thessaloniki, Greece
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5
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Illarregi U, Lopez-Lopez E. LncRNA expression and regulatory networks across pediatric cancers. Transl Pediatr 2024; 13:383-386. [PMID: 38455753 PMCID: PMC10915441 DOI: 10.21037/tp-23-531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/11/2024] [Indexed: 03/09/2024] Open
Affiliation(s)
- Unai Illarregi
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Elixabet Lopez-Lopez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Pediatric Oncology Group, Biobizkaia Health Research Institute, Barakaldo, Spain
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Wang P, Wen X, Li H, Lang P, Li S, Lei Y, Shu H, Gao L, Zhao D, Zeng J. Author Correction: Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON. Nat Commun 2024; 15:1323. [PMID: 38351163 PMCID: PMC10864347 DOI: 10.1038/s41467-024-45929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Affiliation(s)
- Peizhuo Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Xiao Wen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Yipin Lei
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, 710071, Xi'an, Shaanxi Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China.
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7
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Elgaml A, Elshazli R, Miyoshi SI. Editorial: The role of regulatory networks in virulence and antimicrobial resistance of microbial pathogens. Front Microbiol 2024; 15:1370093. [PMID: 38410383 PMCID: PMC10896426 DOI: 10.3389/fmicb.2024.1370093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Affiliation(s)
- Abdelaziz Elgaml
- Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, Horus University - Egypt, New Damietta, Egypt
| | - Rami Elshazli
- Biochemistry and Molecular Genetics Department, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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8
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Bongirwar R, Shukla P. Engineering regulatory networks of cyanobacteria. Trends Biotechnol 2024:S0167-7799(23)00368-2. [PMID: 38296717 DOI: 10.1016/j.tibtech.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
Engineering a cell's regulatory networks to dynamically control gene expression has been considered a new frontier in biological engineering. In cyanobacteria, the lack of well-characterized, modular gene regulatory elements makes regulatory network engineering challenging. Here, we suggest potential tools to modify various gene expression steps in cyanobacterial regulatory networks.
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Affiliation(s)
- Riya Bongirwar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
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Zerrouk N, Alcraft R, Hall BA, Augé F, Niarakis A. Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis. NPJ Syst Biol Appl 2024; 10:10. [PMID: 38272919 PMCID: PMC10811231 DOI: 10.1038/s41540-024-00337-5] [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: 09/18/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Macrophages play an essential role in rheumatoid arthritis. Depending on their phenotype (M1 or M2), they can play a role in the initiation or resolution of inflammation. The M1/M2 ratio in rheumatoid arthritis is higher than in healthy controls. Despite this, no treatment targeting specifically macrophages is currently used in clinics. Thus, devising strategies to selectively deplete proinflammatory macrophages and promote anti-inflammatory macrophages could be a promising therapeutic approach. State-of-the-art molecular interaction maps of M1 and M2 macrophages in rheumatoid arthritis are available and represent a dense source of knowledge; however, these maps remain limited by their static nature. Discrete dynamic modelling can be employed to study the emergent behaviours of these systems. Nevertheless, handling such large-scale models is challenging. Due to their massive size, it is computationally demanding to identify biologically relevant states in a cell- and disease-specific context. In this work, we developed an efficient computational framework that converts molecular interaction maps into Boolean models using the CaSQ tool. Next, we used a newly developed version of the BMA tool deployed to a high-performance computing cluster to identify the models' steady states. The identified attractors are then validated using gene expression data sets and prior knowledge. We successfully applied our framework to generate and calibrate the M1 and M2 macrophage Boolean models for rheumatoid arthritis. Using KO simulations, we identified NFkB, JAK1/JAK2, and ERK1/Notch1 as potential targets that could selectively suppress proinflammatory macrophages and GSK3B as a promising target that could promote anti-inflammatory macrophages in rheumatoid arthritis.
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Affiliation(s)
- Naouel Zerrouk
- GenHotel, Laboratoire Européen de Recherche Pour La Polyarthrite Rhumatoïde, University Paris-Saclay, University Evry, Evry, France
- Sanofi R&D Data and Data Science, Artificial Intelligence & Deep Analytics, Omics Data Science, 1, Av Pierre Brossolette, 91385, Chilly-Mazarin, France
| | - Rachel Alcraft
- Advanced Research Computing Centre, University College London, London, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Franck Augé
- Sanofi R&D Data and Data Science, Artificial Intelligence & Deep Analytics, Omics Data Science, 1, Av Pierre Brossolette, 91385, Chilly-Mazarin, France
| | - Anna Niarakis
- GenHotel, Laboratoire Européen de Recherche Pour La Polyarthrite Rhumatoïde, University Paris-Saclay, University Evry, Evry, France.
- Lifeware Group, Inria Saclay, Palaiseau, France.
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [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: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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Wellman R, Jacobson D, Secrier M, Labbadia J. Distinct patterns of proteostasis network gene expression are associated with different prognoses in melanoma patients. Sci Rep 2024; 14:198. [PMID: 38167612 PMCID: PMC10761826 DOI: 10.1038/s41598-023-50640-0] [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: 09/05/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
The proteostasis network (PN) is a collection of protein folding and degradation pathways that spans cellular compartments and acts to preserve the integrity of the proteome. The differential expression of PN genes is a hallmark of many cancers, and the inhibition of protein quality control factors is an effective way to slow cancer cell growth. However, little is known about how the expression of PN genes differs between patients and how this impacts survival outcomes. To address this, we applied unbiased hierarchical clustering to gene expression data obtained from primary and metastatic cutaneous melanoma (CM) samples and found that two distinct groups of individuals emerge across each sample type. These patient groups are distinguished by the differential expression of genes encoding ATP-dependent and ATP-independent chaperones, and proteasomal subunits. Differences in PN gene expression were associated with increased levels of the transcription factors, MEF2A, SP4, ZFX, CREB1 and ATF2, as well as markedly different survival outcomes. However, surprisingly, similar PN alterations in primary and metastatic samples were associated with discordant survival outcomes in patients. Our findings reveal that the expression of PN genes demarcates CM patients and highlights several new proteostasis sub-networks that could be targeted for more effective suppression of CM within specific individuals.
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Affiliation(s)
- Rachel Wellman
- Division of Biosciences, Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
| | - Daniel Jacobson
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Maria Secrier
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK.
| | - John Labbadia
- Division of Biosciences, Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK.
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12
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He Z, Li M, Pan X, Peng Y, Shi Y, Han Q, Shi M, She L, Borovskii G, Chen X, Gu X, Cheng X, Zhang W. R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice. New Phytol 2024; 241:267-282. [PMID: 37849024 DOI: 10.1111/nph.19315] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment. COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.
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Affiliation(s)
- Zexue He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Mengqi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Xiucai Pan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
- Xiangyang Academy of Agricultural Sciences, Xiangyang, Hubei Province, 441057, China
| | - Yulian Peng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Yining Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Qi Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Manli Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Linwei She
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Gennadii Borovskii
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences (SB RAS) Irkutsk, Lermontova, 664033, Russia
| | - Xiaojun Chen
- Key Lab of Agricultural Biotechnology of Ningxia, Ningxia Academy of Agriculture and Forestry Sciences, YinChuan, 750002, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuejiao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
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13
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Ishikawa M, Sugino S, Masuda Y, Tarumoto Y, Seto Y, Taniyama N, Wagai F, Yamauchi Y, Kojima Y, Kiryu H, Yusa K, Eiraku M, Mochizuki A. RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations. Commun Biol 2023; 6:1290. [PMID: 38155269 PMCID: PMC10754834 DOI: 10.1038/s42003-023-05594-4] [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: 12/08/2022] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.
