1
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Picazo I, Espeso EA. Interconnections between the Cation/Alkaline pH-Responsive Slt and the Ambient pH Response of PacC/Pal Pathways in Aspergillus nidulans. Cells 2024; 13:651. [PMID: 38607089 PMCID: PMC11011638 DOI: 10.3390/cells13070651] [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: 02/13/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
In the filamentous ascomycete Aspergillus nidulans, at least three high hierarchy transcription factors are required for growth at extracellular alkaline pH: SltA, PacC and CrzA. Transcriptomic profiles depending on alkaline pH and SltA function showed that pacC expression might be under SltA regulation. Additional transcriptional studies of PacC and the only pH-regulated pal gene, palF, confirmed both the strong dependence on ambient pH and the function of SltA. The regulation of pacC expression is dependent on the activity of the zinc binuclear (C6) cluster transcription factor PacX. However, we found that the ablation of sltA in the pacX- mutant background specifically prevents the increase in pacC expression levels without affecting PacC protein levels, showing a novel specific function of the PacX factor. The loss of sltA function causes the anomalous proteolytic processing of PacC and a reduction in the post-translational modifications of PalF. At alkaline pH, in a null sltA background, PacC72kDa accumulates, detection of the intermediate PacC53kDa form is extremely low and the final processed form of 27 kDa shows altered electrophoretic mobility. Constitutive ubiquitination of PalF or the presence of alkalinity-mimicking mutations in pacC, such as pacCc14 and pacCc700, resembling PacC53kDa and PacC27kDa, respectively, allowed the normal processing of PacC but did not rescue the alkaline pH-sensitive phenotype caused by the null sltA allele. Overall, data show that Slt and PacC/Pal pathways are interconnected, but the transcription factor SltA is on a higher hierarchical level than PacC on regulating the tolerance to the ambient alkalinity in A. nidulans.
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Affiliation(s)
| | - Eduardo A. Espeso
- Department of Molecular and Cellular Biology, Centro de Investigaciones Biológicas (CIB) Margarita Salas, Spanish Research Council (CSIC), Ramiro de Maeztu, 9, 28040 Madrid, Spain;
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2
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Ahmed M, Tóth Z, Decsi K. The Impact of Salinity on Crop Yields and the Confrontational Behavior of Transcriptional Regulators, Nanoparticles, and Antioxidant Defensive Mechanisms under Stressful Conditions: A Review. Int J Mol Sci 2024; 25:2654. [PMID: 38473901 DOI: 10.3390/ijms25052654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
One of the most significant environmental challenges to crop growth and yield worldwide is soil salinization. Salinity lowers soil solution water potential, causes ionic disequilibrium and specific ion effects, and increases reactive oxygen species (ROS) buildup, causing several physiological and biochemical issues in plants. Plants have developed biological and molecular methods to combat salt stress. Salt-signaling mechanisms regulated by phytohormones may provide additional defense in salty conditions. That discovery helped identify the molecular pathways that underlie zinc-oxide nanoparticle (ZnO-NP)-based salt tolerance in certain plants. It emphasized the need to study processes like transcriptional regulation that govern plants' many physiological responses to such harsh conditions. ZnO-NPs have shown the capability to reduce salinity stress by working with transcription factors (TFs) like AP2/EREBP, WRKYs, NACs, and bZIPs that are released or triggered to stimulate plant cell osmotic pressure-regulating hormones and chemicals. In addition, ZnO-NPs have been shown to reduce the expression of stress markers such as malondialdehyde (MDA) and hydrogen peroxide (H2O2) while also affecting transcriptional factors. Those systems helped maintain protein integrity, selective permeability, photosynthesis, and other physiological processes in salt-stressed plants. This review examined how salt stress affects crop yield and suggested that ZnO-NPs could reduce plant salinity stress instead of osmolytes and plant hormones.
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Affiliation(s)
- Mostafa Ahmed
- Festetics Doctoral School, Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
- Department of Agricultural Biochemistry, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Zoltán Tóth
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
| | - Kincső Decsi
- Institute of Agronomy, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary
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3
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Zhang J, Wang Y, Guo J, Zhang N, He J, Zhou Z, Wu F. Direct Reprogramming of Mouse Fibroblasts to Osteoblast-like Cells Using Runx2/Dlx5 Factors on Engineered Stiff Hydrogels. ACS Appl Mater Interfaces 2023; 15:59209-59223. [PMID: 38102996 DOI: 10.1021/acsami.3c14777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Direct reprogramming of somatic cells into functional cells still faces major limitations in terms of efficiency and achieving functional maturity of the reprogramed cells. While different approaches have been developed commonly based on exploiting biochemical signals, introducing appropriate mechanical cues that stimulate the reprogramming process is rarely reported. In this study, collagen-coated polyacrylamide (PAM) hydrogels with stiffness close to that of collagenous bone (40 kPa) were adopted to augment the direct reprogramming process of mouse fibroblasts to osteoblastic-like cells. The results suggested that culturing cells on a hydrogel substrate enhanced the overexpression of osteogenic transcription factors using nonviral vectors and improved the yield of osteoblast-like cells. Particularly, a synergistic effect on achieving osteogenic functionality has been observed for the mechanical cues and overexpression of transcriptional factors, leading to enhanced osteogenic transformation and production of bone mineral matrix. Animal experiments suggested that reprogramed cells generated on matrix hydrogels accelerated bone regeneration and stimulated ectopic osteogenesis. Mechanism analysis suggested the critical involvement of actomyosin contraction and mechanical signal-mediated pathways like the RhoA-ROCK pathway, leading to a synergistic effect on the key transcriptional processes, including chromatin remodeling, nuclear translocation, and epigenetic transition. This study provides insights into the mechanical cue-enhanced direct reprogramming and cell therapy.
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Affiliation(s)
- Junwei Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Yao Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing Guo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Nihui Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Jing He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
| | - Zongke Zhou
- Orthopedic Research Institute & Department of Orthopedics, West China Hospital of Sichuan University, Chengdu 610041, Sichuan, China
| | - Fang Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, PR China
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4
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Li C, Zhou Y, Zou Y, Jiang T, Gong X, Yan Y. Identifying, Characterizing, and Engineering a Phenolic Acid-Responsive Transcriptional Factor from Bacillus amyloliquefaciens. ACS Synth Biol 2023; 12:2382-2392. [PMID: 37499217 PMCID: PMC10443031 DOI: 10.1021/acssynbio.3c00206] [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: 04/03/2023] [Indexed: 07/29/2023]
Abstract
Transcriptional factors-based biosensors are commonly used in metabolic engineering for inducible control of gene expression and related applications such as high-throughput screening and dynamic pathway regulations. Mining for novel transcriptional factors is essential for expanding the usability of these toolsets. Here, we report the identification, characterization, and engineering of a phenolic acid responsive regulator PadR from Bacillus amyloliquefaciens (BaPadR). This BaPadR-based biosensor system showed a unique ligand preference and exhibited a high output strength comparable to that of commonly used inducible expression systems. Through engineering the DNA binding region of BaPadR, we further enhanced the dynamic range of the biosensor system. The DNA sequences that are responsible for BaPadR recognition were located by promoter truncation and hybrid promoter building. To further explore the tunability of the sensor system, base substitutions were performed on the BaPadR binding region of the phenolic acid decarboxylase promoter (PpadC) and the hybrid promoter. This novel biosensor system can serve as a valuable tool in future synthetic biology applications.
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Affiliation(s)
- Chenyi Li
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yuyang Zhou
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yusong Zou
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Tian Jiang
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Xinyu Gong
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Yajun Yan
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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5
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Wrede D, Bordak M, Abraham Y, Mehedi M. Pulmonary Pathogen-Induced Epigenetic Modifications. Epigenomes 2023; 7:13. [PMID: 37489401 PMCID: PMC10366755 DOI: 10.3390/epigenomes7030013] [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: 05/23/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023] Open
Abstract
Epigenetics generally involves genetic control by factors other than our own DNA sequence. Recent research has focused on delineating the mechanisms of two major epigenetic phenomena: DNA methylation and histone modification. As epigenetics involves many cellular processes, it is no surprise that it can also influence disease-associated gene expression. A direct link between respiratory infections, host cell epigenetic regulations, and chronic lung diseases is still unknown. Recent studies have revealed bacterium- or virus-induced epigenetic changes in the host cells. In this review, we focused on respiratory pathogens (viruses, bacteria, and fungi) induced epigenetic modulations (DNA methylation and histone modification) that may contribute to lung disease pathophysiology by promoting host defense or allowing pathogen persistence.
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Affiliation(s)
- Dylan Wrede
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Mika Bordak
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Yeabtsega Abraham
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Masfique Mehedi
- School of Medicine & Health Sciences, University of North Dakota, Grand Forks, ND 58202, USA
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6
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Martini P, Mingardi J, Carini G, Mattevi S, Ndoj E, La Via L, Magri C, Gennarelli M, Russo I, Popoli M, Musazzi L, Barbon A. Transcriptional Profiling of Rat Prefrontal Cortex after Acute Inescapable Footshock Stress. Genes (Basel) 2023; 14:genes14030740. [PMID: 36981011 PMCID: PMC10048409 DOI: 10.3390/genes14030740] [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: 12/30/2022] [Revised: 01/31/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Stress is a primary risk factor for psychiatric disorders such as Major Depressive Disorder (MDD) and Post Traumatic Stress Disorder (PTSD). The response to stress involves the regulation of transcriptional programs, which is supposed to play a role in coping with stress. To evaluate transcriptional processes implemented after exposure to unavoidable traumatic stress, we applied microarray expression analysis to the PFC of rats exposed to acute footshock (FS) stress that were sacrificed immediately after the 40 min session or 2 h or 24 h after. While no substantial changes were observed at the single gene level immediately after the stress session, gene set enrichment analysis showed alterations in neuronal pathways associated with glia development, glia-neuron networking, and synaptic function. Furthermore, we found alterations in the expression of gene sets regulated by specific transcription factors that could represent master regulators of the acute stress response. Of note, these pathways and transcriptional programs are activated during the early stress response (immediately after FS) and are already turned off after 2 h-while at 24 h, the transcriptional profile is largely unaffected. Overall, our analysis provided a transcriptional landscape of the early changes triggered by acute unavoidable FS stress in the PFC of rats, suggesting that the transcriptional wave is fast and mild, but probably enough to activate a cellular response to acute stress.
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Affiliation(s)
- Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Jessica Mingardi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Giulia Carini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Stefania Mattevi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elona Ndoj
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca La Via
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Isabella Russo
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Maurizio Popoli
- Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy
| | - Laura Musazzi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Alessandro Barbon
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
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7
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Nocera R, Eletto D, Santoro V, Parisi V, Bellone ML, Izzo M, Tosco A, Dal Piaz F, Donadio G, De Tommasi N. Design of an Herbal Preparation Composed by a Combination of Ruscus aculeatus L. and Vitis vinifera L. Extracts, Magnolol and Diosmetin to Address Chronic Venous Diseases through an Anti-Inflammatory Effect and AP-1 Modulation. Plants (Basel) 2023; 12:1051. [PMID: 36903912 PMCID: PMC10004780 DOI: 10.3390/plants12051051] [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: 12/05/2022] [Revised: 02/10/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Chronic venous disease (CVD) is an often underestimated inflammatory pathological condition that can have a serious impact on quality of life. Many therapies have been proposed to deal with CVD, but unfortunately the symptoms recur with increasing frequency and intensity as soon as treatments are stopped. Previous studies have shown that the common inflammatory transcription factor AP-1 (activator protein-1) and nuclear factor kappa-activated B-cell light chain enhancer (NF-kB) play key roles in the initiation and progression of this vascular dysfunction. The aim of this research was to develop a herbal product that acts simultaneously on different aspects of CVD-related inflammation. Based on the evidence that several natural components of plant origin are used to treat venous insufficiency and that magnolol has been suggested as a putative modulator of AP-1, two herbal preparations based on Ruscus aculeatus root extracts, and Vitis vinifera seed extracts, as well as diosmetin and magnolol, were established. A preliminary MTT-based evaluation of the possible cytotoxic effects of these preparations led to the selection of one of them, named DMRV-2, for further investigation. First, the anti-inflammatory efficacy of DMRV-2 was demonstrated by monitoring its ability to reduce cytokine secretion from endothelial cells subjected to LPS-induced inflammation. Furthermore, using a real-time PCR-based protocol, the effect of DMRV-2 on AP-1 expression and activity was also evaluated; the results obtained demonstrated that the incubation of the endothelial cells with this preparation almost completely nullified the effects exerted by the treatment with LPS on AP-1. Similar results were also obtained for NF-kB, whose activation was evaluated by monitoring its distribution between the cytosol and the nucleus of endothelial cells after the different treatments.
