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Geng A, Lian W, Wang Y, Liu M, Zhang Y, Wang X, Chen G. Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice. Int J Mol Sci 2024; 25:1185. [PMID: 38256261 PMCID: PMC10817035 DOI: 10.3390/ijms25021185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.
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Affiliation(s)
- Anjing Geng
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Wenli Lian
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yihan Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Minghao Liu
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Yue Zhang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
| | - Guang Chen
- Institute of Quality Standard and Monitoring Technology for Agro-Products of Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory of Testing and Evaluation for Agro-Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Quality & Safety Risk Assessment for Agro-Products, Guangzhou 510640, China
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Mandel N, Büttner M, Poschet G, Kuner R, Agarwal N. SUMOylation Modulates Reactive Oxygen Species (ROS) Levels and Acts as a Protective Mechanism in the Type 2 Model of Diabetic Peripheral Neuropathy. Cells 2023; 12:2511. [PMID: 37947589 PMCID: PMC10648122 DOI: 10.3390/cells12212511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Diabetic peripheral neuropathy (DPN) is the prevalent type of peripheral neuropathy; it primarily impacts extremity nerves. Its multifaceted nature makes the molecular mechanisms of diabetic neuropathy intricate and incompletely elucidated. Several types of post-translational modifications (PTMs) have been implicated in the development and progression of DPN, including phosphorylation, glycation, acetylation and SUMOylation. SUMOylation involves the covalent attachment of small ubiquitin-like modifier (SUMO) proteins to target proteins, and it plays a role in various cellular processes, including protein localization, stability, and function. While the specific relationship between high blood glucose and SUMOylation is not extensively studied, recent evidence implies its involvement in the development of DPN in type 1 diabetes. In this study, we investigated the impact of SUMOylation on the onset and progression of DPN in a type 2 diabetes model using genetically modified mutant mice lacking SUMOylation, specifically in peripheral sensory neurons (SNS-Ubc9-/-). Behavioural measurement for evoked pain, morphological analyses of nerve fibre loss in the epidermis, measurement of reactive oxygen species (ROS) levels, and antioxidant molecules were analysed over several months in SUMOylation-deficient and control mice. Our longitudinal analysis at 30 weeks post-high-fat diet revealed that SNS-Ubc9-/- mice exhibited earlier and more pronounced thermal and mechanical sensation loss and accelerated intraepidermal nerve fibre loss compared to control mice. Mechanistically, these changes are associated with increased levels of ROS both in sensory neuronal soma and in peripheral axonal nerve endings in SNS-Ubc9-/- mice. In addition, we observed compromised detoxifying potential, impaired respiratory chain complexes, and reduced levels of protective lipids in sensory neurons upon deletion of SUMOylation in diabetic mice. Importantly, we also identified mitochondrial malate dehydrogenase (MDH2) as a SUMOylation target, the activity of which is negatively regulated by SUMOylation. Our results indicate that SUMOylation is an essential neuroprotective mechanism in sensory neurons in type 2 diabetes, the deletion of which causes oxidative stress and an impaired respiratory chain, resulting in energy depletion and subsequent damage to sensory neurons.