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Affiliation(s)
- Masato Ishikawa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Seiichi Sugino
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yoshie Masuda
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Tarumoto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yusuke Seto
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Nobuko Taniyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Fumi Wagai
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuhei Yamauchi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Yasuhiro Kojima
- Laboratory of Computational Life Science, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Kosuke Yusa
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
| | - Mototsugu Eiraku
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, 606-8507, Japan
| | - Atsushi Mochizuki
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan
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14
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Chen L, Liu L, Yang G, Li X, Dai X, Xue L, Yin T. Expression Quantitative Trait Locus of Wood Formation-Related Genes in Salix suchowensis. Int J Mol Sci 2023; 25:247. [PMID: 38203430 PMCID: PMC10778782 DOI: 10.3390/ijms25010247] [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: 11/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Shrub willows are widely planted for landscaping, soil remediation, and biomass production, due to their rapid growth rates. Identification of regulatory genes in wood formation would provide clues for genetic engineering of willows for improved growth traits on marginal lands. Here, we conducted an expression quantitative trait locus (eQTL) analysis, using a full sibling F1 population of Salix suchowensis, to explore the genetic mechanisms underlying wood formation. Based on variants identified from simplified genome sequencing and gene expression data from RNA sequencing, 16,487 eQTL blocks controlling 5505 genes were identified, including 2148 cis-eQTLs and 16,480 trans-eQTLs. eQTL hotspots were identified, based on eQTL frequency in genomic windows, revealing one hotspot controlling genes involved in wood formation regulation. Regulatory networks were further constructed, resulting in the identification of key regulatory genes, including three transcription factors (JAZ1, HAT22, MYB36) and CLV1, BAM1, CYCB2;4, CDKB2;1, associated with the proliferation and differentiation activity of cambium cells. The enrichment of genes in plant hormone pathways indicates their critical roles in the regulation of wood formation. Our analyses provide a significant groundwork for a comprehensive understanding of the regulatory network of wood formation in S. suchowensis.
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Affiliation(s)
| | | | | | | | | | - Liangjiao Xue
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- State Key Laboratory of Tree Genetics and Breeding, Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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15
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Wang P, Wen X, Li H, Lang P, Li S, Lei Y, Shu H, Gao L, Zhao D, Zeng J. Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON. Nat Commun 2023; 14:8459. [PMID: 38123534 PMCID: PMC10733330 DOI: 10.1038/s41467-023-44103-3] [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: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell technologies enable the dynamic analyses of cell fate mapping. However, capturing the gene regulatory relationships and identifying the driver factors that control cell fate decisions are still challenging. We present CEFCON, a network-based framework that first uses a graph neural network with attention mechanism to infer a cell-lineage-specific gene regulatory network (GRN) from single-cell RNA-sequencing data, and then models cell fate dynamics through network control theory to identify driver regulators and the associated gene modules, revealing their critical biological processes related to cell states. Extensive benchmarking tests consistently demonstrated the superiority of CEFCON in GRN construction, driver regulator identification, and gene module identification over baseline methods. When applied to the mouse hematopoietic stem cell differentiation data, CEFCON successfully identified driver regulators for three developmental lineages, which offered useful insights into their differentiation from a network control perspective. Overall, CEFCON provides a valuable tool for studying the underlying mechanisms of cell fate decisions from single-cell RNA-seq data.
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Affiliation(s)
- Peizhuo Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Xiao Wen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Yipin Lei
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, 710071, Xi'an, Shaanxi Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China.
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16
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Yakubovich E, Cook DP, Rodriguez GM, Vanderhyden BC. Mesenchymal ovarian cancer cells promote CD8 + T cell exhaustion through the LGALS3-LAG3 axis. NPJ Syst Biol Appl 2023; 9:61. [PMID: 38086828 PMCID: PMC10716312 DOI: 10.1038/s41540-023-00322-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cancer cells often metastasize by undergoing an epithelial-mesenchymal transition (EMT). Although abundance of CD8+ T-cells in the tumor microenvironment correlates with improved survival, mesenchymal cancer cells acquire greater resistance to antitumor immunity in some cancers. We hypothesized the EMT modulates the immune response to ovarian cancer. Here we show that cancer cells from infiltrated/inflamed tumors possess more mesenchymal cells, than excluded and desert tumors. We also noted high expression of LGALS3 is associated with EMT in vivo, a finding validated with in vitro EMT models. Dissecting the cellular communications among populations in the tumor revealed that mesenchymal cancer cells in infiltrated tumors communicate through LGALS3 to LAG3 receptor expressed by CD8+ T cells. We found CD8+ T cells express high levels of LAG3, a marker of T cell exhaustion. The results indicate that EMT in ovarian cancer cells promotes interactions between cancer cells and T cells through the LGALS3 - LAG3 axis, which could increase T cell exhaustion in infiltrated tumors, dampening antitumor immunity.
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Affiliation(s)
- Edward Yakubovich
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.
| | - David P Cook
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Galaxia M Rodriguez
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Barbara C Vanderhyden
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
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17
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Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C, Chao Y. In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub. Nat Commun 2023; 14:8106. [PMID: 38062076 PMCID: PMC10703908 DOI: 10.1038/s41467-023-43632-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Small noncoding RNAs (sRNAs) are crucial regulators of gene expression in bacteria. Acting in concert with major RNA chaperones such as Hfq or ProQ, sRNAs base-pair with multiple target mRNAs and form large RNA-RNA interaction networks. To systematically investigate the RNA-RNA interactome in living cells, we have developed a streamlined in vivo approach iRIL-seq (intracellular RIL-seq). This generic approach is highly robust, illustrating the dynamic sRNA interactomes in Salmonella enterica across multiple stages of growth. We have identified the OmpD porin mRNA as a central regulatory hub that is targeted by a dozen sRNAs, including FadZ cleaved from the conserved 3'UTR of fadBA mRNA. Both ompD and FadZ are activated by CRP, constituting a type I incoherent feed-forward loop in the fatty acid metabolism pathway. Altogether, we have established an approach to profile RNA-RNA interactomes in live cells, highlighting the complexity of RNA regulatory hubs and RNA networks.
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Affiliation(s)
- Fang Liu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ziying Chen
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center & Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shuo Zhang
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kejing Wu
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Bei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China
| | - Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200033, China.
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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18
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Zhao S, Zhang T, Hasunuma T, Kondo A, Zhao XQ, Feng JX. Every road leads to Rome: diverse biosynthetic regulation of plant cell wall-degrading enzymes in filamentous fungi Penicillium oxalicum and Trichoderma reesei. Crit Rev Biotechnol 2023:1-21. [PMID: 38035670 DOI: 10.1080/07388551.2023.2280810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Cellulases and xylanases are plant cell wall-degrading enzymes (CWDEs) that are critical to sustainable bioproduction based on renewable lignocellulosic biomass to reduce carbon dioxide emission. Currently, these enzymes are mainly produced from filamentous fungi, especially Trichoderma reesei and Penicillium oxalicum. However, an in-depth comparison of these two producers has not been performed. Although both P. oxalicum and T. reesei harbor CWDE systems, they exhibit distinct features regulating the production of these enzymes, mainly through different transcriptional regulatory networks. This review presents the strikingly different modes of genome-wide regulation of cellulase and xylanase biosynthesis in P. oxalicum and T. reesei, including sugar transporters, signal transduction cascades, transcription factors, chromatin remodeling, and three-dimensional organization of chromosomes. In addition, different molecular breeding approaches employed, based on the understanding of the regulatory networks, are summarized. This review highlights the existence of very different regulatory modes leading to the efficient regulation of CWDE production in filamentous fungi, akin to the adage that "every road leads to Rome." An understanding of this divergence may help further improvements in fungal enzyme production through the metabolic engineering and synthetic biology of certain fungal species.