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Affiliation(s)
- Raffaella Nocera
- Ph.D. Program in Drug Discovery & Development, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Daniela Eletto
- Department of Pharmacy, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Valentina Santoro
- Department of Pharmacy, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Valentina Parisi
- Ph.D. Program in Drug Discovery & Development, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Maria Laura Bellone
- Ph.D. Program in Drug Discovery & Development, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Marcello Izzo
- Department of Medicine and Surgery, Univesità degli Studi di Ferrara, 44121 Ferrara, Italy
| | - Alessandra Tosco
- Department of Pharmacy, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine, Surgery and Dentistry, Università degli Studi di Salerno, 84081 Baronissi, Italy
| | - Giuliana Donadio
- Department of Pharmacy, Università degli Studi di Salerno, 84084 Fisciano, Italy
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8
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Zeng N, Jian Z, Zhu W, Xu J, Fan Y, Xiao F. KLF13 overexpression protects sepsis-induced myocardial injury and LPS-induced inflammation and apoptosis. Int J Exp Pathol 2023; 104:23-32. [PMID: 36583453 PMCID: PMC9845607 DOI: 10.1111/iep.12459] [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: 02/14/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 12/31/2022] Open
Abstract
Sepsis remains a worldwide public health problem. This study aims to explore the role and mechanism of transcriptional factors (TFs) in sepsis-induced myocardial injury. Firstly, TF KLF13 was selected to explore its role in sepsis-induced myocardial injury. The caecal ligation and puncture (CLP) -induced sepsis mouse model was established and the septic mice were examined using standard histopathological methods. KLF13 expression was detected in the septic mouse heart and was also seen in a lipoploysaccharide (LPS) -induced cellular inflammation model. To explore this further both pro-apoptotic cleaved-caspase3/caspase3 and Bax levels and anti-apoptotic Bcl2 levels were examined, also in both models, In addition inflammatory cytokine (IL-1β, TNF-α, IL-8 and MCP-1) production and IκB-α protein level and p65 phosphorylation were examined in both septic mice and LPS-induced cells. Thus three parameters - cardiomyocyte apoptosis, inflammatory response and NF-κB pathway activation were evaluated under similar conditions. The septic mice showed significant oedema, disordered myofilament arrangement and degradation and necrosis to varying degrees in the myocardial cells. KLF13 was downregulated in both the septic mouse heart and the LPS-induced cellular inflammation model. Furthermore, both models showed abnormally increased cardiomyocyte apoptosis (increased cleaved-caspase3/caspase and Bax protein levels and decreased Bcl2 level), elevated inflammation (increased production of inflammatory cytokines) and the activated NF-κB pathway (increased p65 phosphorylation and decreased IκB-α protein level). KLF13 overexpression notably ameliorated sepsis-induced myocardial injury in vivo and in vitro. KLF13 overexpression protected against sepsis-induced myocardial injury and LPS-induced cellular inflammation and apoptosis via inhibiting the inflammatory pathways (especially NF-κB signalling) and cardiomyocyte apoptosis.
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Affiliation(s)
- Ni Zeng
- Department of AnesthesiologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Zaijin Jian
- Department of AnesthesiologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Wenxin Zhu
- Department of AnesthesiologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Junmei Xu
- Department of AnesthesiologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Yongmei Fan
- Department of Rehabilitationthe Second Xiangya Hospital, Central South UniversityChangshaChina
| | - Feng Xiao
- Department of AnesthesiologyThe Second Xiangya Hospital, Central South UniversityChangshaChina
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9
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Liao Z, Zhang L, Vázquez-Flota F. Editorial: Plant specialized metabolism for plant protection: Genomics and biotechnology. Front Plant Sci 2022; 13:1080939. [PMID: 36457519 PMCID: PMC9706228 DOI: 10.3389/fpls.2022.1080939] [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] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Zhihua Liao
- State Key Laboratory of Silkworm Genome Biology, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & Southwest University, SWU-TAAHC Medicinal Plant Joint R&D Centre, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Academy of Science and Technology, Chongqing, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, China
| | - Felipe Vázquez-Flota
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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10
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Li C, Zhang Y, Leng L, Pan X, Zhao D, Li X, Huang J, Bolund L, Lin G, Luo Y, Xu F. The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development. Front Cell Dev Biol 2022; 10:1020490. [PMID: 36438554 PMCID: PMC9691860 DOI: 10.3389/fcell.2022.1020490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/17/2022] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) and transcription factors (TFs) are involved in the precise regulation of gene expression during the preimplantation stage. Activation of TEs is a key event for mammalian embryonic genome activation and preimplantation early embryonic development. TFs are involved in the regulation of drastic changes in gene expression patterns, but an inventory of the interplay between TEs and TFs during normal/abnormal human embryonic development is still lacking. Here we used single-cell RNA sequencing data generated from biparental and uniparental embryos to perform an integrative analysis of TE and TF expression. Our results showed that endogenous retroviruses (ERVs) are mainly expressed during the minor embryonic genome activation (EGA) process of early embryos, while Alu is gradually expressed in the middle and later stages. Some important ERVs (e.g., LTR5_Hs, MLT2A1) and Alu TEs are expressed at significantly lower levels in androgenic embryos. Integrative analysis revealed that the expression of the transcription factors CTCF and POU5F1 is correlated with the differential expression of ERV TEs. Comparative coexpression network analysis further showed distinct expression levels of important TFs (e.g., LEUTX and ZSCAN5A) in dizygotic embryos vs. parthenogenetic and androgenic embryos. This systematic investigation of TE and TF expression in human early embryonic development by single-cell RNA sequencing provides valuable insights into mammalian embryonic development.
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Affiliation(s)
- Conghui Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Xiaoguang Pan
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xuemei Li
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jinrong Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bolund
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yonglun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Fengping Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI Cell, BGI-Shenzhen, Shenzhen, China
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11
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Sun T, Cao Y, Huang T, Sang Y, Dai Y, Tao Z. Comprehensive analysis of fifteen hub genes to identify a promising diagnostic model, regulated networks, and immune cell infiltration in acute kidney injury. J Clin Lab Anal 2022; 36:e24709. [PMID: 36125921 DOI: 10.1002/jcla.24709] [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: 08/07/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Acute kidney injury is a common clinical problem with no sensitive and specific diagnostic biomarkers and definitive treatments. The underlying molecular mechanisms of acute kidney injury are unclear. Therefore, it is pivotal to explore the underlying mechanisms and screen for novel diagnostic biomarkers, and therapeutic targets. METHODS The present study identified 15 hub genes by WGCNA analysis. LASSO-based logistic regression analysis was used to select key features and construct a diagnostic model of AKI. In addition, GO and KEGG analyses were performed and TF-mRNA and miRNA-mRNA network analysis and immune infiltration analysis of hub genes were performed to reveal the underlying mechanisms of AKI. RESULTS A diagnostic model was constructed by LASSO-based logistic regression analysis and was validated by RT-qPCR based on 15 hub genes. GO and KEGG analyses revealed DEGs were enriched in oxidation-reduction process, cell adhesion, proliferation, migration, and metabolic process. The enriched TFs were BRD2, EP300, ETS1, MYC, SPI1, and ZNF263. The enriched miRNAs were miR-181c-5p, miR-218-5p, miR-485-5p, miR-532-5p and miR-6884-5p. The immune infiltration analysis showed that Macrophages M2 was decreasing significantly revealing a protective factor for further AKI treatment. CONCLUSIONS The present study identified 15 hub genes based on WGCNA. Development and validation of a potentially diagnostic model based on 15 hub genes. In addition, exploring the interaction between transcriptional factors and 15 hub genes, and miRNA-mRNA relationship pairs. Furthermore, immune infiltration analysis was performed by analyzing gene expression profiles of AKI. Our study provides some basis for further experimental studies.
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Affiliation(s)
- Tao Sun
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Ying Cao
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Tiancha Huang
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Yiwen Sang
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Yibei Dai
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
| | - Zhihua Tao
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, China
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Bhat KA, Mahajan R, Pakhtoon MM, Urwat U, Bashir Z, Shah AA, Agrawal A, Bhat B, Sofi PA, Masi A, Zargar SM. Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops. Front Plant Sci 2022; 13:888710. [PMID: 35720588 PMCID: PMC9204169 DOI: 10.3389/fpls.2022.888710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 05/27/2023]
Abstract
The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.
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Affiliation(s)
- Kaisar Ahmad Bhat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Zaffar Bashir
- Deparment of Microbiology, University of Kashmir, Srinagar, India
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ankit Agrawal
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
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13
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Huang J, Cao H, Cui B, Ma X, Gao L, Yu C, Shen F, Yang X, Liu N, Qiu A, Cai G, Zhuang S. Mesenchymal Stem Cells-Derived Exosomes Ameliorate Ischemia/Reperfusion Induced Acute Kidney Injury in a Porcine Model. Front Cell Dev Biol 2022; 10:899869. [PMID: 35686052 PMCID: PMC9171021 DOI: 10.3389/fcell.2022.899869] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/26/2022] [Indexed: 12/14/2022] Open
Abstract
Exosomes are membrane-enclosed vesicles secreted by cells, containing a variety of biologically active ingredients including proteins, nucleic acids and lipids. In this study, we investigated the therapeutic effects of the exosomes and underlying mechanisms in a miniature pig model of ischemia/reperfusion-induced acute kidney injury (I/R-AKI). The exosomes were extracted from cultured human umbilical cord derived mesenchymal stem cells (hUC-MSCs) and infused into a miniature pig model of I/R AKI. Our results showed that 120 min of unilateral ischemia followed by reperfusion and contralateral nephrectomy resulted in renal dysfunction, severe kidney damage, apoptosis and necroptosis. Intravenous infusion of one dose of exosomes collected from about 4 × 108 hUC-MSCs significantly improved renal function and reduced apoptosis and necroptosis. Administration of hUC-MSC exosomes also reduced the expression of some pro-inflammatory cytokines/chemokines, decreased infiltration of macrophages to the injured kidneys and suppressed the phosphorylation of nuclear factor-κB and signal transducer and activator of transcription 3, two transcriptional factors related to inflammatory regulation. Moreover, hUC-MSC exosomes could promote proliferation of renal tubular cells, angiogenesis and upregulation of Klotho and Bone Morphogenetic Protein 7, two renoprotective molecules and vascular endothelial growth factor A and its receptor. Collectively, our results suggest that injection of hUC-MSC exosomes could ameliorate I/R-AKI and accelerate renal tubular cell repair and regeneration, and that hUC-MSC exosomes may be used as a potential biological therapy for Acute kidney injury patients.