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Affiliation(s)
- Nicolas Mandel
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
| | - Michael Büttner
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Rohini Kuner
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
| | - Nitin Agarwal
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
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Gmeiner WH, Okechukwu CC. Review of 5-FU resistance mechanisms in colorectal cancer: clinical significance of attenuated on-target effects. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2023; 6:257-272. [PMID: 37457133 PMCID: PMC10344727 DOI: 10.20517/cdr.2022.136] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/01/2023] [Accepted: 04/17/2023] [Indexed: 07/18/2023]
Abstract
The emergence of chemoresistant disease during chemotherapy with 5-Fluorouracil-based (5-FU-based) regimens is an important factor in the mortality of metastatic CRC (mCRC). The causes of 5-FU resistance are multi-factorial, and besides DNA mismatch repair deficiency (MMR-D), there are no widely accepted criteria for determining which CRC patients are not likely to be responsive to 5-FU-based therapy. Thus, there is a need to systematically understand the mechanistic basis for 5-FU treatment failure and an urgent need to develop new approaches for circumventing the major causes of 5-FU resistance. In this manuscript, we review mechanisms of 5-FU resistance with an emphasis on: (1) altered anabolic metabolism limiting the formation of the primary active metabolite Fluorodeoxyuridylate (5-Fluoro-2'-deoxyuridine-5'-O-monophosphate; FdUMP); (2) elevated expression or activity of the primary enzymatic target thymidylate synthase (TS); and (3) dysregulated programmed cell death as important causes of 5-FU resistance. Importantly, these causes of 5-FU resistance can potentially be overcome through the use of next-generation fluoropyrimidine (FP) polymers (e.g., CF10) that display reduced dependence on anabolic metabolism and more potent TS inhibitory activity.
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Affiliation(s)
- William H. Gmeiner
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Integrative Physiology and Pharmacology Graduate Program, Institution, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Charles Chidi Okechukwu
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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4
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Reduced SUMOylation of Nrf2 signaling contributes to its inhibition induced by amyloid-β. Neurosci Lett 2023; 799:137118. [PMID: 36764479 DOI: 10.1016/j.neulet.2023.137118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/15/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Oxidative stress induced by amyloid-β (Aβ) has been considered as one of the important mechanisms in the development of Alzheimer disease (AD). The inhibition of endogenous antioxidant Nrf2 signaling in the brain of AD patients aggravates the oxidative damage, however, the causes of Nrf2 signaling inhibition are unclear. It is reported that smallubiquitin-like modification (SUMOylation) is involved in the process of oxidative injury. To investigate whether and how SUMOylation was involved in the inhibition of Nrf2 signaling pathway induced by Aβ, Aβ intrahippocampal injection rat model and Aβ treated SH-SY5Y cell model were used in the current study. Small interfering RNA and lentivirus transfection were used to intervene SUMOylation, and the level of SUMOylation was assessed by immunoprecipitation. The present in vivo and in vitro studies revealed that SUMOylation levels of Nrf2 and MafF, as well as the overall SUMOylation level were reduced under long-term Aβ insult. Meanwhile, the binding of Nrf2 to MafF was decreased, accompanied by low interaction with antioxidant response element (ARE) area of gene. Down-regulation of SUMO protein exacerbated the Aβ-induced inhibition of Nrf2 signaling pathway, while, enhancement of SUMOylation of Nrf2 and MafF by overexpression of Ubc9 reversed this process. These results imply that reduction in SUMOylation induced by Aβ contributed to the inhibition of Nrf2 signaling, and SUMOylation might be a potential therapeutic target of AD.
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Acuña ML, García-Morin A, Orozco-Sepúlveda R, Ontiveros C, Flores A, Diaz AV, Gutiérrez-Zubiate I, Patil AR, Alvarado LA, Roy S, Russell WK, Rosas-Acosta G. Alternative splicing of the SUMO1/2/3 transcripts affects cellular SUMOylation and produces functionally distinct SUMO protein isoforms. Sci Rep 2023; 13:2309. [PMID: 36759644 PMCID: PMC9911741 DOI: 10.1038/s41598-023-29357-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Substantial increases in the conjugation of the main human SUMO paralogs, SUMO1, SUMO2, and SUMO3, are observed upon exposure to different cellular stressors, and such increases are considered important to facilitate cell survival to stress. Despite their critical cellular role, little is known about how the levels of the SUMO modifiers are regulated in the cell, particularly as it relates to the changes observed upon stress. Here we characterize the contribution of alternative splicing towards regulating the expression of the main human SUMO paralogs under normalcy and three different stress conditions, heat-shock, cold-shock, and Influenza A Virus infection. Our data reveal that the normally spliced transcript variants are the predominant mature mRNAs produced from the SUMO genes and that the transcript coding for SUMO2 is by far the most abundant of all. We also provide evidence that alternatively spliced transcripts coding for protein isoforms of the prototypical SUMO proteins, which we refer to as the SUMO alphas, are also produced, and that their abundance and nuclear export are affected by stress in a stress- and cell-specific manner. Additionally, we provide evidence that the SUMO alphas are actively synthesized in the cell as their coding mRNAs are found associated with translating ribosomes. Finally, we provide evidence that the SUMO alphas are functionally different from their prototypical counterparts, with SUMO1α and SUMO2α being non-conjugatable to protein targets, SUMO3α being conjugatable but targeting a seemingly different subset of protein from those targeted by SUMO3, and all three SUMO alphas displaying different cellular distributions from those of the prototypical SUMOs. Thus, alternative splicing appears to be an important contributor to the regulation of the expression of the SUMO proteins and the cellular functions of the SUMOylation system.