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Affiliation(s)
- Shuai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
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19
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Sukko N, Kalapanulak S, Saithong T. Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation. Sci Rep 2023; 13:19973. [PMID: 37968317 PMCID: PMC10651926 DOI: 10.1038/s41598-023-47095-8] [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: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.
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Affiliation(s)
- Nattavat Sukko
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
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20
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Sanders JG, Akl H, Hagen SJ, Xue B. Crosstalk enables mutual activation of coupled quorum sensing pathways through "jump-start" and "push-start" mechanisms. Sci Rep 2023; 13:19230. [PMID: 37932382 PMCID: PMC10628186 DOI: 10.1038/s41598-023-46399-z] [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: 05/24/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Many quorum sensing microbes produce more than one chemical signal and detect them using interconnected pathways that crosstalk with each other. While there are many hypotheses for the advantages of sensing multiple signals, the prevalence and functional significance of crosstalk between pathways are much less understood. We explore the effect of intracellular signal crosstalk using a simple model that captures key features of typical quorum sensing pathways: multiple pathways in a hierarchical configuration, operating with positive feedback, with crosstalk at the receptor and promoter levels. We find that crosstalk enables activation or inhibition of one output by the non-cognate signal, broadens the dynamic range of the outputs, and allows one pathway to modulate the feedback circuit of the other. Our findings show how crosstalk between quorum sensing pathways can be viewed not as a detriment to the processing of information, but as a mechanism that enhances the functional range of the full regulatory system. When positive feedback systems are coupled through crosstalk, several new modes of activation or deactivation become possible.
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Affiliation(s)
| | - Hoda Akl
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA
| | - Stephen J Hagen
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA
| | - BingKan Xue
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA.
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21
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Abstract
Enhancer RNAs (eRNAs) are non-coding RNAs produced by transcriptional enhancers that are highly correlated with their activity. Using a capped nascent RNA sequencing (PRO-cap) dataset in human lymphoblastoid cell lines across 67 individuals, we identified inter-individual variation in the expression of over 80 thousand transcribed transcriptional regulatory elements (tTREs), in both enhancers and promoters. Co-expression analysis of eRNAs from tTREs across individuals revealed how enhancers are associated with each other and with promoters. Mid- to long-range co-expression showed a distance-dependent decay that was modified by TF occupancy. In particular, we found a class of "bivalent" TFs, including Cohesin, that both facilitate and isolate the interaction between enhancers and/or promoters, depending on their topology. At short distances, we observed strand-specific correlations between nearby eRNAs in both convergent and divergent orientations. Our results support a cooperative model of convergent eRNAs, consistent with eRNAs facilitating adjacent enhancers rather than interfering with each other. Therefore, our approach to infer functional interactions from co-expression analyses provided novel insights into the principles of enhancer interactions as a function of distance, orientation, and binding landscapes of TFs.
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Affiliation(s)
- Seungha Alisa Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Katla Kristjánsdóttir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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22
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Massacci G, Perfetto L, Sacco F. The Cyclin-dependent kinase 1: more than a cell cycle regulator. Br J Cancer 2023; 129:1707-1716. [PMID: 37898722 PMCID: PMC10667339 DOI: 10.1038/s41416-023-02468-8] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/26/2023] [Accepted: 10/13/2023] [Indexed: 10/30/2023] Open
Abstract
The Cyclin-dependent kinase 1, as a serine/threonine protein kinase, is more than a cell cycle regulator as it was originally identified. During the last decade, it has been shown to carry out versatile functions during the last decade. From cell cycle control to gene expression regulation and apoptosis, CDK1 is intimately involved in many cellular events that are vital for cell survival. Here, we provide a comprehensive catalogue of the CDK1 upstream regulators and substrates, describing how this kinase is implicated in the control of key 'cell cycle-unrelated' biological processes. Finally, we describe how deregulation of CDK1 expression and activation has been closely associated with cancer progression and drug resistance.
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Affiliation(s)
- Giorgia Massacci
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Livia Perfetto
- Department of Biology and Biotechnologies "Charles Darwin", University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy.
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23
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Ozen M, Lopez CF. Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways. NPJ Syst Biol Appl 2023; 9:55. [PMID: 37907529 PMCID: PMC10618210 DOI: 10.1038/s41540-023-00316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/02/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive disease and challenging to treat due to its mixture of transcriptional subtypes and subtype transitions. Transcription factor (TF) networks have been the focus of studies to identify SCLC subtype regulators via systems approaches. Yet, their structures, which can provide clues on subtype drivers and transitions, are barely investigated. Here, we analyze the structure of an SCLC TF network by using graph theory concepts and identify its structurally important components responsible for complex signal processing, called hubs. We show that the hubs of the network are regulators of different SCLC subtypes by analyzing first the unbiased network structure and then integrating RNA-seq data as weights assigned to each interaction. Data-driven analysis emphasizes MYC as a hub, consistent with recent reports. Furthermore, we hypothesize that the pathways connecting functionally distinct hubs may control subtype transitions and test this hypothesis via network simulations on a candidate pathway and observe subtype transition. Overall, structural analyses of complex networks can identify their functionally important components and pathways driving the network dynamics. Such analyses can be an initial step for generating hypotheses and can guide the discovery of target pathways whose perturbation may change the network dynamics phenotypically.
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Affiliation(s)
- Mustafa Ozen
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA
| | - Carlos F Lopez
- Dept. of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Multiscale Modeling Group, SI3, Altos Labs, Redwood City, CA, USA.
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24
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Berenson A, Lane R, Soto-Ugaldi LF, Patel M, Ciausu C, Li Z, Chen Y, Shah S, Santoso C, Liu X, Spirohn K, Hao T, Hill DE, Vidal M, Fuxman Bass JI. Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors. Nat Commun 2023; 14:6570. [PMID: 37853017 PMCID: PMC10584920 DOI: 10.1038/s41467-023-42445-6] [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: 04/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA region-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage and identify cooperativity and antagonism between human TFs and viral proteins from human papillomaviruses, Epstein-Barr virus, and other viruses. Altogether, pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.
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Affiliation(s)
- Anna Berenson
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Mahir Patel
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Cosmin Ciausu
- Department of Computer Science, Boston University, Boston, MA, 02215, USA
| | - Zhaorong Li
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Yilin Chen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Sakshi Shah
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Xing Liu
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, 02215, USA.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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25
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Flores-Garza E, Hernández-Pando R, García-Zárate I, Aguirre P, Domínguez-Hüttinger E. Bifurcation analysis of a tuberculosis progression model for drug target identification. Sci Rep 2023; 13:17567. [PMID: 37845271 PMCID: PMC10579266 DOI: 10.1038/s41598-023-44569-7] [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: 05/22/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023] Open
Abstract
Tuberculosis (TB) is a major cause of morbidity and mortality worldwide. The emergence and rapid spread of drug-resistant M. tuberculosis strains urge us to develop novel treatments. Experimental trials are constrained by laboratory capacity, insufficient funds, low number of laboratory animals and obsolete technology. Systems-level approaches to quantitatively study TB can overcome these limitations. Previously, we proposed a mathematical model describing the key regulatory mechanisms underlying the pathological progression of TB. Here, we systematically explore the effect of parameter variations on disease outcome. We find five bifurcation parameters that steer the clinical outcome of TB: number of bacteria phagocytosed per macrophage, macrophages death, macrophage killing by bacteria, macrophage recruitment, and phagocytosis of bacteria. The corresponding bifurcation diagrams show all-or-nothing dose-response curves with parameter regions mapping onto bacterial clearance, persistent infection, or history-dependent clearance or infection. Importantly, the pathogenic stage strongly affects the sensitivity of the host to these parameter variations. We identify parameter values corresponding to a latent-infection model of TB, where disease progression occurs significantly slower than in progressive TB. Two-dimensional bifurcation analyses uncovered synergistic parameter pairs that could act as efficient compound therapeutic approaches. Through bifurcation analysis, we reveal how modulation of specific regulatory mechanisms could steer the clinical outcome of TB.