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Affiliation(s)
- Jianni Huang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hao Cao
- Department of Cardiac Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Binbin Cui
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoyan Ma
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ling Gao
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chao Yu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fengchen Shen
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xinyu Yang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Na Liu
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Andong Qiu
- School of Life Science and Technology, Advanced Institute of Translational Medicine, Tongji University, Shanghai, China
| | - Guangyan Cai
- Department of Nephrology, Chinese PLA General Hospital, Beijing, China
| | - Shougang Zhuang
- Department of Nephrology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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14
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Li S, Han X, Lu Z, Qiu W, Yu M, Li H, He Z, Zhuo R. MAPK Cascades and Transcriptional Factors: Regulation of Heavy Metal Tolerance in Plants. Int J Mol Sci 2022; 23:ijms23084463. [PMID: 35457281 PMCID: PMC9032930 DOI: 10.3390/ijms23084463] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/20/2022] Open
Abstract
In nature, heavy metal (HM) stress is one of the most destructive abiotic stresses for plants. Heavy metals produce toxicity by targeting key molecules and important processes in plant cells. The mitogen-activated protein kinase (MAPK) cascade transfers the signals perceived by cell membrane surface receptors to cells through phosphorylation and dephosphorylation and targets various effector proteins or transcriptional factors so as to result in the stress response. Signal molecules such as plant hormones, reactive oxygen species (ROS), and nitric oxide (NO) can activate the MAPK cascade through differentially expressed genes, the activation of the antioxidant system and synergistic crosstalk between different signal molecules in order to regulate plant responses to HMs. Transcriptional factors, located downstream of MAPK, are key factors in regulating plant responses to heavy metals and improving plant heavy metal tolerance and accumulation. Thus, understanding how HMs activate the expression of the genes related to the MAPK cascade pathway and then phosphorylate those transcriptional factors may allow us to develop a regulation network to increase our knowledge of HMs tolerance and accumulation. This review highlighted MAPK pathway activation and responses under HMs and mainly focused on the specificity of MAPK activation mediated by ROS, NO and plant hormones. Here, we also described the signaling pathways and their interactions under heavy metal stresses. Moreover, the process of MAPK phosphorylation and the response of downstream transcriptional factors exhibited the importance of regulating targets. It was conducive to analyzing the molecular mechanisms underlying heavy metal accumulation and tolerance.
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Affiliation(s)
- Shaocui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Forestry Faculty, Nanjing Forestry University, Nanjing 210037, China
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaojiao Han
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhuchou Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Wenmin Qiu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Miao Yu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Haiying Li
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetic and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443002, China
- Correspondence: (Z.H.); (R.Z.); Tel.: +86-717-6397188 (Z.H.); +86-0571-63311860 (R.Z.)
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; (S.L.); (X.H.); (Z.L.); (W.Q.); (M.Y.)
- Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Correspondence: (Z.H.); (R.Z.); Tel.: +86-717-6397188 (Z.H.); +86-0571-63311860 (R.Z.)
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15
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Abstract
![]()
Next-generation DNA vectors for cancer
immunotherapies and vaccine
development require promoters eliciting predefined transcriptional
activities specific to target cell types, such as dendritic cells
(DCs), which underpin immune response. In this study, we describe
the de novo design of DC-specific synthetic promoters via in silico assembly of cis-transcription
factor response elements (TFREs) that harness the DC transcriptional
landscape. Using computational genome mining approaches, candidate
TFREs were identified within promoter sequences of highly expressed
DC-specific genes or those exhibiting an upregulated expression during
DC maturation. Individual TFREs were then screened in vitro in a target DC line and off-target cell lines derived from skeletal
muscle, fibroblast, epithelial, and endothelial cells using homotypic
(TFRE repeats in series) reporter constructs. Based on these data,
a library of heterotypic promoter assemblies varying in the TFRE composition,
copy number, and sequential arrangement was constructed and tested in vitro to identify DC-specific promoters. Analysis of
the transcriptional activity and specificity of these promoters unraveled
underlying design rules, primarily TFRE composition, which govern
the DC-specific synthetic promoter activity. Using these design rules,
a second library of exclusively DC-specific promoters exhibiting varied
transcriptional activities was generated. All DC-specific synthetic
promoter assemblies exhibited >5-fold activity in the target DC
line
relative to off-target cell lines, with transcriptional activities
ranging from 8 to 67% of the nonspecific human cytomegalovirus (hCMV-IE1)
promoter. We show that bioinformatic analysis of a mammalian cell
transcriptional landscape is an effective strategy for de
novo design of cell-type-specific synthetic promoters with
precisely controllable transcriptional activities.
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Affiliation(s)
- Abayomi O. Johnson
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
| | - Susan B. Fowler
- Antibody Discovery and Protein Engineering, R&D, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Carl I. Webster
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB21 6GH, U.K
| | - Adam J. Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
| | - David C. James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
- SynGenSys Limited, Freeths LLP, Norfolk Street, Sheffield S1 2JE, U.K
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16
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Mossine VV, Waters JK, Gu Z, Sun GY, Mawhinney TP. Bidirectional Responses of Eight Neuroinflammation-Related Transcriptional Factors to 64 Flavonoids in Astrocytes with Transposable Insulated Signaling Pathway Reporters. ACS Chem Neurosci 2022; 13:613-623. [PMID: 35147416 DOI: 10.1021/acschemneuro.1c00750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neuroinflammation is implicated in a variety of pathologies and is mechanistically linked to hyperactivation of glial cells in the central nervous system (CNS), predominantly in response to external stimuli. Multiple dietary factors were reported to alter neuroinflammation, but their actions on the relevant transcription factors in glia are not sufficiently understood. Here, an in vitro protocol employing cultured astroglial cells, which carry reporters of multiple signaling pathways associated with inflammation, was developed for screening environmental factors and synthetic drugs. Immortalized rat astrocyte line DI TNC1 was stably transfected with piggyBac transposon vectors containing a series of insulated reporters for the transcriptional activity of NF-κB, AP-1, signal transducer and activator of transcription 1 (STAT1), signal transducer and activator of transcription 3 (STAT3), aromatic hydrocarbon receptor (AhR), Nrf2, peroxisome proliferator-activated receptor γ (PPARγ), and HIF-1α, which is quantified via luciferase assay. Concatenated green fluorescent protein (GFP) expression was employed for simultaneous evaluation of cellular viability. Responses to a set of 64 natural and synthetic monomeric flavonoids representing six main structural classes (flavan-3-ols, flavanones, flavones, flavonols, isoflavones, and anthocyan(id)ins) were obtained at 10 and 50 μM concentrations. Except for HIF-1α, the activity of NF-κB and other transcription factors (TFs) in astrocytes was predominantly inhibited by flavan-3-ols and anthocyan(id)ins, while flavones and isoflavones generally activated these TFs. In addition, we obtained dose-response profiles for 11 flavonoids (apigenin, baicalein, catechin, cyanidin, epigallocatechin gallate, genistein, hesperetin, kaempferol, luteolin, naringenin, and quercetin) within the 1-100 μM range and in the presence of immune-stimulants and immune-suppressors. The flavonoid concentration profiles for TF-activation reveal biphasic response curves from the astrocytes. Apart from epigallocatechin gallate (EGCG), flavonoids failed to inhibit the NF-κB activation by proinflammatory agents [lipopolysaccharide (LPS), cytokines], but most of the tested polyphenols synergized with STAT3 inhibitors (stattic, ruxolitinib) against the activation of this TF in the astrocytes. We conclude that transposable insulated reporters of transcriptional activation represent a convenient neurochemistry tool in screening for activators/inhibitors of signaling pathways.
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Affiliation(s)
- Valeri V. Mossine
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - James K. Waters
- Agriculture Experiment Station Chemical Laboratories, University of Missouri, Columbia, Missouri 65211, United States
| | - Zezong Gu
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, Missouri 65211, United States
| | - Grace Y. Sun
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Thomas P. Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Child Health, University of Missouri, Columbia, Missouri 65211, United States
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Yao Y, Uddin MN, Manley K, Lawrence DA. Constitutive activation of Notch signalling and T cell activation characterize a mouse model of autism. Cell Biochem Funct 2022; 40:150-162. [PMID: 34978084 DOI: 10.1002/cbf.3684] [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: 09/12/2021] [Revised: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 11/08/2022]
Abstract
Gene and protein expression of BTBR T+ Itpr3tf /J (BTBR) mice with autistic-like behaviours were compared with the C57BL/6J strain, which is considered to have normal immunity and behaviour. Notch signalling pathway was constitutively activated in the immune system and liver of BTBR T+ Itpr3tf /J (BTBR) mice. Notch ligand 4 (Dll4), Notch receptors (Notch1 Notch2 and Notch3) and recombination signal binding protein for immunoglobulin κ j region (RBPJ) were increased both at gene and protein levels in BTBR spleens and thymi. Notch downstream transcriptional factors, Tbx21, Gata3, Rorc and FoxP3 were increased in BTBR spleens, Gata3 and FoxP3 were increased in BTBR thymi and BTBR mice have a high blood CD4/CD8 T cell ratio. Reduced nucleotide excision repair ability in BTBR spleens was associated with increased 8-oxoguanine, Ogg1 inhibition, an enhanced level of apoptotic thymocytes and higher expression of GATA-3. Ogg1 inhibition and enhanced GATA-3 expression also were detected in BTBR brain. Notch signal promoted mitochondrial dynamics switching to enhanced fission with an increased number and mass of mitochondria in immune cells of BTBR mice, but not in livers and brains. Constitutive influences on mitochondria exist in this mouse model of autism spectrum disorder; similar outcomes from environmental exposures might occur perinatally in susceptible individuals to affect the development of autism.
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Affiliation(s)
- Yunyi Yao
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | | | - Kevin Manley
- New York State Department of Health, Wadsworth Center, Albany, New York, USA
| | - David A Lawrence
- New York State Department of Health, Wadsworth Center, Albany, New York, USA.,Department of Environmental Health Sciences, School of Public Health, University at Albany, Rensselaer, New York, USA
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Ming J, Sana SRGL, Deng X. Identification of copper-related biomarkers and potential molecule mechanism in diabetic nephropathy. Front Endocrinol (Lausanne) 2022; 13:978601. [PMID: 36329882 PMCID: PMC9623046 DOI: 10.3389/fendo.2022.978601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) is a chronic microvascular complication in patients with diabetes mellitus, which is the leading cause of end-stage renal disease. However, the role of copper-related genes (CRGs) in DN development remains unclear. MATERIALS AND METHODS CRGs were acquired from the GeneCards and NCBI databases. Based on the GSE96804 and GSE111154 datasets from the GEO repository, we identified hub CRGs for DN progression by taking the intersection of differentially expressed CRGs (DECRGs) and genes in the key module from Weighted Gene Co-expression Network Analysis. The Maximal Clique Centrality algorithm was used to identify the key CRGs from hub CRGs. Transcriptional factors (TFs) and microRNAs (miRNAs) targeting hub CRGs were acquired from publicly available databases. The CIBERSORT algorithm was used to perform comparative immune cell infiltration analysis between normal and DN samples. RESULTS Eighty-two DECRGs were identified between normal and DN samples, as were 10 hub CRGs, namely PTGS2, DUSP1, JUN, FOS, S100A8, S100A12, NAIP, CLEC4E, CXCR1, and CXCR2. Thirty-nine TFs and 165 miRNAs potentially targeted these 10 hub CRGs. PTGS2 was identified as the key CRG and FOS as the most significant gene among all of DECRGs. RELA was identified as the hub TF interacting with PTGS2 by taking the intersection of potential TFs from the ChEA and JASPAR public databases. let-7b-5p was identified as the hub miRNA targeting PTGS2 by taking the intersection of miRNAs from the miRwalk, RNA22, RNAInter, TargetMiner, miRTarBase, and ENCORI databases. Similarly, CREB1, E2F1, and RELA were revealed as hub TFs for FOS, and miR-338-3p as the hub miRNA. Finally, compared with those in healthy samples, there are more infiltrating memory B cells, M1 macrophages, M2 macrophages, and resting mast cells and fewer infiltrating activated mast cells and neutrophils in DN samples (all p< 0.05). CONCLUSION The 10 identified hub copper-related genes provide insight into the mechanisms of DN development. It is beneficial to examine and understand the interaction between hub CRGs and potential regulatory molecules in DN. This knowledge may provide a novel theoretical foundation for the development of diagnostic biomarkers and copper-related therapy targets in DN.