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Affiliation(s)
- Myriah L Acuña
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Andrea García-Morin
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Rebeca Orozco-Sepúlveda
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Carlos Ontiveros
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Graduate School of Biomedical Sciences, University of Texas Health, San Antonio, TX, 78229, USA
| | - Alejandra Flores
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Arely V Diaz
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | | | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Luis A Alvarado
- Biostatistics and Epidemiology Consulting Lab, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Sourav Roy
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Germán Rosas-Acosta
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA.
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, 79968, USA.
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Ning Q, Qi Z, Wang Y, Deng A, Chen C. FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites. Brief Bioinform 2022; 23:6720406. [PMID: 36168700 DOI: 10.1093/bib/bbac421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/15/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In recent years, many computational methods of glutarylation sites have emerged one after another, but there are still many limitations, among which noisy data and the class imbalance problem caused by the uncertainty of non-glutarylation sites are great challenges. In this study, we propose a new semi-supervised learning algorithm, named FCCCSR, to identify reliable non-glutarylation lysine sites from unlabeled samples as negative samples. FCCCSR first finds core objects from positive samples according to reverse nearest neighbor information, and then clusters core objects based on natural neighbor structure. Finally, reliable negative samples are selected according to clustering result. With FCCCSR algorithm, we propose a new method named FCCCSR_Glu for glutarylation sites identification. In this study, multi-view features are extracted and fused to describe peptides, including amino acid composition, BLOSUM62, amino acid factors and composition of k-spaced amino acid pairs. Then, reliable negative samples selected by FCCCSR and positive samples are combined to establish models and XGBoost optimized by differential evolution algorithm is used as the classifier. On the independent testing dataset, FCCCSR_Glu achieves 85.18%, 98.36%, 94.31% and 0.8651 in sensitivity, specificity, accuracy and Matthew's Correlation Coefficient, respectively, which is superior to state-of-the-art methods in predicting glutarylation sites. Therefore, FCCCSR_Glu can be a useful tool for glutarylation sites prediction and FCCCSR algorithm can effectively select reliable negative samples from unlabeled samples. The data and code are available on https://github.com/xbbxhbc/FCCCSR_Glu.git.