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Affiliation(s)
- Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico, Mexico
| | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, 14080, Mexico City, Mexico
| | - Ibrahim García-Zárate
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | - Pablo Aguirre
- Departamento de Matemática, Universidad Técnica Federico Santa María, Casilla 110-V, Valparaíso, Chile
| | - Elisa Domínguez-Hüttinger
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico, Mexico.
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26
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Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs. Nat Commun 2023; 14:6319. [PMID: 37813857 PMCID: PMC10562459 DOI: 10.1038/s41467-023-41882-7] [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: 02/23/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.
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Affiliation(s)
- Alaksh Choudhury
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Laboratoire Biophysique et Évolution (LBE), UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France.
| | - Benoit Gachet
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
| | - Zoya Dixit
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France
| | - Roland Faure
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado-Boulder, Boulder, CO, 80309-0027, USA
- Novo Nordisk Foundation, Denmark Technical University, 2800 Kgs, Lyngby, Denmark
| | - Olivier Tenaillon
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France.
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27
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Sahoo S, Ramu S, Nair MG, Pillai M, San Juan BP, Milioli HZ, Mandal S, Naidu CM, Mavatkar AD, Subramaniam H, Neogi AG, Chaffer CL, Prabhu JS, Somarelli JA, Jolly MK. Multi-modal transcriptomic analysis unravels enrichment of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer. bioRxiv 2023:2023.09.30.558960. [PMID: 37873432 PMCID: PMC10592858 DOI: 10.1101/2023.09.30.558960] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Intra-tumoral phenotypic heterogeneity promotes tumor relapse and therapeutic resistance and remains an unsolved clinical challenge. It manifests along multiple phenotypic axes and decoding the interconnections among these different axes is crucial to understand its molecular origins and to develop novel therapeutic strategies to control it. Here, we use multi-modal transcriptomic data analysis - bulk, single-cell and spatial transcriptomics - from breast cancer cell lines and primary tumor samples, to identify associations between epithelial-mesenchymal transition (EMT) and luminal-basal plasticity - two key processes that enable heterogeneity. We show that luminal breast cancer strongly associates with an epithelial cell state, but basal breast cancer is associated with hybrid epithelial/mesenchymal phenotype(s) and higher phenotypic heterogeneity. These patterns were inherent in methylation profiles, suggesting an epigenetic crosstalk between EMT and lineage plasticity in breast cancer. Mathematical modelling of core underlying gene regulatory networks representative of the crosstalk between the luminal-basal and epithelial-mesenchymal axes recapitulate and thus elucidate mechanistic underpinnings of the observed associations from transcriptomic data. Our systems-based approach integrating multi-modal data analysis with mechanism-based modeling offers a predictive framework to characterize intra-tumor heterogeneity and to identify possible interventions to restrict it.
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Affiliation(s)
- Sarthak Sahoo
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Soundharya Ramu
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Madhumathy G Nair
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Maalavika Pillai
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
- Current affiliation: Feinberg School of Medicine, Northwestern University, Chicago, 60611, USA
| | - Beatriz P San Juan
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | | | - Susmita Mandal
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Chandrakala M Naidu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Apoorva D Mavatkar
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | - Harini Subramaniam
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Arpita G Neogi
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
| | - Christine L Chaffer
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- University of New South Wales, UNSW Medicine, UNSW Sydney, NSW, 2052, Australia
| | - Jyothi S Prabhu
- Division of Molecular Medicine, St. John’s Research Institute, St. John’s Medical College, Bangalore, 560012, India
| | | | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore, 560012, India
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28
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Oliva M, Lister R. Exploring the identity of individual plant cells in space and time. New Phytol 2023; 240:61-67. [PMID: 37483019 PMCID: PMC10952157 DOI: 10.1111/nph.19153] [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] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/17/2023] [Indexed: 07/25/2023]
Abstract
In recent years, single-cell genomics, coupled to imaging techniques, have become the state-of-the-art approach for characterising biological systems. In plant sciences, a variety of tissues and species have been profiled, providing an enormous quantity of data on cell identity at an unprecedented resolution, but what biological insights can be gained from such data sets? Using recently published studies in plant sciences, we will highlight how single-cell technologies have enabled a better comprehension of tissue organisation, cell fate dynamics in development or in response to various stimuli, as well as identifying key transcriptional regulators of cell identity. We discuss the limitations and technical hurdles to overcome, as well as future directions, and the promising use of single-cell omics to understand, predict, and manipulate plant development and physiology.
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Affiliation(s)
- Marina Oliva
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular SciencesUniversity of Western AustraliaPerthWA6009Australia
- The Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical ResearchThe University of Western AustraliaPerthWA6009Australia
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29
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Wang Z, Song G, Zhang F, Shu X, Wang N. Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris. Int J Mol Sci 2023; 24:14464. [PMID: 37833913 PMCID: PMC10572147 DOI: 10.3390/ijms241914464] [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: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.
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Affiliation(s)
- Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Guowei Song
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybeans (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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30
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Han Y, Li W, Filko A, Li J, Zhang F. Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli. Nat Commun 2023; 14:5757. [PMID: 37717013 PMCID: PMC10505187 DOI: 10.1038/s41467-023-41572-4] [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: 12/07/2022] [Accepted: 09/08/2023] [Indexed: 09/18/2023] Open
Abstract
Elucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. We perform PPTP-seq for E. coli growing in three different media. The PPTP-seq data reveal robust steady-state promoter activities under most single TF knockdown conditions. PPTP-seq also enables identifications of, to the best of our knowledge, previously unknown TF autoregulatory responses and complex transcriptional control on one-carbon metabolism. We further find context-dependent promoter regulation by multiple TFs whose relative binding strengths determined promoter activities. Additionally, PPTP-seq reveals different promoter responses in different growth media, suggesting condition-specific gene regulation. Overall, PPTP-seq provides a powerful method to examine genome-wide transcriptional regulatory networks and can be potentially expanded to reveal gene expression responses to other genetic elements.
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Affiliation(s)
- Yichao Han
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Wanji Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Alden Filko
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA.
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri, USA.
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA.
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31
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Fleck JS, Jansen SMJ, Wollny D, Zenk F, Seimiya M, Jain A, Okamoto R, Santel M, He Z, Camp JG, Treutlein B. Inferring and perturbing cell fate regulomes in human brain organoids. Nature 2023; 621:365-372. [PMID: 36198796 PMCID: PMC10499607 DOI: 10.1038/s41586-022-05279-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [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: 10/06/2021] [Accepted: 08/25/2022] [Indexed: 02/06/2023]
Abstract
Self-organizing neural organoids grown from pluripotent stem cells1-3 combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology.