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Affiliation(s)
- Jie Ming
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Si Ri Gu Leng Sana
- Department of Anaesthesiology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Si Ri Gu Leng Sana,
| | - Xijin Deng
- Department of Anaesthesiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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19
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Biagi CAO, Cury SS, Alves CP, Rabhi N, Silva WA, Farmer SR, Carvalho RF, Batista ML. Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Adipocyte Plasticity Underlying Thermogenic Response. Cells 2021; 10:cells10113073. [PMID: 34831295 PMCID: PMC8618495 DOI: 10.3390/cells10113073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
Adipose tissue has been classified based on its morphology and function as white, brown, or beige/brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, going beyond simply defined morphology but also by their cellular origin, adaptation to metabolic stress, and plasticity. Here, we performed an in-depth analysis of publicly available single-nuclei RNAseq from adipose tissue and utilized a workflow template to characterize adipocyte plasticity, heterogeneity, and secretome profiles. The reanalyzed dataset led to the identification of different subtypes of adipocytes including three subpopulations of thermogenic adipocytes, and provided a characterization of distinct transcriptional profiles along the adipocyte trajectory under thermogenic challenges. This study provides a useful resource for further investigations regarding mechanisms related to adipocyte plasticity and trans-differentiation.
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Affiliation(s)
- Carlos Alberto Oliveira Biagi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, Brazil; (C.A.O.B.J.); (W.A.S.J.)
- Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto 14051-140, Brazil
- Institute for Cancer Research, IPEC, Guarapuava 85100-000, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
| | - Cleidson Pádua Alves
- Department of Translational Genomics, Medical Faculty, University of Cologne, 50923 Cologne, Germany;
| | - Nabil Rabhi
- Department of Biochemistry, School of Medicine, Boston University, Boston, MA 02215, USA; (N.R.); (S.R.F.)
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14051-140, Brazil; (C.A.O.B.J.); (W.A.S.J.)
- Center for Cell-Based Therapy (CEPID/FAPESP), National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Ribeirão Preto 14051-140, Brazil
| | - Stephen R. Farmer
- Department of Biochemistry, School of Medicine, Boston University, Boston, MA 02215, USA; (N.R.); (S.R.F.)
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, Brazil;
- Correspondence: (R.F.C.); (M.L.B.J.)
| | - Miguel Luiz Batista
- Department of Biochemistry, School of Medicine, Boston University, Boston, MA 02215, USA; (N.R.); (S.R.F.)
- Department of Integrated Biotechnology, University of Mogi das Cruzes, São Paulo 08747-000, Brazil
- Correspondence: (R.F.C.); (M.L.B.J.)
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20
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Spirina L, Avgustinovich A, Afanas'ev S, Volkov M, Dobrodeev A, Cheremisina O, Kostromitsky D. PD-L1 Status in Gastric Cancers, Association with the Transcriptional, Growth Factors, AKT/mTOR Components Change, and Autophagy Initiation. Int J Mol Sci 2021; 22:11176. [PMID: 34681840 DOI: 10.3390/ijms222011176] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction: The programmed death receptor ligand 1 (PD-L1) immunohistochemistry (IHC) assay is a widely used selection method for pembrolizumab treatment in gastric cancer (GC) patients. PD-L1 is the main regulator of immunity in oncogenesis. Material and methods: The study included 38 patients with GC. The combined treatment consisted of neoadjuvant FOLFOX6, or FLOT, chemotherapy and surgery. PD-L1 + tumor status was recorded in 12 patients (CPS > 5), with a negative status recorded in 26 patients. RT-PCR determined the expression of molecular markers. The level of LC3B protein was detected by Western Blotting analysis. Results: An overexpression of PD-1, PD-L2 in the tumor is associated with AKT/mTOR mRNA profile change and autophagy initiation in IHC PD-L1 positive GCs. NACT influences these biological features, modifying the expression of AKT/mTOR components and autophagic flux. In PD-L1 positive cancers, the effect of NACT and molecular markers rearrangements are essential compared to the PD-L1 negative cancers. Conclusion: The IHC PD-L1 status in gastric cancers is the significant marker of cancer progression, recovering the multiple inner mechanisms of cancer spreading and leading to ineffective therapy. Autophagy induction and angiogenesis are found in PD-L1 positive gastric cancers.
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21
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Siemens N, Lütticken R. Streptococcus pyogenes ("Group A Streptococcus"), a Highly Adapted Human Pathogen-Potential Implications of Its Virulence Regulation for Epidemiology and Disease Management. Pathogens 2021; 10:776. [PMID: 34205500 DOI: 10.3390/pathogens10060776] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022] Open
Abstract
Streptococcus pyogenes (group A streptococci; GAS) is an exclusively human pathogen. It causes a variety of suppurative and non-suppurative diseases in people of all ages worldwide. Not all can be successfully treated with antibiotics. A licensed vaccine, in spite of its global importance, is not yet available. GAS express an arsenal of virulence factors responsible for pathological immune reactions. The transcription of all these virulence factors is under the control of three types of virulence-related regulators: (i) two-component systems (TCS), (ii) stand-alone regulators, and (iii) non-coding RNAs. This review summarizes major TCS and stand-alone transcriptional regulatory systems, which are directly associated with virulence control. It is suggested that this treasure of knowledge on the genetics of virulence regulation should be better harnessed for new therapies and prevention methods for GAS infections, thereby changing its global epidemiology for the better.
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22
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Kurylenko O, Ruchala J, Kruk B, Vasylyshyn R, Szczepaniak J, Dmytruk K, Sibirny A. The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha. FEMS Yeast Res 2021; 21:6275188. [PMID: 33983391 DOI: 10.1093/femsyr/foab029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 05/07/2021] [Indexed: 01/20/2023] Open
Abstract
Glucose is a preferred carbon source for most living organisms. The metabolism and regulation of glucose utilization are well studied mostly for Saccharomyces cerevisiae. Xylose is the main pentose sugar released from the lignocellulosic biomass, which has a high potential as a renewable feedstock for bioethanol production. The thermotolerant yeast Ogataea (Hansenula) polymorpha, in contrast to S. cerevisiae, is able to metabolize and ferment not only glucose but also xylose. However, in non-conventional yeasts, the regulation of glucose and xylose metabolism remains poorly understood. In this study, we characterize the role of transcriptional factors Mig1, Mig2, Tup1 and Hap4 in the natural xylose-fermenting yeast O. polymorpha. The deletion of MIG1 had no significant influence on ethanol production either from xylose or glucose, however the deletion of both MIG1 and MIG2 reduced the amount of ethanol produced from these sugars. The deletion of HAP4-A and TUP1 genes resulted in increased ethanol production from xylose. Inversely, the overexpression of HAP4-A and TUP1 genes reduced ethanol production during xylose alcoholic fermentation. Thus, HAP4-A and TUP1 are involved in repression of xylose metabolism and fermentation in yeast O. polymorpha and their deletion could be a viable strategy to improve ethanol production from this pentose.
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Affiliation(s)
- Olena Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Barbara Kruk
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Roksolana Vasylyshyn
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Szczepaniak
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
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23
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Morales-Lange B, Nombela I, Ortega-Villaizán MDM, Imarai M, Schmitt P, Mercado L. Induction of foxp3 during the Crosstalk between Antigen Presenting Like-Cells MHCII +CD83 + and Splenocytes CD4 +IgM - in Rainbow Trout. Biology (Basel) 2021; 10:biology10040324. [PMID: 33924548 PMCID: PMC8069158 DOI: 10.3390/biology10040324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary In aquatic biological models, the communication between cells from the immune system remains poorly characterized. In this work, to determine the gene expression of master transcriptional factors that coordinate the polarization of T cells, co-cultures of rainbow trout splenocytes are analyzed after stimulation with Interferon-gamma and/or Piscirickettsia salmonis. The results showed an upregulation of foxp3 compared to the other transcriptional factors, suggesting a potential communication between cells in the spleen, which may induce a Treg phenotype. Abstract In fish, the spleen is one of the major immune organs in the animal, and the splenocytes could play a key role in the activation and modulation of the immune response, both innate and adaptive. However, the crosstalk between different types of immune cells in the spleen has been poorly understood. In this work, an in vitro strategy is carried out to obtain and characterize mononuclear splenocytes from rainbow trout, using biomarkers associated with lymphocytes (CD4 and IgM) and antigen-presenting cells (CD83 and MHC II). Using these splenocytes, co-cultures of 24 and 48 h are used to determine the gene expression of master transcriptional factors that coordinate the polarization of T cells (t-bet, gata3, and foxp3). The results show a proportional upregulation of foxp3 (compared to t-bet and gata3) in co-cultures (at 24 h) of IFNγ-induced splenocytes with and without stimulation of Piscirickettsia salmonis proteins. In addition, foxp3 upregulation was established in co-cultures with IFNγ-induced cells and in cells only stimulated previously with P. salmonis proteins at 48 h of co-culture. These results show a potential communication between antigen-presenting-like cells and lymphocyte in the spleen, which could be induced towards a Treg phenotype.
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Affiliation(s)
- Byron Morales-Lange
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, 2340000 Valparaíso, Chile; (B.M.-L.); (P.S.)
| | - Ivan Nombela
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain; (I.N.); (M.D.M.O.-V.)
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000 Flanders, Belgium
| | - María Del Mar Ortega-Villaizán
- Instituto de Biología Molecular y Celular (IBMC) and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández (UMH), 03202 Elche, Spain; (I.N.); (M.D.M.O.-V.)
| | - Mónica Imarai
- Centro de Biotecnología Acuícola, Departamento de Biología, Universidad de Santiago de Chile, Estación Central, 9160000 Santiago, Chile;
| | - Paulina Schmitt
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, 2340000 Valparaíso, Chile; (B.M.-L.); (P.S.)
| | - Luis Mercado
- Grupo de Marcadores Inmunológicos en Organismos Acuáticos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, 2340000 Valparaíso, Chile; (B.M.-L.); (P.S.)