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Affiliation(s)
- Qiao Ning
- Department of Information Science and Technology, Dalian Maritime University, Lingshui Street, 116026, Dalian, China
| | - Zedong Qi
- Department of Information Science and Technology, Dalian Maritime University, Lingshui Street, 116026, Dalian, China
| | - Yue Wang
- Department of Information Science and Technology, Dalian Maritime University, Lingshui Street, 116026, Dalian, China
| | - Ansheng Deng
- Department of Information Science and Technology, Dalian Maritime University, Lingshui Street, 116026, Dalian, China
| | - Chen Chen
- Naval Architecture and Ocean Engineering college, Dalian Maritime University, Lingshui Street, 116026, Dalian, China
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Nan J, Lee JS, Moon JH, Lee SA, Park YJ, Lee DS, Chung SS, Park KS. SENP2 regulates mitochondrial function and insulin secretion in pancreatic β cells. Exp Mol Med 2022; 54:72-80. [PMID: 35064188 PMCID: PMC8814193 DOI: 10.1038/s12276-021-00723-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 01/01/2023] Open
Abstract
AbstractIncreasing evidence has shown that small ubiquitin-like modifier (SUMO) modification plays an important role in metabolic regulation. We previously demonstrated that SUMO-specific protease 2 (SENP2) is involved in lipid metabolism in skeletal muscle and adipogenesis. In this study, we investigated the function of SENP2 in pancreatic β cells by generating a β cell-specific knockout (Senp2-βKO) mouse model. Glucose tolerance and insulin secretion were significantly impaired in the Senp2-βKO mice. In addition, glucose-stimulated insulin secretion (GSIS) was decreased in the islets of the Senp2-βKO mice without a significant change in insulin synthesis. Furthermore, islets of the Senp2-βKO mice exhibited enlarged mitochondria and lower oxygen consumption rates, accompanied by lower levels of S616 phosphorylated DRP1 (an active form of DRP1), a mitochondrial fission protein. Using a cell culture system of NIT-1, an islet β cell line, we found that increased SUMO2/3 conjugation to DRP1 due to SENP2 deficiency suppresses the phosphorylation of DRP1, which possibly induces mitochondrial dysfunction. In addition, SENP2 overexpression restored GSIS impairment induced by DRP1 knockdown and increased DRP1 phosphorylation. Furthermore, palmitate treatment decreased phosphorylated DRP1 and GSIS in β cells, which was rescued by SENP2 overexpression. These results suggest that SENP2 regulates mitochondrial function and insulin secretion at least in part by modulating the phosphorylation of DRP1 in pancreatic β cells.
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Arafat ME, Ahmad MW, Shovan S, Dehzangi A, Dipta SR, Hasan MAM, Taherzadeh G, Shatabda S, Sharma A. Accurately Predicting Glutarylation Sites Using Sequential Bi-Peptide-Based Evolutionary Features. Genes (Basel) 2020; 11:E1023. [PMID: 32878321 PMCID: PMC7565944 DOI: 10.3390/genes11091023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Post Translational Modification (PTM) is defined as the alteration of protein sequence upon interaction with different macromolecules after the translation process. Glutarylation is considered one of the most important PTMs, which is associated with a wide range of cellular functioning, including metabolism, translation, and specified separate subcellular localizations. During the past few years, a wide range of computational approaches has been proposed to predict Glutarylation sites. However, despite all the efforts that have been made so far, the prediction performance of the Glutarylation sites has remained limited. One of the main challenges to tackle this problem is to extract features with significant discriminatory information. To address this issue, we propose a new machine learning method called BiPepGlut using the concept of a bi-peptide-based evolutionary method for feature extraction. To build this model, we also use the Extra-Trees (ET) classifier for the classification purpose, which, to the best of our knowledge, has never been used for this task. Our results demonstrate BiPepGlut is able to significantly outperform previously proposed models to tackle this problem. BiPepGlut achieves 92.0%, 84.8%, 95.6%, 0.82, and 0.88 in accuracy, sensitivity, specificity, Matthew's Correlation Coefficient, and F1-score, respectively. BiPepGlut is implemented as a publicly available online predictor.