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Affiliation(s)
- Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | | | - Damian Wollny
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fides Zenk
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Akanksha Jain
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ryoko Okamoto
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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32
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Harris R, Karimi M. Dissecting the regulatory network of transcription factors in T cell phenotype/functioning during GVHD and GVT. Front Immunol 2023; 14:1194984. [PMID: 37441063 PMCID: PMC10333690 DOI: 10.3389/fimmu.2023.1194984] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Transcription factors play a major role in regulation and orchestration of immune responses. The immunological context of the response can alter the regulatory networks required for proper functioning. While these networks have been well-studied in canonical immune contexts like infection, the transcription factor landscape during alloactivation remains unclear. This review addresses how transcription factors contribute to the functioning of mature alloactivated T cells. This review will also examine how these factors form a regulatory network to control alloresponses, with a focus specifically on those factors expressed by and controlling activity of T cells of the various subsets involved in graft-versus-host disease (GVHD) and graft-versus-tumor (GVT) responses.
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Affiliation(s)
- Rebecca Harris
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Mobin Karimi
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
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Premkumar T, Sajitha Lulu S. Molecular crosstalk between COVID-19 and Alzheimer's disease using microarray and RNA-seq datasets: A system biology approach. Front Med (Lausanne) 2023; 10:1151046. [PMID: 37359008 PMCID: PMC10286240 DOI: 10.3389/fmed.2023.1151046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/20/2023] [Indexed: 06/28/2023] Open
Abstract
Objective Coronavirus disease 2019 (COVID-19) is an infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The clinical and epidemiological analysis reported the association between SARS-CoV-2 and neurological diseases. Among neurological diseases, Alzheimer's disease (AD) has developed as a crucial comorbidity of SARS-CoV-2. This study aimed to understand the common transcriptional signatures between SARS-CoV-2 and AD. Materials and methods System biology approaches were used to compare the datasets of AD and COVID-19 to identify the genetic association. For this, we have integrated three human whole transcriptomic datasets for COVID-19 and five microarray datasets for AD. We have identified differentially expressed genes for all the datasets and constructed a protein-protein interaction (PPI) network. Hub genes were identified from the PPI network, and hub genes-associated regulatory molecules (transcription factors and miRNAs) were identified for further validation. Results A total of 9,500 differentially expressed genes (DEGs) were identified for AD and 7,000 DEGs for COVID-19. Gene ontology analysis resulted in 37 molecular functions, 79 cellular components, and 129 biological processes were found to be commonly enriched in AD and COVID-19. We identified 26 hub genes which includes AKT1, ALB, BDNF, CD4, CDH1, DLG4, EGF, EGFR, FN1, GAPDH, INS, ITGB1, ACTB, SRC, TP53, CDC42, RUNX2, HSPA8, PSMD2, GFAP, VAMP2, MAPK8, CAV1, GNB1, RBX1, and ITGA2B. Specific miRNA targets associated with Alzheimer's disease and COVID-19 were identified through miRNA target prediction. In addition, we found hub genes-transcription factor and hub genes-drugs interaction. We also performed pathway analysis for the hub genes and found that several cell signaling pathways are enriched, such as PI3K-AKT, Neurotrophin, Rap1, Ras, and JAK-STAT. Conclusion Our results suggest that the identified hub genes could be diagnostic biomarkers and potential therapeutic drug targets for COVID-19 patients with AD comorbidity.
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Moschonas NK, Klapa MI. Editorial: Exploring GWAS data by biomolecular network analysis in revealing genetic disease mechanisms. Front Genet 2023; 14:1223913. [PMID: 37323675 PMCID: PMC10262209 DOI: 10.3389/fgene.2023.1223913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Nicholas K. Moschonas
- Laboratory of General Biology, School of Medicine, University of Patras, Patras, Greece
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
| | - Maria I. Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT), Patras, Greece
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Fu G, Ren Y, Kang J, Wang B, Zhang J, Fang J, Wu W. Integrative analysis of grapevine ( Vitis vinifera L) transcriptome reveals regulatory network for Chardonnay quality formation. Front Nutr 2023; 10:1187842. [PMID: 37324731 PMCID: PMC10265639 DOI: 10.3389/fnut.2023.1187842] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
Anthocyanins, total phenols, soluble sugar and fruit shape plays a significant role in determining the distinct fruit quality and customer preference. However, for the majority of fruit species, little is known about the transcriptomics and underlying regulatory networks that control the generation of overall quality during fruit growth and ripening. This study incorporated the quality-related transcriptome data from 6 ecological zones across 3 fruit development and maturity phases of Chardonnay cultivars. With the help of this dataset, we were able to build a complex regulatory network that may be used to identify important structural genes and transcription factors that control the anthocyanins, total phenols, soluble sugars and fruit shape in grapes. Overall, our findings set the groundwork to improve grape quality in addition to offering novel views on quality control during grape development and ripening.
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Affiliation(s)
- Guangqing Fu
- Research Institute of Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Yanhua Ren
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Horticultural College, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jun Kang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Bo Wang
- Research Institute of Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Junxiang Zhang
- Food and Wine Academy, Ningxia University, Yinchuan, Ningxia, China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Food and Wine Academy, Ningxia University, Yinchuan, Ningxia, China
| | - Weimin Wu
- Research Institute of Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
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Thompson MJ, Young CA, Munnamalai V, Umulis DM. Early radial positional information in the cochlea is optimized by a precise linear BMP gradient and enhanced by SOX2. Sci Rep 2023; 13:8567. [PMID: 37237002 PMCID: PMC10219982 DOI: 10.1038/s41598-023-34725-4] [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: 01/23/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Positional information encoded in signaling molecules is essential for early patterning in the prosensory domain of the developing cochlea. The sensory epithelium, the organ of Corti, contains an exquisite repeating pattern of hair cells and supporting cells. This requires precision in the morphogen signals that set the initial radial compartment boundaries, but this has not been investigated. To measure gradient formation and morphogenetic precision in developing cochlea, we developed a quantitative image analysis procedure measuring SOX2 and pSMAD1/5/9 profiles in mouse embryos at embryonic day (E)12.5, E13.5, and E14.5. Intriguingly, we found that the pSMAD1/5/9 profile forms a linear gradient up to the medial ~ 75% of the PSD from the pSMAD1/5/9 peak in the lateral edge during E12.5 and E13.5. This is a surprising activity readout for a diffusive BMP4 ligand secreted from a tightly constrained lateral region since morphogens typically form exponential or power-law gradient shapes. This is meaningful for gradient interpretation because while linear profiles offer the theoretically highest information content and distributed precision for patterning, a linear morphogen gradient has not yet been observed. Furthermore, this is unique to the cochlear epithelium as the pSMAD1/5/9 gradient is exponential in the surrounding mesenchyme. In addition to the information-optimized linear profile, we found that while pSMAD1/5/9 is stable during this timeframe, an accompanying gradient of SOX2 shifts dynamically. Last, through joint decoding maps of pSMAD1/5/9 and SOX2, we see that there is a high-fidelity mapping between signaling activity and position in the regions that will become Kölliker's organ and the organ of Corti. Mapping is ambiguous in the prosensory domain precursory to the outer sulcus. Altogether, this research provides new insights into the precision of early morphogenetic patterning cues in the radial cochlea prosensory domain.
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Affiliation(s)
- Matthew J Thompson
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Caryl A Young
- University of Maine, 168 College Ave, Orono, ME, 04469, USA
| | - Vidhya Munnamalai
- University of Maine, 168 College Ave, Orono, ME, 04469, USA.
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - David M Umulis
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr, West Lafayette, IN, 47907, USA.