- Correspondence:
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24
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Martín JF, Liras P, Sánchez S. Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes. Front Microbiol 2021; 12:630694. [PMID: 33796086 PMCID: PMC8007912 DOI: 10.3389/fmicb.2021.630694] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. There are two types of phosphorylations involved in the control of transcriptional factors: (1) phosphorylation of sensor kinases and transfer of the phosphate group to the receiver domain of response regulators, which alters the expression of regulator target genes. (2) Phosphorylation systems involving promiscuous serine/threonine/tyrosine kinases that modify proteins at several amino acid residues, e.g., the phosphorylation of the global nitrogen regulator GlnR. Another post-translational modification is the acetylation at the epsilon amino group of lysine residues. The protein acetylation/deacetylation controls the activity of many short and long-chain acyl-CoA synthetases, transcriptional factors, key proteins of bacterial metabolism, and enzymes for the biosynthesis of non-ribosomal peptides, desferrioxamine, streptomycin, or phosphinic acid-derived antibiotics. Acetyltransferases catalyze acetylation reactions showing different specificity for the acyl-CoA donor. Although it functions as acetyltransferase, there are examples of malonylation, crotonylation, succinylation, or in a few cases acylation activities using bulky acyl-CoA derivatives. Substrates activation by nucleoside triphosphates is one of the central reactions inhibited by lysine acetyltransferases. Phosphorylation/dephosphorylation or acylation/deacylation reactions on global regulators like PhoP, GlnR, AfsR, and the carbon catabolite regulator glucokinase strongly affects the expression of genes controlled by these regulators. Finally, a different type of post-translational protein modification is the phosphopantetheinylation, catalized by phosphopantetheinyl transferases (PPTases). This reaction is essential to modify those enzymes requiring phosphopantetheine groups like non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. Up to five PPTases are present in S. tsukubaensis and S. avermitilis. Different PPTases modify substrate proteins in the PCP or ACP domains of tacrolimus biosynthetic enzymes. Directed mutations of genes encoding enzymes involved in the post-translational modification is a promising tool to enhance the production of bioactive metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico
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25
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Gong W, Song Q, Ji K, Gong S, Wang L, Chen L, Zhang J, Yuan D. Full-Length Transcriptome from Camellia oleifera Seed Provides Insight into the Transcript Variants Involved in Oil Biosynthesis. J Agric Food Chem 2020; 68:14670-14683. [PMID: 33249832 DOI: 10.1021/acs.jafc.0c05381] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Camellia oleifera Abel., belonging to the genus Camellia of Theaceae, has been widely used as a cooking oil, lubricant, and in cosmetics. Because of complicated polyploidization and large genomes, reference genome information is still lacking. Systematic characterization of gene models based on transcriptome data is a fast and economical approach for C. oleifera. Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq) and Illumina RNA-Seq combined with gas chromatography were performed for exploration of oil biosynthesis, accumulation, and comprehensive transcriptome analysis in C. oleifera seeds at five different developmental stages. We report the first full-length transcriptome data set of C. oleifera seeds comprising 40,143 deredundant high-quality isoforms. Among these isoforms, 37,982 were functionally annotated, and 271 (2.43%) belonged to fatty acid metabolism. A total of 8,344 full-length unique transcript models were obtained, and 8,151 (97.69%) of them produced more than two isoforms, suggesting a high degree of transcriptome complexity in C. oleifera seeds. A total of 783 alternative splicing (AS) events were identified, among which the retained intron was the most abundant. We also obtained 1,910 long noncoding RNAs (lncRNAs) and found that AS events occurred in these lncRNAs. Potential transcript variants of genes involved in oil biosynthesis were also investigated. After performing weighted correlation network analysis, we found seven "gene modules" and hub genes for each module showing a significant association with oil content. The series test of clusters classified these modules into four significant profiles based on gene expression patterns. Protein-protein interaction network analysis showed that upregulated WRI1 interacted with 17 genes encoding the enzymes playing key roles in oil synthesis. MYB and ZIP transcriptional factors also showed significant interactions with key genes involved in oil synthesis. Collectively, our data advance the knowledge of RNA isoform diversity in seeds at different developmental stages and provide a rich resource for functional studies on oil synthesis in C. oleifera.
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Affiliation(s)
- Wenfang Gong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Qiling Song
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ke Ji
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - ShouFu Gong
- Xinyang Agriculture and Forestry University, Xinyang, Henan 464000, China
| | - Lingkai Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Le Chen
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Jian Zhang
- Xinyang Agriculture and Forestry University, Xinyang, Henan 464000, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of Ministry of Education and the Key Laboratory of Non-Wood Forest Products of Forestry Ministry, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
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26
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Abstract
One common and reversible type of post-translational modification (PTM) is the addition of O-linked β-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), and its dynamic balance is controlled by O-GlcNAc transferase (OGT) and glycoside hydrolase O-GlcNAcase (OGA) through the addition or removal of O-GlcNAc groups. A large amount of research data confirms that proteins regulated by O-GlcNAcylation play a pivotal role in cells. In particularly, imbalanced levels of OGT and O-GlcNAcylation have been found in various types of cancers. Recently, increasing evidence shows that imbalanced O-GlcNAcylation directly or indirectly impacts the process of cancer metastasis. This review summarizes the current understanding of the influence of O-GlcNAc-proteins on the regulation of cancer metastasis. It will provide a theoretical basis to further elucidate of the molecular mechanisms underlying cancer emergence and progression.
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Affiliation(s)
- Donglu Wu
- School of Clinical Medical, Changchun University of Chinese Medicine, Changchun, China.,Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jingji Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhidong Qiu
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Da Liu
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Haoming Luo
- Key Laboratory of Effective Components of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China.,School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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27
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Shtratnikova VY, Schelkunov MI, Fokina VV, Bragin EY, Lobastova TG, Shutov AA, Kazantsev AV, Donova MV. Genome-Wide Transcriptome Profiling Provides Insight on Cholesterol and Lithocholate Degradation Mechanisms in Nocardioides simplex VKM Ac-2033D. Genes (Basel) 2020; 11:E1229. [PMID: 33092158 DOI: 10.3390/genes11101229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Steroid microbial degradation plays a significant ecological role for biomass decomposition and removal/detoxification of steroid pollutants. In this study, the initial steps of cholesterol degradation and lithocholate bioconversion by a strain with enhanced 3-ketosteroid dehydrogenase (3-KSD) activity, Nocardioides simplex VKM Ac-2033D, were studied. Biochemical, transcriptomic, and bioinformatic approaches were used. Among the intermediates of sterol sidechain oxidation cholest-5-en-26-oic acid and 3-oxo-cholesta-1,4-dien-26-oic acid were identified as those that have not been earlier reported for N. simplex and related species. The transcriptomic approach revealed candidate genes of cholesterol and lithocholic acid (LCA) catabolism by the strain. A separate set of genes combined in cluster and additional 3-ketosteroid Δ1-dehydrogenase and 3-ketosteroid 9α-hydroxylases that might be involved in LCA catabolism were predicted. Bioinformatic calculations based on transcriptomic data showed the existence of a previously unknown transcription factor, which regulates cholate catabolism gene orthologs. The results contribute to the knowledge on diversity of steroid catabolism regulation in actinobacteria and might be used at the engineering of microbial catalysts for ecological and industrial biotechnology.
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28
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Spirina LV, Chizhevskaya SY, Kondakova IV. Molecular Profiling of Follicular Variant of Papillary Thyroid Cancer. Bull Exp Biol Med 2020; 169:85-8. [PMID: 32495172 DOI: 10.1007/s10517-020-04830-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 10/24/2022]
Abstract
The molecular features of the follicular variant of papillary thyroid cancer are closely related to the clinical behavior of the tumor and the prognosis of the disease. BRAF-V600E mutations in patients with a follicular variant of papillary thyroid cancer have not been identified; however, the majority of patients had T3-4N0M0 stage of the disease. Changes in the expression of transcription and growth factors and AKT/m-TOR signaling pathway components were detected. In addition, hyperexpression of m-TOR and 4EBP1 kinases and CAIX enzyme was shown compared to the classical variant of papillary thyroid cancer, where an increase in the nuclear factor NF-κB p65 and c-RAF kinase expression was observed.
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29
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Liu H, Ni S, Wang H, Zhang Q, Weng W. Charactering tumor microenvironment reveals stromal-related transcription factors promote tumor carcinogenesis in gastric cancer. Cancer Med 2020; 9:5247-5257. [PMID: 32463580 PMCID: PMC7367614 DOI: 10.1002/cam4.3133] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Transcription factors represent the crucial role of controlling gene transcription in cancer development and progression. However, their functions in gastric cancer have not been thoroughly characterized. For this study, we comprehensively evaluated the correlation between infiltration patterns of tumor microenvironment (TME) cells and TFs expression in the cohort of stomach adenocarcinoma (STAD) from TCGA database. We integrally explored differential expression panel and prognostic value of candidate TFs in TCGA‐STAD cohort. Notably, we found a key transcription factor named HEYL, which its expression level was correlated with stromal component transformation of TME. HEYL was regularly high expressed in gastric cancer and correlated with patients’ poor prognosis. Knockdown of HEYL prominently abrogated the tendency of cell proliferation, migration, and progression in gastric cancer. Consistently, overexpression of HEYL strikingly accelerated the gastric carcinoma development through activating oncogenic signaling pathways and transcriptional activation of cadherin 11 (CDH11). Our findings not only identified the close relationship between TFs and TME phenotype, but also emphasized the crucial importance of TFs, especially HEYL, which could be identified as a candidate biomarker to evaluate prognostic risk and therapeutic effect in gastric cancer.
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Affiliation(s)
- Haining Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Shujuan Ni
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hanbo Wang
- Jining Medical University, Jining, China
| | - Qiongyan Zhang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Weiwei Weng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
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30
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Kalantari Khandani N, Ghahremanloo A, Hashemy SI. Role of tumor microenvironment in the regulation of PD-L1: A novel role in resistance to cancer immunotherapy. J Cell Physiol 2020; 235:6496-6506. [PMID: 32239707 DOI: 10.1002/jcp.29671] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/08/2020] [Indexed: 12/13/2022]
Abstract
Tumor evasion from the host immune system is a substantial strategy for tumor development and survival. The expression of many immune checkpoint proteins in cancer cells is a mechanism by which tumor cells escape from the immune system. Among the well-known immune checkpoints that can tremendously affect tumor development and cancer therapy are the programmed death-ligand-1/programmed death-1 (PD-L1/PD-1). To tackle this phenomenon and improve the therapeutic strategies in cancer treatment, the blockade of the PD-L1/PD-1 pathway is introduced as a target, but the therapeutic advantage of PD L1/PD-1 blockade has not fulfilled the expectations. This condition may be associated with a different type of resistance in a considerable number of patients. A crucial issue to conquer resistance against immune checkpoint blockade therapy is to understand how PD-L1 level is regulated. However, the mechanisms by which the PD-L1 expression is regulated are complicated, and they can occur at different levels from signaling pathways to posttranscriptional levels. For example, various transcriptional factors, such as hypoxia-inducible factor-1, nuclear factor-κΒ, interferon-γ, STAT3, MYC, and AP-1 can regulate the PD-L1 distribution at the transcriptional level. Herein, we tried to focus on the most important regulatory mechanisms of PD-L1 by inducible agents in the tumor cells, such as signaling pathways, transcriptional factors, and posttranscriptional factors. Finally, these approaches may open up new windows for targeting tumor immune evasion and suggest the novel suppressors of PD-L1 for efficient therapeutics.
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Affiliation(s)
| | - Atefeh Ghahremanloo
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Clinical Biochemistry, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Isaac Hashemy
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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31
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Maliehe M, Ntoi MA, Lahiri S, Folorunso OS, Ogundeji AO, Pohl CH, Sebolai OM. Environmental Factors That Contribute to the Maintenance of Cryptococcus neoformans Pathogenesis. Microorganisms 2020; 8:microorganisms8020180. [PMID: 32012843 PMCID: PMC7074686 DOI: 10.3390/microorganisms8020180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
The ability of microorganisms to colonise and display an intracellular lifestyle within a host body increases their fitness to survive and avoid extinction. This host–pathogen association drives microbial evolution, as such organisms are under selective pressure and can become more pathogenic. Some of these microorganisms can quickly spread through the environment via transmission. The non-transmittable fungal pathogens, such as Cryptococcus, probably return into the environment upon decomposition of the infected host. This review analyses whether re-entry of the pathogen into the environment causes restoration of its non-pathogenic state or whether environmental factors and parameters assist them in maintaining pathogenesis. Cryptococcus (C.) neoformans is therefore used as a model organism to evaluate the impact of environmental stress factors that aid the survival and pathogenesis of C. neoformans intracellularly and extracellularly.