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Affiliation(s)
- Md. Easin Arafat
- Department of Computer Science and Engineering, United International University, Dhaka 1212, Bangladesh; (M.E.A.); (M.W.A.); (S.R.D.)
| | - Md. Wakil Ahmad
- Department of Computer Science and Engineering, United International University, Dhaka 1212, Bangladesh; (M.E.A.); (M.W.A.); (S.R.D.)
| | - S.M. Shovan
- Department of Computer Science and Engineering, Rajshahi University of Engineering and Technology, Rajshahi 6204, Bangladesh; (S.M.S.); (M.A.M.H.)
| | - Abdollah Dehzangi
- Department of Computer Science, Rutgers University, Camden, NJ 08102, USA;
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Shubhashis Roy Dipta
- Department of Computer Science and Engineering, United International University, Dhaka 1212, Bangladesh; (M.E.A.); (M.W.A.); (S.R.D.)
| | - Md. Al Mehedi Hasan
- Department of Computer Science and Engineering, Rajshahi University of Engineering and Technology, Rajshahi 6204, Bangladesh; (S.M.S.); (M.A.M.H.)
| | - Ghazaleh Taherzadeh
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, United International University, Dhaka 1212, Bangladesh; (M.E.A.); (M.W.A.); (S.R.D.)
| | - Alok Sharma
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD 4111, Australia
- Department of Medical Science Mathematics, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
- School of Engineering and Physics, Faculty of Science Technology and Environment, University of the South Pacific, Suva, Fiji
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Tait S, Baldassarre A, Masotti A, Calura E, Martini P, Varì R, Scazzocchio B, Gessani S, Del Cornò M. Integrated Transcriptome Analysis of Human Visceral Adipocytes Unravels Dysregulated microRNA-Long Non-coding RNA-mRNA Networks in Obesity and Colorectal Cancer. Front Oncol 2020; 10:1089. [PMID: 32714872 PMCID: PMC7351520 DOI: 10.3389/fonc.2020.01089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
Obesity, and the obesity-associated inflammation, represents a major risk factor for the development of chronic diseases, including colorectal cancer (CRC). Dysfunctional visceral adipose tissue (AT) is now recognized as key player in obesity-associated morbidities, although the biological processes underpinning the increased CRC risk in obese subjects are still a matter of debate. Recent findings have pointed to specific alterations in the expression pattern of non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), as mechanisms underlying dysfunctional adipocyte phenotype in obesity. Nevertheless, the regulatory networks and interrelated processes relevant for adipocyte functions, that may contribute to a tumor-promoting microenvironment, are poorly known yet. To this end, based on RNA sequencing data, we identified lncRNAs and miRNAs, which are aberrantly expressed in visceral adipocytes from obese and CRC subjects, as compared to healthy lean control, and validated a panel of modulated ncRNAs by real-time qPCR. Furthermore, by combining the differentially expressed lncRNA and miRNA profiles with the transcriptome analysis dataset of adipocytes from lean and obese subjects affected or not by CRC, lncRNA-miRNA-mRNA adipocyte networks were defined for obese and CRC subjects. This analysis highlighted several ncRNAs modulation that are common to both obesity and CRC or unique of each disorder. Functional enrichment analysis of network-related mRNA targets, revealed dysregulated pathways associated with metabolic processes, lipid and energy metabolism, inflammation, and cancer. Moreover, adipocytes from obese subjects affected by CRC exhibited a higher complexity, in terms of number of genes, lncRNAs, miRNAs, and biological processes found to be dysregulated, providing evidence that the transcriptional and post-transcriptional program of adipocytes from CRC patients is deeply affected by obesity. Overall, this study adds further evidence for a central role of visceral adipocyte dysfunctions in the obesity-cancer relationship.