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Ribeiro-dos-Santos A, de Brito LM, de Araújo GS. The fusiform gyrus exhibits differential gene-gene co-expression in Alzheimer's disease. Front Aging Neurosci 2023; 15:1138336. [PMID: 37255536 PMCID: PMC10225579 DOI: 10.3389/fnagi.2023.1138336] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Alzheimer's Disease (AD) is an irreversible neurodegenerative disease clinically characterized by the presence of β-amyloid plaques and tau deposits in various regions of the brain. However, the underlying factors that contribute to the development of AD remain unclear. Recently, the fusiform gyrus has been identified as a critical brain region associated with mild cognitive impairment, which may increase the risk of AD development. In our study, we performed gene co-expression and differential co-expression network analyses, as well as gene-expression-based prediction, using RNA-seq transcriptome data from post-mortem fusiform gyrus tissue samples collected from both cognitively healthy individuals and those with AD. We accessed differential co-expression networks in large cohorts such as ROSMAP, MSBB, and Mayo, and conducted over-representation analyses of gene pathways and gene ontology. Our results comprise four exclusive gene hubs in co-expression modules of Alzheimer's Disease, including FNDC3A, MED23, NRIP1, and PKN2. Further, we identified three genes with differential co-expressed links, namely FAM153B, CYP2C8, and CKMT1B. The differential co-expressed network showed moderate predictive performance for AD, with an area under the curve ranging from 0.71 to 0.76 (+/- 0.07). The over-representation analysis identified enrichment for Toll-Like Receptors Cascades and signaling pathways, such as G protein events, PIP2 hydrolysis and EPH-Epherin mechanism, in the fusiform gyrus. In conclusion, our findings shed new light on the molecular pathophysiology of AD by identifying new genes and biological pathways involved, emphasizing the crucial role of gene regulatory networks in the fusiform gyrus.
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Affiliation(s)
- Arthur Ribeiro-dos-Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Leonardo Miranda de Brito
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
- Centro de Informática, Universidade Federal de Pernambuco, Recife, Brazil
| | - Gilderlanio Santana de Araújo
- Programa de Pós-graduação em Genética e Biologia Molecular, Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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Kim J, Hopper C, Cho KH. Statistical control of structural networks with limited interventions to minimize cellular phenotypic diversity represented by point attractors. Sci Rep 2023; 13:6275. [PMID: 37072458 PMCID: PMC10113376 DOI: 10.1038/s41598-023-33346-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
The underlying genetic networks of cells give rise to diverse behaviors known as phenotypes. Control of this cellular phenotypic diversity (CPD) may reveal key targets that govern differentiation during development or drug resistance in cancer. This work establishes an approach to control CPD that encompasses practical constraints, including model limitations, the number of simultaneous control targets, which targets are viable for control, and the granularity of control. Cellular networks are often limited to the structure of interactions, due to the practical difficulty of modeling interaction dynamics. However, these dynamics are essential to CPD. In response, our statistical control approach infers the CPD directly from the structure of a network, by considering an ensemble average function over all possible Boolean dynamics for each node in the network. These ensemble average functions are combined with an acyclic form of the network to infer the number of point attractors. Our approach is applied to several known biological models and shown to outperform existing approaches. Statistical control of CPD offers a new avenue to contend with systemic processes such as differentiation and cancer, despite practical limitations in the field.
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Affiliation(s)
- Jongwan Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Corbin Hopper
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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Gopalan V, Hannenhalli S. Towards a Synthesis of the Non-Genetic and Genetic Views of Cancer in Understanding Pancreatic Ductal Adenocarcinoma Initiation and Prevention. Cancers (Basel) 2023; 15:cancers15072159. [PMID: 37046820 PMCID: PMC10093726 DOI: 10.3390/cancers15072159] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
While much of the research in oncogenesis and cancer therapy has focused on mutations in key cancer driver genes, more recent work suggests a complementary non-genetic paradigm. This paradigm focuses on how transcriptional and phenotypic heterogeneity, even in clonally derived cells, can create sub-populations associated with oncogenesis, metastasis, and therapy resistance. We discuss this complementary paradigm in the context of pancreatic ductal adenocarcinoma. A better understanding of cellular transcriptional heterogeneity and its association with oncogenesis can lead to more effective therapies that prevent tumor initiation and slow progression.
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Affiliation(s)
- Vishaka Gopalan
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20814, USA
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40
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Al-Aamri A, Kudlicki AS, Maalouf M, Taha K, Homouz D. Inferring Gene Regulatory Networks from RNA-seq Data Using Kernel Classification. Biology (Basel) 2023; 12:518. [PMID: 37106719 PMCID: PMC10135911 DOI: 10.3390/biology12040518] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Gene expression profiling is one of the most recognized techniques for inferring gene regulators and their potential targets in gene regulatory networks (GRN). The purpose of this study is to build a regulatory network for the budding yeast Saccharomyces cerevisiae genome by incorporating the use of RNA-seq and microarray data represented by a wide range of experimental conditions. We introduce a pipeline for data analysis, data preparation, and training models. Several kernel classification models; including one-class, two-class, and rare event classification methods, are used to categorize genes. We test the impact of the normalization techniques on the overall performance of RNA-seq. Our findings provide new insights into the interactions between genes in the yeast regulatory network. The conclusions of our study have significant importance since they highlight the effectiveness of classification and its contribution towards enhancing the present comprehension of the yeast regulatory network. When assessed, our pipeline demonstrates strong performance across different statistical metrics, such as a 99% recall rate and a 98% AUC score.
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Affiliation(s)
- Amira Al-Aamri
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Andrzej S. Kudlicki
- Department of Biochemistry and Molecular Biology, Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maher Maalouf
- Department of Industrial and Systems Engineering, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Kamal Taha
- Department of Electrical and Computer Science, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
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41
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Griffin AT, Vlahos LJ, Chiuzan C, Califano A. NaRnEA: An Information Theoretic Framework for Gene Set Analysis. Entropy (Basel) 2023; 25:e25030542. [PMID: 36981431 PMCID: PMC10048242 DOI: 10.3390/e25030542] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/03/2023] [Accepted: 03/13/2023] [Indexed: 05/26/2023]
Abstract
Gene sets are being increasingly leveraged to make high-level biological inferences from transcriptomic data; however, existing gene set analysis methods rely on overly conservative, heuristic approaches for quantifying the statistical significance of gene set enrichment. We created Nonparametric analytical-Rank-based Enrichment Analysis (NaRnEA) to facilitate accurate and robust gene set analysis with an optimal null model derived using the information theoretic Principle of Maximum Entropy. By measuring the differential activity of ~2500 transcriptional regulatory proteins based on the differential expression of each protein's transcriptional targets between primary tumors and normal tissue samples in three cohorts from The Cancer Genome Atlas (TCGA), we demonstrate that NaRnEA critically improves in two widely used gene set analysis methods: Gene Set Enrichment Analysis (GSEA) and analytical-Rank-based Enrichment Analysis (aREA). We show that the NaRnEA-inferred differential protein activity is significantly correlated with differential protein abundance inferred from independent, phenotype-matched mass spectrometry data in the Clinical Proteomic Tumor Analysis Consortium (CPTAC), confirming the statistical and biological accuracy of our approach. Additionally, our analysis crucially demonstrates that the sample-shuffling empirical null models leveraged by GSEA and aREA for gene set analysis are overly conservative, a shortcoming that is avoided by the newly developed Maximum Entropy analytical null model employed by NaRnEA.