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Martín JF, Liras P. The Balance Metabolism Safety Net: Integration of Stress Signals by Interacting Transcriptional Factors in Streptomyces and Related Actinobacteria. Front Microbiol 2020; 10:3120. [PMID: 32038560 PMCID: PMC6988585 DOI: 10.3389/fmicb.2019.03120] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022] Open
Abstract
Soil dwelling Streptomyces species are faced with large variations in carbon or nitrogen sources, phosphate, oxygen, iron, sulfur, and other nutrients. These drastic changes in key nutrients result in an unbalanced metabolism that have undesirable consequences for growth, cell differentiation, reproduction, and secondary metabolites biosynthesis. In the last decades evidence has accumulated indicating that mechanisms to correct metabolic unbalances in Streptomyces species take place at the transcriptional level, mediated by different transcriptional factors. For example, the master regulator PhoP and the large SARP-type regulator AfsR bind to overlapping sequences in the afsS promoter and, therefore, compete in the integration of signals of phosphate starvation and S-adenosylmethionine (SAM) concentrations. The cross-talk between phosphate control of metabolism, mediated by the PhoR-PhoP system, and the pleiotropic orphan nitrogen regulator GlnR, is very interesting; PhoP represses GlnR and other nitrogen metabolism genes. The mechanisms of control by GlnR of several promoters of ATP binding cassettes (ABC) sugar transporters and carbon metabolism are highly elaborated. Another important cross-talk that governs nitrogen metabolism involves the competition between GlnR and the transcriptional factor MtrA. GlnR and MtrA exert opposite effects on expression of nitrogen metabolism genes. MtrA, under nitrogen rich conditions, represses expression of nitrogen assimilation and regulatory genes, including GlnR, and competes with GlnR for the GlnR binding sites. Strikingly, these sites also bind to PhoP. Novel examples of interacting transcriptional factors, discovered recently, are discussed to provide a broad view of this interactions. Altogether, these findings indicate that cross-talks between the major transcriptional factors protect the cell metabolic balance. A detailed analysis of the transcriptional factors binding sequences suggests that the transcriptional factors interact with specific regions, either by overlapping the recognition sequence of other factors or by binding to adjacent sites in those regions. Additional interactions on the regulatory backbone are provided by sigma factors, highly phosphorylated nucleotides, cyclic dinucleotides, and small ligands that interact with cognate receptor proteins and with TetR-type transcriptional regulators. We propose to define the signal integration DNA regions (so called integrator sites) that assemble responses to different stress, nutritional or environmental signals. These integrator sites constitute nodes recognized by two, three, or more transcriptional factors to compensate the unbalances produced by metabolic stresses. This interplay mechanism acts as a safety net to prevent major damage to the metabolism under extreme nutritional and environmental conditions.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Paloma Liras
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
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He M, Qin CX, Wang X, Ding NZ. Plant Unsaturated Fatty Acids: Biosynthesis and Regulation. Front Plant Sci 2020; 11:390. [PMID: 32425958 PMCID: PMC7212373 DOI: 10.3389/fpls.2020.00390] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 05/11/2023]
Abstract
In most plants, major unsaturated fatty acids (UFAs) are three C18 species, namely, oleic (18:1), linoleic (18:2), and α-linolenic (18:3) acids. These simple compounds play multiple crucial roles in planta and are also important economic traits of oil crops. The enzymatic steps of C18 UFA biosynthesis have been well established. However, the associated FA/lipid trafficking between the plastid and the endoplasmic reticulum remains largely unclear, as does the regulation of the expression and activities of the involved enzymes. In this review, we will revisit the biosynthesis of C18 UFAs with an emphasis on the trafficking, and present an overview of the key enzymes and their regulation. Of particular interest is the emerging regulatory network composed of transcriptional factors and upstream signaling pathways. The review thereby provides the promise of using physical, biochemical and/or genetic means to manipulate FA composition and increase oil yield in crop improvement.
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Toptygina AP, Zakirov RS, Kapitanova KS, Semikina EL. Detection of Small Subsets of CD4 + Lymphocytes with SmartFlare Nanoprobes. Bull Exp Biol Med 2019; 168:270-274. [PMID: 31784846 DOI: 10.1007/s10517-019-04689-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/04/2019] [Indexed: 01/15/2023]
Abstract
SmartFlare technology allows detection of mRNA in single living cells. We studied the possibility of using SmartFlare nanoprobes for detection of small subsets of CD4+ lymphocytes. It was found that SmartFlare allows detection of transcriptional master regulators of major CD4+T helper subsets in living human lymphocytes. Nanoprobes labeled with Cy5 fluorophore were better detected by flow cytometry than nanoprobes labeled with Cy3. Appropriate time of lymphocyte incubation with SmartFlare probes was 24 h.
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Affiliation(s)
- A P Toptygina
- G. N. Gabrichevsky Moscow Research Institute for Epidemiology and Microbiology, Federal Service on Surveillance for Consumer Rights Protection and Human Well-Being, Moscow, Russia.
| | - R Sh Zakirov
- National Medical Research Center for Children's Health, Ministry of Health of the Russian Federation, Moscow, Russia
| | - K S Kapitanova
- G. N. Gabrichevsky Moscow Research Institute for Epidemiology and Microbiology, Federal Service on Surveillance for Consumer Rights Protection and Human Well-Being, Moscow, Russia
| | - E L Semikina
- National Medical Research Center for Children's Health, Ministry of Health of the Russian Federation, Moscow, Russia
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Ahmed MZ, Bhardwaj N, Sharma S, Pande V, Anvikar AR. Transcriptional Modulation of the Host Immunity Mediated by Cytokines and Transcriptional Factors in Plasmodium falciparum-Infected Patients of North-East India. Biomolecules 2019; 9:E600. [PMID: 31614626 DOI: 10.3390/biom9100600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/20/2019] [Accepted: 09/21/2019] [Indexed: 11/17/2022] Open
Abstract
Complications due to malaria are caused mostly by host immunological responses. Plasmodium falciparum subverts host immunity by various strategies, including modulation in the host immune responses by regulating cytokines. The transcriptional alterations of major cytokines and immunoregulators were analyzed in this study through gene expression profiling in clinically defined subgroups of P. falciparum patients. Malaria patients were included from Dhalai district hospital of Tripura with uncomplicated malaria (UC) and severe malaria (SM) and healthy controls from endemic and non-endemic areas of India. qPCR gene expression analysis was performed for all factors and they were grouped into three clusters based on their altered expressions. The first cluster was downregulated with an increased parasitic burden which included T-BET, GATA3, EOMES, TGF-β, STAT4, STAT6 and cytokines IFN-γ, IL-12, IL-4, IL-5, and IL-13. RANTES, IL-8, CCR8, and CXCR3 were decreased in the SM group. The second cluster was upregulated with severity and included TNF-α, IL-10, IL-1β and IL-7. PD-1 and BCL6 were increased in the SM group. The third cluster comprised of NF-κB and was not altered. The level of perforin was suppressed while GrB expression was elevated in SM. P. falciparum malaria burden is characterized by the modulation of host immunity via compromization of T cell-mediated responses and suppression of innate immune-regulators.
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Rodríguez-Enríquez S, Marín-Hernández Á, Gallardo-Pérez JC, Pacheco-Velázquez SC, Belmont-Díaz JA, Robledo-Cadena DX, Vargas-Navarro JL, Corona de la Peña NA, Saavedra E, Moreno-Sánchez R. Transcriptional Regulation of Energy Metabolism in Cancer Cells. Cells 2019; 8:cells8101225. [PMID: 31600993 PMCID: PMC6830338 DOI: 10.3390/cells8101225] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/19/2019] [Accepted: 10/01/2019] [Indexed: 01/17/2023] Open
Abstract
Cancer development, growth, and metastasis are highly regulated by several transcription regulators (TRs), namely transcription factors, oncogenes, tumor-suppressor genes, and protein kinases. Although TR roles in these events have been well characterized, their functions in regulating other important cancer cell processes, such as metabolism, have not been systematically examined. In this review, we describe, analyze, and strive to reconstruct the regulatory networks of several TRs acting in the energy metabolism pathways, glycolysis (and its main branching reactions), and oxidative phosphorylation of nonmetastatic and metastatic cancer cells. Moreover, we propose which possible gene targets might allow these TRs to facilitate the modulation of each energy metabolism pathway, depending on the tumor microenvironment.
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Affiliation(s)
| | | | | | | | | | | | | | - Norma Angélica Corona de la Peña
- Unidad de Investigación Médica en Trombosis, Hemostasia y Aterogénesis, Hospital General Regional Carlos McGregor-Sánchez, México CP 03100, Mexico.
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México 14080, Mexico.
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología, México 14080, Mexico.
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Sun X, Zhang L, Jiang J, Ng M, Cui Z, Mai J, Ahn SK, Liu J, Zhang J, Liu J, Li Y. Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis. Virulence 2019; 9:1468-1482. [PMID: 30165798 PMCID: PMC6177252 DOI: 10.1080/21505594.2018.1514237] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (M. tb) to survive and persist in the host for decades in an asymptomatic state is an important aspect of tuberculosis pathogenesis. Although adaptation to hypoxia is thought to play a prominent role underlying M. tb persistence, how the bacteria achieve this goal is largely unknown. Rv0081, a member of the DosR regulon, is induced at the early stage of hypoxia while Rv3334 is one of the enduring hypoxic response genes. In this study, we uncovered genetic interactions between these two transcription factors. RNA-seq analysis of ΔRv0081 and ΔRv3334 revealed that the gene expression profiles of these two mutants were highly similar. We also found that under hypoxia, Rv0081 positively regulated the expression of Rv3334 while Rv3334 repressed transcription of Rv0081. In addition, we demonstrated that Rv0081 formed dimer and bound to the promoter region of Rv3334. Taken together, these data suggest that Rv0081 and Rv3334 work in the same regulatory pathway and that Rv3334 functions immediately downstream of Rv0081. We also found that Rv3334 is a bona fide regulator of the enduring hypoxic response genes. Our study has uncovered a regulatory pathway that connects the early and the enduring hypoxic response, revealing a transcriptional cascade that coordinates the temporal response of M. tb to hypoxia.