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Affiliation(s)
- Sabrina Tait
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Research Laboratories, Rome, Italy
| | - Enrica Calura
- Department of Biology, University of Padua, Padua, Italy
| | - Paolo Martini
- Department of Biology, University of Padua, Padua, Italy
| | - Rosaria Varì
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Sandra Gessani
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Manuela Del Cornò
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
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Abstract
Objective: Small ubiquitin-related modifiers (SUMOs) are a group of post-translational modification proteins extensively expressed in eukaryotes. Abnormal SUMOylation can lead to the development of various diseases. This article summarizes the progress on research of the role of SUMOs in various types of kidney diseases to further increase the understanding of the regulatory functions of SUMOylation in the pathogenesis of kidney diseases. Data sources: This review was based on articles published in the PubMed databases up to January 2018, using the keywords including “SUMOs,” “SUMOylation,” and “kidney diseases.” Study selection: Original articles and critical reviews about SUMOs and kidney disease were selected for this review. A total of 50 studies were in English. Results: SUMO participates in the activation of NF-κB inflammatory signaling pathway, playing a central regulatory role in the inflammation and progression of DN, and the secretion of various chemokines in AKI. SUMO involves in the regulation of TG2 and Nrf2 antioxidant stress, affecting renal tubular injury in AKI. SUMO affects the MAPK/ERK pathway, regulating intracellular signal transduction, modulating the transcription and expression of effector molecules in DN. SUMO contributes to the TGF-β/Smad pathway, leading to fibrosis of the kidney. The conjugate combination of SUMO and p53 regulates cell proliferation and apoptosis, and participates in the regulation of tumorigenesis. In addition, SUMOylation of MITF modulates renal tumors secondary to melanoma, Similarly, SUMOylation of tumor suppressor gene VHL regulates the occurrence of renal cell carcinoma in VHL syndrome. Conclusions: Tissue injury, inflammatory responses, fibrosis, apoptosis, and tumor proliferation in kidney diseases all involve SUMOs. Further research of the substrate SUMOylation and regulatory mechanisms of SUMO in kidney diseases will improve and develop new treatment measures and strategies targeting kidney diseases.
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AL-barakati HJ, Saigo H, Newman RH, KC DB. RF-GlutarySite: a random forest based predictor for glutarylation sites. Mol Omics 2019; 15:189-204. [DOI: 10.1039/c9mo00028c] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glutarylation, which is a newly identified posttranslational modification that occurs on lysine residues, has recently emerged as an important regulator of several metabolic and mitochondrial processes. Here, we describe the development of RF-GlutarySite, a random forest-based predictor designed to predict glutarylation sites based on protein primary amino acid sequence.
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Affiliation(s)
- Hussam J. AL-barakati
- Department of Computational Science and Engineering
- North Carolina Agricultural & Technical State University
- Greensboro
- USA
| | - Hiroto Saigo
- Department of Informatics
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Robert H. Newman
- Department of Biology
- North Carolina Agricultural & Technical State University
- Greensboro
- USA
| | - Dukka B. KC
- Department of Computational Science and Engineering
- North Carolina Agricultural & Technical State University
- Greensboro
- USA
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Elizondo G, Vega L. Ubiquitination/sumoylation: An alternative pathway to modify gene regulation directed by xenosensors. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling. Sci Rep 2018; 8:1139. [PMID: 29348603 PMCID: PMC5773548 DOI: 10.1038/s41598-018-19424-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/02/2018] [Indexed: 02/07/2023] Open
Abstract
Post-translational modification by small ubiquitin-related modifier (SUMO) is a key regulator of cell physiology, modulating protein-protein and protein-DNA interactions. Recently, SUMO modifications were postulated to be involved in response to various stress stimuli. We aimed to identify the near complete set of proteins modified by SUMO and the dynamics of the modification in stress conditions in the higher eukaryote, Caenorhabditis elegans. We identified 874 proteins modified by SUMO in the worm. We have analyzed the SUMO modification in stress conditions including heat shock, DNA damage, arsenite induced cellular stress, ER and osmotic stress. In all these conditions the global levels of SUMOylation was significantly increased. These results show the evolutionary conservation of SUMO modifications in reaction to stress. Our analysis showed that SUMO targets are highly conserved throughout species. By comparing the SUMO targets among species, we approximated the total number of proteins modified in a given proteome to be at least 15–20%. We developed a web server designed for convenient prediction of potential SUMO modification based on experimental evidences in other species.
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Is Tattooing a Risk Factor for Hepatitis C Transmission?: An Updated Systematic Review and Meta-Analysis. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.14308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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