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Affiliation(s)
- Aaron T. Griffin
- Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lukas J. Vlahos
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Codruta Chiuzan
- Department of Biostatistics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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Hammami F, Tichit L, Py B, Barras F, Mandin P, Remy E. Analysis of a logical regulatory network reveals how Fe-S cluster biogenesis is controlled in the face of stress. Microlife 2023; 4:uqad003. [PMID: 37223744 PMCID: PMC10117729 DOI: 10.1093/femsml/uqad003] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/16/2022] [Accepted: 03/01/2023] [Indexed: 05/25/2023]
Abstract
Iron-sulfur (Fe-S) clusters are important cofactors conserved in all domains of life, yet their synthesis and stability are compromised in stressful conditions such as iron deprivation or oxidative stress. Two conserved machineries, Isc and Suf, assemble and transfer Fe-S clusters to client proteins. The model bacterium Escherichia coli possesses both Isc and Suf, and in this bacterium utilization of these machineries is under the control of a complex regulatory network. To better understand the dynamics behind Fe-S cluster biogenesis in E. coli, we here built a logical model describing its regulatory network. This model comprises three biological processes: 1) Fe-S cluster biogenesis, containing Isc and Suf, the carriers NfuA and ErpA, and the transcription factor IscR, the main regulator of Fe-S clusters homeostasis; 2) iron homeostasis, containing the free intracellular iron regulated by the iron sensing regulator Fur and the non-coding regulatory RNA RyhB involved in iron sparing; 3) oxidative stress, representing intracellular H2O2 accumulation, which activates OxyR, the regulator of catalases and peroxidases that decompose H2O2 and limit the rate of the Fenton reaction. Analysis of this comprehensive model reveals a modular structure that displays five different types of system behaviors depending on environmental conditions, and provides a better understanding on how oxidative stress and iron homeostasis combine and control Fe-S cluster biogenesis. Using the model, we were able to predict that an iscR mutant would present growth defects in iron starvation due to partial inability to build Fe-S clusters, and we validated this prediction experimentally.
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Affiliation(s)
- Firas Hammami
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, CNRS, Aix-Marseille University, 13009 Marseille, France
- I2M, CNRS, Aix-Marseille University, 13009 Marseille, France
| | - Laurent Tichit
- I2M, CNRS, Aix-Marseille University, 13009 Marseille, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne (UMR7283), IMM, IM2B, CNRS, Aix-Marseille University, 13009 Marseille, France
| | - Frédéric Barras
- Institut Pasteur, Département de Microbiologie, Université Paris‐Cité, UMR CNRS 6047, SAMe Unit, F-75015 Paris, France
| | - Pierre Mandin
- Corresponding author. LCB, CNRS, Aix-Marseile University, 13009 Marseille, Tel: +33 4 91 16 46 39; E-mail:
| | - Elisabeth Remy
- Corresponding author. 12M, CNRS, Aix-Marseile University, 13009 Marseille, Tel: +33 4 91 26 95 65; E-mail:
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Zuo Q, Gong W, Yao Z, Xia Q, Zhang Y, Li B. Identification of key events and regulatory networks in the formation process of primordial germ cell based on proteomics. J Cell Physiol 2023; 238:610-630. [PMID: 36745473 DOI: 10.1002/jcp.30952] [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: 08/24/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 02/07/2023]
Abstract
Currently, studies have analyzed the formation mechanism of primordial germ cell (PGC) at the transcriptional level, but few at the protein level, which made the mechanism study of PGC formation not systematic. Here, we screened differential expression proteins (DEPs) regulated PGC formation by label-free proteomics with a novel sampling strategy of embryonic stem cells and PGC. Analysis of DEPs showed that multiple key events were involved, such as the transition from glycolysis to oxidative phosphorylation, activation of autophagy, low DNA methylation ensured the normal formation of PGC, beyond that, protein ubiquitination also played an important role in PGC formation. Importantly, the progression of such events was attributed to the inconsistency between transcription and translation. Interestingly, MAPK, PPAR, Wnt, and JAK signaling pathways not only interact with each other but also interact with different events to participate in the formation of PGC, which formed the PGC regulatory network. According to the regulatory network, the efficiency of PGC formation in induction system can be significantly improved. In conclusion, our results indicate that chicken PGC formation is a complex process involving multiple events and signals, which provide technical support for the specific application in PGC research.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Wei Gong
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Zeling Yao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Qian Xia
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P.R. China
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, P.R. China
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Nakazato Y, Shimoyama M, Cohen AA, Watanabe A, Kobayashi H, Shimoyama H, Shimoyama H. Intercorrelated variability in blood and hemodynamic biomarkers reveals physiological network in hemodialysis patients. Sci Rep 2023; 13:1660. [PMID: 36717578 DOI: 10.1038/s41598-023-28345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/17/2023] [Indexed: 01/31/2023] Open
Abstract
Increased intra-individual variability of a variety of biomarkers is generally associated with poor health and reflects physiological dysregulation. Correlations among these biomarker variabilities should then represent interactions among heterogeneous biomarker regulatory systems. Herein, in an attempt to elucidate the network structure of physiological systems, we probed the inter-variability correlations of 22 biomarkers. Time series data on 19 blood-based and 3 hemodynamic biomarkers were collected over a one-year period for 334 hemodialysis patients, and their variabilities were evaluated by coefficients of variation. The network diagram exhibited six clusters in the physiological systems, corresponding to the regulatory domains for metabolism, inflammation, circulation, liver, salt, and protein. These domains were captured as latent factors in exploratory and confirmatory factor analyses (CFA). The 6-factor CFA model indicates that dysregulation in each of the domains manifests itself as increased variability in a specific set of biomarkers. Comparison of a diabetic and non-diabetic group within the cohort by multi-group CFA revealed that the diabetic cohort showed reduced capacities in the metabolism and salt domains and higher variabilities of the biomarkers belonging to these domains. The variability-based network analysis visualizes the concept of homeostasis and could be a valuable tool for exploring both healthy and pathological conditions.
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Zhao Y, Jiang D, Xia Y. Corrigendum: Editorial: Epigenetic and transcriptional networks underlying ventricular and atrial arrhythmias. Front Cardiovasc Med 2023; 10:1140389. [PMID: 36742074 PMCID: PMC9895926 DOI: 10.3389/fcvm.2023.1140389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fcvm.2022.978891.].
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Affiliation(s)
- Yuanyuan Zhao
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation of Ministry of Education, National Health Commission and Chinese Academy of Medical Sciences, Wuhan, China,*Correspondence: Yuanyuan Zhao ✉
| | - Dingsheng Jiang
- Division of Cardiothoracic and Vascular Surgery Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, China,Dingsheng Jiang ✉
| | - Yong Xia
- Division of Cardiology, Department of Molecular and Cellular Biochemistry, Davis Heart & Lung Research Institute, The Ohio State University, Columbus, OH, United States,Yong Xia ✉
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46
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Cahill T, da Silveira WA, Renaud L, Wang H, Williamson T, Chung D, Chan S, Overton I, Hardiman G. Investigating the effects of chronic low-dose radiation exposure in the liver of a hypothermic zebrafish model. Sci Rep 2023; 13:918. [PMID: 36650199 PMCID: PMC9845366 DOI: 10.1038/s41598-022-26976-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/22/2022] [Indexed: 01/18/2023] Open
Abstract
Mankind's quest for a manned mission to Mars is placing increased emphasis on the development of innovative radio-protective countermeasures for long-term space travel. Hibernation confers radio-protective effects in hibernating animals, and this has led to the investigation of synthetic torpor to mitigate the deleterious effects of chronic low-dose-rate radiation exposure. Here we describe an induced torpor model we developed using the zebrafish. We explored the effects of radiation exposure on this model with a focus on the liver. Transcriptomic and behavioural analyses were performed. Radiation exposure resulted in transcriptomic perturbations in lipid metabolism and absorption, wound healing, immune response, and fibrogenic pathways. Induced torpor reduced metabolism and increased pro-survival, anti-apoptotic, and DNA repair pathways. Coupled with radiation exposure, induced torpor led to a stress response but also revealed maintenance of DNA repair mechanisms, pro-survival and anti-apoptotic signals. To further characterise our model of induced torpor, the zebrafish model was compared with hepatic transcriptomic data from hibernating grizzly bears (Ursus arctos horribilis) and active controls revealing conserved responses in gene expression associated with anti-apoptotic processes, DNA damage repair, cell survival, proliferation, and antioxidant response. Similarly, the radiation group was compared with space-flown mice revealing shared changes in lipid metabolism.