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Affiliation(s)
- Xian Sun
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Lu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Jiang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Mark Ng
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Zhenling Cui
- c Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Medical School , Tongji University , Shanghai , China
| | - Juntao Mai
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Sang Kyun Ahn
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jingqian Liu
- b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Jinyu Zhang
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
| | - Jun Liu
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China.,b Department of Molecular Genetics , University of Toronto , Toronto , Canada
| | - Yao Li
- a State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science , Fudan University , Shanghai , China
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Deng YN, Bellanti JA, Zheng SG. Essential Kinases and Transcriptional Regulators and Their Roles in Autoimmunity. Biomolecules 2019; 9:E145. [PMID: 30974919 DOI: 10.3390/biom9040145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Kinases and transcriptional regulators are fundamental components of cell signaling that are expressed on many types of immune cells which are involved in secretion of cytokines, cell proliferation, differentiation, and apoptosis. Both play important roles in biological responses in health as well as in illnesses such as the autoimmune diseases which comprise at least 80 disorders. These diseases are caused by complex genetic and environmental interactions that lead to a breakage of immunologic tolerance and a disruption of the balance between self-reactive cells and regulatory cells. Kinases or transcriptional regulatory factors often have an abnormal expression in the autoimmune cells that participate in the pathogenesis of autoimmune disease. These abnormally expressed kinases or transcriptional regulators can over-activate the function of self-reactive cells to produce inflammatory cytokines or down-regulate the activity of regulatory cells, thus causing autoimmune diseases. In this review we introduce five kinds of kinase and transcriptional regulator related to autoimmune diseases, namely, members of the Janus kinase (JAK) family (JAK3 and/or tyrosine kinase 2 (TYK2)), fork head box protein 3 (Foxp3), the retinoic acid-related orphan receptor gamma t (RORγt), and T-box expressed in T cells (T-bet) factors. We also provide a mechanistic insight into how these kinases and transcriptional regulators affect the function of the immune cells related to autoimmune diseases, as well as a description of a current drug design targeting these kinases and transcriptional regulators. Understanding their exact role helps offer new therapies for control of the inflammatory responses that could lead to clinical improvement of the autoimmune diseases.
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Ren F, Gao WC, Ke ZP, Xu Y, Liu Y. Identification of six miRNAs serving as predictive biomarkers in coronary artery disease. J Cell Biochem 2019; 120:1932-1942. [PMID: 30362594 DOI: 10.1002/jcb.27476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/25/2018] [Indexed: 01/24/2023]
Abstract
Coronary artery disease (CAD) is quite a common disease with high risk. It was reported that microRNAs (miRNAs) had significant effect on the occurrence of CAD. The previously published results are inconsistent due to the parameters, such as sequencing platform, samples selection, and the filter conditions. Here we aimed to explore the critical miRNAs in the occurrence of CAD, which may function as the potential biomarkers. A total of 12 representative datasets of miRNAs related to the occurrence of miRNAs were finally selected, and the critical miRNAs were determined by the comparison of the overlap relations. TargetScan software was used to predict the target genes of these critical miRNAs. Besides, DAVID and Tfacts dataset were used to analyze the functional enrichment and the transcriptional factors analysis. At last, a total of six signature miRNAs were identified, among which five were significantly upregulated and one was downregulated. The target gene of upregulated miRNAs was mostly enriched in the process of RNA Polymerase II promoter and the transcription of DNA template, whereas the target genes of downregulated miRNAs were mostly enriched in the regulation of transcription, DNA-templated. Besides, the result of the transcriptional factor analysis showed that there were 43 factors coexisting in two kinds of target genes. In summary, six critical miRNAs, as well as the corresponding target genes and transcriptional factors, were identified in the occurrence of CAD by bioinformatics analysis. These identified miRNAs may function as potential biomarkers in the clinical management of CAD.
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Affiliation(s)
- Fei Ren
- Department of Cardiology, The First People's Hospital of Jingmen, Jingmen, China
| | - Wen-Chuang Gao
- Department of Thoracic Surgery, Lian Shui People's Hospital, Huai'an, China
| | - Zun-Ping Ke
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Shanghai, China
| | - Yong Xu
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huaian Shi, China
| | - Yu Liu
- Department of Cardiology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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Abstract
Context The inhibition of adipocyte differentiation has a significant role on the prevention of obesity and obesity-associated complications. Objective In this study, we aimed to detect whether hyperoside is able to inhibit the conversion of pre-adiposits into mature adiposits. Design and Methods 3T3-L1 pre-adipocytes were stimulated so as to differentiate into mature adipocytes. Hyperoside in non-cytotoxic concentrations (1, 2, 5, and 10 µM) were separately applied to differentiated 3T3-L1 cells. Oil red O staining was performed and triacylglycerol contents were measured. Furthermore, gene and protein expressions of transcription factors, adipogenic genes and adipokines were examined in order to investigate the effect of hyperoside on adipocyte differentiation. Results Hyperoside in high concentrations significantly suppressed the adipogenic process by inhibiting the expression of transcription factors and adipogenic genes and reducing lipid accumulation in adipocytes (p<0.05). Low doses of hyperoside are able to inhibit adipogenesis, but higher doses are needed to reduce fat accumulation in mature adipocytes. In the case of maturing preadipocytes, 5 μM of hyperoside exerts its antiadipogenic effect at the early stages of adipogenesis, whereas 10 μM of hyperoside acts at the later stages (p<0.05). Conclusion These results suggest that hyperoside has a beneficial effect on the prevention and treatment of obesity.
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Affiliation(s)
- M Berkoz
- Yuzuncu Yil University, Faculty of Pharmacy - Department of Biochemistry, Van, Turkey
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Zhou C, Li X, Zhou Z, Li C, Zhang Y. Comparative Transcriptome Analysis Identifies Genes Involved in Diosgenin Biosynthesis in Trigonella foenum-graecum L. Molecules 2019; 24:molecules24010140. [PMID: 30609669 PMCID: PMC6337231 DOI: 10.3390/molecules24010140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023] Open
Abstract
Trigonella foenum-graecum L. (fenugreek) is a valuable resource of producing diosgenin which serves as a substrate for synthesizing more than two hundred kinds of steroidal drugs. Phytochemical analysis indicated that methyl jasmonate (MeJA) efficiently induced diosgenin biosynthesis in fenugreek seedlings. Though early steps up to cholesterol have recently been elucidated in plants, cytochrome P450 (CYP)- and glycosyltransferase (GT)-encoding genes involved in the late steps from cholesterol to diosgenin remain unknown. This study established comparative fenugreek transcriptome datasets from the MeJA-treated seedlings and the corresponding control lines. Differential gene expression analysis identified a number of MeJA-induced CYP and GT candidate genes. Further gene expression pattern analysis across a different MeJA-treating time points, together with a phylogenetic analysis, suggested specific family members of CYPs and GTs that may participate in the late steps during diosgenin biosynthesis. MeJA-induced transcription factors (TFs) that may play regulatory roles in diosgenin biosynthesis were also discussed. This study provided a valuable genetic resource to functionally characterize the genes involved in diosgenin biosynthesis, which will push forward the production of diosgenin in microbial organisms using a promising synthetic biology strategy.
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Affiliation(s)
- Chen Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zilin Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Changfu Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yansheng Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
- Shanghai Key Laboratory of Bio-Energy Crops, Research Center for Natural Products, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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Dai H, Zhou J, Zhu B. Gene co-expression network analysis identifies the hub genes associated with immune functions for nocturnal hemodialysis in patients with end-stage renal disease. Medicine (Baltimore) 2018; 97:e12018. [PMID: 30212930 PMCID: PMC6156040 DOI: 10.1097/md.0000000000012018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/28/2018] [Indexed: 01/14/2023] Open
Abstract
End-stage renal disease (ESRD) is the final stage of chronic kidney disease in which the kidney is not sufficient to meet the needs of daily life. It is necessary to understand the role of genes expression involved in ESRD patient responses to nocturnal hemodialysis (NHD) and to improve the immunity responsiveness. The aim of this study was to investigate novel immune-associated genes that may play important roles in patients with ESRD.The microarray expression profiles of peripheral blood in patients with ESRD before and after NHD were analyzed by network-based approaches, and then using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis to explore the biological process and molecular functions of differentially expressed genes. Subsequently, a transcriptional regulatory network of the core genes and the connected transcriptional regulators was constructed. We found that NHD had a significant effect on neutrophil activation and immune response in patients with ESRD.In addition, Our findings suggest that MAPKAPK3, RHOA, ARRB2, FLOT1, MYH9, PRKCD, RHOG, PTPN6, MAPK3, CNPY3, PI3KCG, and PYGL genes maybe potential targets regulated by core transcriptional factors, including ARNT, C/EBPalpha, CEBPA, CREB1, PSG1, DAND5, SP1, GATA1, MYC, EGR2, and EGR3.
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Shi Y, Ding Y, Yang S. Molecular Regulation of CBF Signaling in Cold Acclimation. Trends Plant Sci 2018; 23:623-637. [PMID: 29735429 DOI: 10.1016/j.tplants.2018.04.002] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/28/2018] [Accepted: 04/05/2018] [Indexed: 05/19/2023]
Abstract
Cold stress restricts plant growth, development, and distribution. Understanding how plants transduce and respond to cold signals has long been a topic of interest. Traditional genetic and molecular analyses have identified C-repeat/DREB binding factors (CBFs) as key transcription factors that function in cold acclimation. Recent studies revealed the involvement of pivotal protein kinases and transcription factors in CBF-dependent signaling, expanding our knowledge of cold signal transduction from perception to downstream gene expression events. In this review, we summarize recent advances in our understanding of the molecular regulation of these core components of the CBF cold signaling pathway. Knowledge of the mechanism underlying the ability of plants to survive freezing temperatures will facilitate the development of crop plants with increased freezing tolerance.
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Affiliation(s)
- Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Abstract
Cold stress restricts plant growth, development, and distribution. Understanding how plants transduce and respond to cold signals has long been a topic of interest. Traditional genetic and molecular analyses have identified C-repeat/DREB binding factors (CBFs) as key transcription factors that function in cold acclimation. Recent studies revealed the involvement of pivotal protein kinases and transcription factors in CBF-dependent signaling, expanding our knowledge of cold signal transduction from perception to downstream gene expression events. In this review, we summarize recent advances in our understanding of the molecular regulation of these core components of the CBF cold signaling pathway. Knowledge of the mechanism underlying the ability of plants to survive freezing temperatures will facilitate the development of crop plants with increased freezing tolerance.
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Affiliation(s)
- Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China; These authors contributed equally
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Raposo-Ferreira TMM, Brisson BK, Durham AC, Laufer-Amorim R, Kristiansen V, Puré E, Volk SW, Sorenmo K. Characteristics of the Epithelial-Mesenchymal Transition in Primary and Paired Metastatic Canine Mammary Carcinomas. Vet Pathol 2018; 55:622-633. [PMID: 29788797 DOI: 10.1177/0300985818776054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is a dynamic process linked to metastasis in many tumor types, including mammary tumors. In this study, we evaluated E-cadherin and vimentin immunolocalization in primary canine mammary carcinomas (20 cases) and their respective metastases, as well as their relationship with the core regulators SNAIL/SLUG. To assess the number of cells undergoing the process of EMT, we quantitated double-positive (E-cadherin+/vimentin+) cells using immunofluorescence, via cell counting and image analysis. In addition, SNAIL/SLUG expression was evaluated by established immunohistochemical methods. Primary tumors had significantly more E-cadherin+/vimentin+ co-expression than their paired respective lymph node or distant metastasis, respectively. Furthermore, the percentage of E-cadherin+/vimentin+ cells in grade II and III carcinomas was significantly higher than in grade I tumors. Primary tumors had significantly higher SNAIL/SLUG expression when analyzed based on the percentage of positive cells compared with their respective distant metastases in pairwise comparisons. An inverse correlation was noted between SNAIL/SLUG immunoreactivity and percentage of E-cadherin+/vimentin+ immunopositive cells in primary tumor samples when SNAIL/SLUG immunoreactivity was grouped into 2 categories (high versus low) based on percentage-positive staining. These results show a positive correlation between E-cadherin+/vimentin+ cells and higher tumor grade, establish differences between primary tumor and their respective metastases, and provide further support that EMT plays a critical role in the metastasis of canine mammary carcinoma. Furthermore, these data suggest that modulation of this process could provide greater therapeutic control and provide support for further research to determine if E-cadherin+/vimentin+ co-immunoreactivity imparts predictive value in the clinical outcome of patients with canine mammary carcinomas.