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Affiliation(s)
- Thomas Cahill
- School of Biological Sciences and Institute for Global Food Security, Queens University Belfast, Belfast, BT9 5DL, UK
| | - Willian Abraham da Silveira
- School of Health, Science and Wellbeing, Department of Biological Sciences, Science Centre, Staffordshire University, Leek Road, Stoke-On-Trent, ST4 2DF, UK
- International Space University, 1 Rue Jean-Dominique Cassini, 67400, Illkirch-Graffenstaden, France
| | - Ludivine Renaud
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Hao Wang
- School of Biological Sciences and Institute for Global Food Security, Queens University Belfast, Belfast, BT9 5DL, UK
| | - Tucker Williamson
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sherine Chan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
- JLABS at the Children's National Research and Innovation Campus, Washington, DC, 20012, USA
| | - Ian Overton
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, BT9 7AE, UK
| | - Gary Hardiman
- School of Biological Sciences and Institute for Global Food Security, Queens University Belfast, Belfast, BT9 5DL, UK.
- Department of Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA.
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47
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Wang N, Shu X, Zhang F, Wang Z. Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA. Front Plant Sci 2023; 13:975530. [PMID: 36704164 PMCID: PMC9872026 DOI: 10.3389/fpls.2022.975530] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.
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48
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Yang J, Yang M, Sheng G. Dysregulated lncRNAs are involved in the progress of myocardial infarction by constructing regulatory networks. Open Med (Wars) 2023; 18:20230657. [PMID: 36910851 PMCID: PMC9999115 DOI: 10.1515/med-2023-0657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 01/08/2023] [Accepted: 02/07/2023] [Indexed: 03/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes. However, the effect of all dysregulated lncRNAs in myocardial infarction (MI) is not clear. Whole transcriptome sequencing analysis was used to characterize the dynamic changes in lncRNA and mRNA expression. A gene network was constructed, and genes were classified into different modules using WGCNA. In addition, for all dysregulated lncRNAs, gene ontology analysis and cis-regulatory analysis were applied. The results demonstrated that a large number of the differentially co-expressed genes were primarily linked to the immune system process, inflammatory response, and innate immune response. The functional pathway analysis of the MEblue module included immune system process and apoptosis, and MEbrown included the T-cell receptor signal pathway by WGCNA. In addition, through cis-acting analysis of lncRNA regulation, the cis-regulated mRNAs were mainly enriched in immune system processes, innate immune responses, and VEGF signal pathways. We found that lncRNA regulation of mRNAs plays an important role in immune and inflammatory pathways. Our study provides a foundation to further understand the role and potential mechanism of dysregulated lncRNAs in the regulation of MI, in which many of them could be potential targets for MI.
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Affiliation(s)
- Jingqi Yang
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
| | - Ming Yang
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
| | - Guotai Sheng
- Department of Cardiovascular Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330000, China
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49
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Saha S, Moon HR, Han B, Mugler A. Deduction of signaling mechanisms from cellular responses to multiple cues. NPJ Syst Biol Appl 2022; 8:48. [PMID: 36450797 PMCID: PMC9712676 DOI: 10.1038/s41540-022-00262-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022] Open
Abstract
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models themselves are often complex, and it is not always clear how to extract falsifiable predictions. Here we take an inverse approach, using experimental data at the cell level to deduce the minimal signaling network. We focus on cells' response to multiple cues, specifically on the surprising case in which the response is antagonistic: the response to multiple cues is weaker than the response to the individual cues. We systematically build candidate signaling networks one node at a time, using the ubiquitous ingredients of (i) up- or down-regulation, (ii) molecular conversion, or (iii) reversible binding. In each case, our method reveals a minimal, interpretable signaling mechanism that explains the antagonistic response. Our work provides a systematic way to deduce molecular mechanisms from cell-level data.
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Affiliation(s)
- Soutick Saha
- grid.169077.e0000 0004 1937 2197Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907 USA
| | - Hye-ran Moon
- grid.169077.e0000 0004 1937 2197School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907 USA
| | - Bumsoo Han
- grid.169077.e0000 0004 1937 2197School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907 USA
| | - Andrew Mugler
- grid.169077.e0000 0004 1937 2197Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907 USA ,grid.21925.3d0000 0004 1936 9000Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260 USA
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50
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Zhang Y, Li Z, Liu J, Zhang Y, Ye L, Peng Y, Wang H, Diao H, Ma Y, Wang M, Xie Y, Tang T, Zhuang Y, Teng W, Tong Y, Zhang W, Lang Z, Xue Y, Zhang Y. Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat. Nat Commun 2022; 13:6940. [PMID: 36376315 PMCID: PMC9663577 DOI: 10.1038/s41467-022-34290-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
The success of common wheat as a global staple crop was largely attributed to its genomic diversity and redundancy due to the merge of different genomes, giving rise to the major question how subgenome-divergent and -convergent transcription is mediated and harmonized in a single cell. Here, we create a catalog of genome-wide transcription factor-binding sites (TFBSs) to assemble a common wheat regulatory network on an unprecedented scale. A significant proportion of subgenome-divergent TFBSs are derived from differential expansions of particular transposable elements (TEs) in diploid progenitors, which contribute to subgenome-divergent transcription. Whereas subgenome-convergent transcription is associated with balanced TF binding at loci derived from TE expansions before diploid divergence. These TFBSs have retained in parallel during evolution of each diploid, despite extensive unbalanced turnover of the flanking TEs. Thus, the differential evolutionary selection of paleo- and neo-TEs contribute to subgenome-convergent and -divergent regulation in common wheat, highlighting the influence of TE repertory plasticity on transcriptional plasticity in polyploid.
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Affiliation(s)
- Yuyun Zhang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Zijuan Li
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jinyi Liu
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu’e Zhang
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Luhuan Ye
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuan Peng
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Haoyu Wang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.256922.80000 0000 9139 560XHenan University, School of Life Science, Kaifeng, Henan 457000 China
| | - Huishan Diao
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yu Ma
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Meiyue Wang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yilin Xie
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Tengfei Tang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.256922.80000 0000 9139 560XHenan University, School of Life Science, Kaifeng, Henan 457000 China
| | - Yili Zhuang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China
| | - Wan Teng
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yiping Tong
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
| | - Wenli Zhang
- grid.27871.3b0000 0000 9750 7019State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095 China
| | - Zhaobo Lang
- grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.263817.90000 0004 1773 1790Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Yongbiao Xue
- grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, Beijing, 100049 China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China ,grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing, 100101 China ,grid.268415.cJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China
| | - Yijing Zhang
- grid.8547.e0000 0001 0125 2443State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438 China
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