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Affiliation(s)
- Talita M M Raposo-Ferreira
- 1 Department of Veterinary Clinic and Surgery, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Becky K Brisson
- 2 Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy C Durham
- 3 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,4 Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Renee Laufer-Amorim
- 5 Department of Veterinary Clinic, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, Brazil
| | - Veronica Kristiansen
- 6 Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Ellen Puré
- 4 Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.,7 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan W Volk
- 2 Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.,4 Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.,7 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karin Sorenmo
- 4 Penn Vet Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.,7 Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Cheon KS, Nakatsuka A, Tasaki K, Kobayashi N. Long-lasting Corolla Cultivars in Japanese Azaleas: A Mutant AP3/DEF Homolog Identified in Traditional Azalea Cultivars from More Than 300 Years Ago. Front Plant Sci 2018; 8:2239. [PMID: 29375608 PMCID: PMC5767231 DOI: 10.3389/fpls.2017.02239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
Floral shape in higher plants typically requires genetic regulation through MADS transcription factors. In Japan, hundreds of azalea cultivars including flower shape mutations have been selected from the diversity of endogenous species and natural hybrids since the early 17th century, the Edo era (1603-1867). The long-lasting trait, known as "Misome-shō" in Japanese, has been identified in several species and cultivar groups of evergreen azaleas (Rhododendron L.) from three hundred years ago in Japan. However, the natural mutation conferring the long-lasting trait in azalea remains unknown. Here, we showed MADS-box gene mutations in long-lasting flowers, R. kaempferi 'Nikkō-misome,' R. macrosepalum 'Kochō-zoroi,' R. indicum 'Chōjyu-hō,' and R. × hannoense 'Amagi-beni-chōjyu.' All of the long-lasting flowers exhibited small-sized corollas with stomata during long blooming. In the long-lasting flowers, transcript of the APETALA3 (AP3)/DEFICIENS (DEF) homolog was reduced, and an LTR-retrotransposon was independently inserted into exons 1, 2, and 7 or an unknown sequence in exon 1 in gDNA of each cultivar. This insertion apparently abolished the normal mRNA sequence of the AP3/DEF homolog in long-lasting flowers. Also, long-lasting flowers were shown from F2 hybrids that had homozygous ap3/def alleles. Therefore, we concluded that the loss of function of the AP3/DEF homolog through a transposable element insertion may confer a stable long-lasting mutation in evergreen azaleas.
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Affiliation(s)
- Kyeong-Seong Cheon
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Akira Nakatsuka
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
| | - Keisuke Tasaki
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Nobuo Kobayashi
- Faculty of Life and Environmental Science, Shimane University, Matsue, Japan
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Melo BP, Fraga OT, Silva JCF, Ferreira DO, Brustolini OJB, Carpinetti PA, Machado JPB, Reis PAB, Fontes EPB. Revisiting the Soybean GmNAC Superfamily. Front Plant Sci 2018; 9:1864. [PMID: 30619426 PMCID: PMC6305603 DOI: 10.3389/fpls.2018.01864] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/04/2018] [Indexed: 05/07/2023]
Abstract
The NAC (NAM, ATAF, and CUC) genes encode transcription factors involved with the control of plant morph-physiology and stress responses. The release of the last soybean (Glycine max) genome assembly (Wm82.a2.v1) raised the possibility that new NAC genes would be present in the soybean genome. Here, we interrogated the last version of the soybean genome against a conserved NAC domain structure. Our analysis identified 32 putative novel NAC genes, updating the superfamily to 180 gene members. We also organized the genes in 15 phylogenetic subfamilies, which showed a perfect correlation among sequence conservation, expression profile, and function of orthologous Arabidopsis thaliana genes and NAC soybean genes. To validate our in silico analyses, we monitored the stress-mediated gene expression profiles of eight new NAC-genes by qRT-PCR and monitored the GmNAC senescence-associated genes by RNA-seq. Among ER stress, osmotic stress and salicylic acid treatment, all the novel tested GmNAC genes responded to at least one type of stress, displaying a complex expression profile under different kinetics and extension of the response. Furthermore, we showed that 40% of the GmNACs were differentially regulated by natural leaf senescence, including eight (8) newly identified GmNACs. The developmental and stress-responsive expression profiles of the novel NAC genes fitted perfectly with their phylogenetic subfamily. Finally, we examined two uncharacterized senescence-associated proteins, GmNAC065 and GmNAC085, and a novel, previously unidentified, NAC protein, GmNAC177, and showed that they are nuclear localized, and except for GmNAC065, they display transactivation activity in yeast. Consistent with a role in leaf senescence, transient expression of GmNAC065 and GmNAC085 induces the appearance of hallmarks of leaf senescence, including chlorophyll loss, leaf yellowing, lipid peroxidation and accumulation of H2O2. GmNAC177 was clustered to an uncharacterized subfamily but in close proximity to the TIP subfamily. Accordingly, it was rapidly induced by ER stress and by salicylic acid under late kinetic response and promoted cell death in planta. Collectively, our data further substantiated the notion that the GmNAC genes display functional and expression profiles consistent with their phylogenetic relatedness and established a complete framework of the soybean NAC superfamily as a foundation for future analyses.
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Affiliation(s)
- Bruno P. Melo
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otto T. Fraga
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José Cleydson F. Silva
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Dalton O. Ferreira
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otávio J. B. Brustolini
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Paola A. Carpinetti
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Pedro A. B. Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P. B. Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
- *Correspondence: Elizabeth P. B. Fontes
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Min L, Zhang C, Qu L, Huang J, Jiang L, Liu J, Pinello L, Yuan GC, Shou C. Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. Oncotarget 2017; 8:21938-53. [PMID: 28423538 DOI: 10.18632/oncotarget.15749] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/10/2017] [Indexed: 12/31/2022] Open
Abstract
Background Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype. Genome-scale molecular characteristics and regulatory mechanisms that distinguish TNBC from other subtypes remain incompletely characterized. Results By combining gene expression analysis and PANDA network, we defined three different TF regulatory patterns. A core TNBC-Specific TF Activation Driven Pattern (TNBCac) was specifically identified in TNBC by computational analysis. The essentialness of core TFs (ZEB1, MZF1, SOX10) in TNBC was highlighted and validated by cell proliferation analysis. Furthermore, 13 out of 35 co-targeted genes were also validated to be targeted by ZEB1, MZF1 and SOX10 in TNBC cell lines by real-time quantitative PCR. In three breast cancer cohorts, non-TNBC patients could be stratified into two subgroups by the 35 co-targeted genes along with 5 TFs, and the subgroup that more resembled TNBC had a worse prognosis. Methods We constructed gene regulatory networks in breast cancer by Passing Attributes between Networks for Data Assimilation (PANDA). Co-regulatory modules were specifically identified in TNBC by computational analysis, while the essentialness of core translational factors (TF) in TNBC was highlighted and validated by in vitro experiments. Prognostic effects of different factors were measured by Log-rank test and displayed by Kaplan-Meier plots. Conclusions We identified a core co-regulatory module specifically existing in TNBC, which enabled subtype re-classification and provided a biologically feasible view of breast cancer.
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Krzanowski J, Madzio J, Pastorczak A, Tracz A, Braun M, Tabarkiewicz J, Pluta A, Młynarski W, Zawlik I. Selected miRNA levels are associated with IKZF1 microdeletions in pediatric acute lymphoblastic leukemia. Oncol Lett 2017; 14:3853-3861. [PMID: 28927157 DOI: 10.3892/ol.2017.6599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 12/14/2016] [Accepted: 04/28/2017] [Indexed: 01/19/2023] Open
Abstract
The clinical outcome of children with high-risk relapsed B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is poor. The present study assessed the utility and prognostic value of selected microRNA (miRNA/miR) in BCP-ALL. The changes in the expression levels of these miRNAs regarding known gene lesions affecting lymphoid development [early B-cell factor 1 (EBF1), ETS variant 6 (ETV6), IKAROS family zinc finger 1 (IKZF1), paired box 5 (PAX5), cyclin dependent kinase inhibitor (CDKN) 2A/CDKN2B, retinoblastoma 1 (RB1), pseudoautosomal region 1 (PAR1), B-cell translocation gene 1 protein (BTG1)] were analyzed. The following miRNAs were analyzed: miR-24, miR-31, miR-128, miR-542, and miR-708. The present study focused on patients with deletions of the IKAROS transcriptional factor gene IKZF1, which is currently considered to be an independent negative prognostic factor for ALL outcome. It was demonstrated that the expression level of miR-128 was significantly lower in patients with IKZF1 deletion compared with patients without IKZF1 deletion. Additionally, low expression of miR-542 was associated with CDKN2A/B and miR-31deletions, and low expression of miR-24 was associated with miR-31 deletion. Low expression of miR-31, miR-24, miR-708 and miR-128 was associated with PAX5 deletion, high expression of miR-24 and miR-542 was associated with PAR1 deletion and high expression of miR-708 was associated with ETV6 deletion. The expression of the selected miRNAs was not associated with deletions of BTG1, EBF1 and RB1. These data, by emphasizing the association of miRNAs expression level with microdeletions, may assist to elucidate ALL biology and contribute to future studies on the possible applications of the miRNA profile for diagnosis.
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Affiliation(s)
- J Krzanowski
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland
| | - J Madzio
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - A Pastorczak
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - A Tracz
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - M Braun
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland.,Department of Pathology, Chair of Oncology, Medical University of Łódź, 92-213 Łódź, Poland
| | - J Tabarkiewicz
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland.,Department of Immunology, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszów, 35-959 Rzeszów, Poland
| | - A Pluta
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland
| | - W Młynarski
- Department of Pediatrics, Hematology, Oncology and Diabetology, Medical University of Łódź, 91-738 Łódź, Poland
| | - I Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35-959 Rzeszów, Poland.,Department of Genetics, Chair of Molecular Medicine, Faculty of Medicine, University of Rzeszów, 35-959 Rzeszów, Poland
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50
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Mao L, Wang H, Ma F, Guo Z, He H, Zhou H, Wang N. Exposure to static magnetic fields increases insulin secretion in rat INS-1 cells by activating the transcription of the insulin gene and up-regulating the expression of vesicle-secreted proteins. Int J Radiat Biol 2017; 93:831-840. [PMID: 28593826 DOI: 10.1080/09553002.2017.1332439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PURPOSE To evaluate the effect of static magnetic fields (SMFs) on insulin secretion and explore the mechanisms underlying exposure to SMF-induced insulin secretion in rat insulinoma INS-1 cells. MATERIALS AND METHODS INS-1 cells were exposed to a 400 mT SMF for 72 h, and the proliferation of INS-1 cells was detected by (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The secretion of insulin was measured with an enzyme linked immunosorbent assays (ELISA), the expression of genes was detected by real-time PCR, and the expression of proteins was measured by Western blotting. RESULTS Exposure to an SMF increased the expression and secretion of insulin by INS-1 cells but did not affect cell proliferation. Moreover, SMF exposure up-regulated the expression of several pancreas-specific transcriptional factors. Specifically, the activity of the rat insulin promoter was enhanced in INS-1 cells exposed to an SMF, and the expression levels of synaptosomal-associated protein 25 (SNAP-25) and syntaxin-1A were up-regulated after exposure to an SMF. CONCLUSIONS SMF exposure can promote insulin secretion in rat INS-1 cells by activating the transcription of the insulin gene and up-regulating the expression of vesicle-secreted proteins.
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Affiliation(s)
- Libin Mao
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Huiqin Wang
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Fenghui Ma
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Zhixia Guo
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Hongpeng He
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Hao Zhou
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
| | - Nan Wang
- a Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education and Tianjin, College of Biotechnology , Tianjin University of Science and Technology , Tianjin , P.R. China
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