1
|
Zhang L, Zhao J, Peng Z, Zhang Z, Huang S, Dong X, Gao J, Guo X. Anti-adipogenesis effect of indole-3-acrylic acid on human preadipocytes and HFD-induced zebrafish. Acta Diabetol 2024:10.1007/s00592-024-02256-7. [PMID: 38598139 DOI: 10.1007/s00592-024-02256-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Obesity, defined as excessive or abnormal body fat accumulation, which could significantly increase the risk of cardiovascular disease, type 2 diabetes mellitus (T2DM) diseases and seriously affect people's quality of life. More than 2 billion people are overweight, and the incidence of obesity is increasing rapidly worldwide, it has become a widely concerned public health issue in the world. Diverse evidence show that active metabolites are involved in the pathophysiological processes of obesity. AIMS However, whether the downstream catabolite of tryptophan, 3-indole acrylic acid (IA), is involved in obesity remains unclear. METHODS We collected the samples of serum from peripheral blood of obesity and health controls, and liquid chromatography-mass spectrometry (LC-MS) was performed to identify the plasma levels of IA. Additionally, we verified the potential benefits of IA on human preadipocytes and HFD- induced zebrafish by cell viability assay, flow cytometry assay, Oil red O staining, total cholesterol (T-CHO), triglyceride (TG) and nonesterified free fatty acids (NEFA) measurements and Nile Red staining. RNA-Seq, functional analysis and western blot revealed the mechanisms underlying the function of IA. RESULTS We found that the content of IA in peripheral blood serum of overweight people was significantly lower than that of normal people. In addition, supplementation with IA in zebrafish larvae induced by a high fat diet (HFD) dramatically reduced HFD induced lipid accumulation. IA had no effect on proliferation and apoptosis of preadipocytes, but significantly inhibited adipogenesis of preadipocytes by down-regulate CEBPα and PPARγ. RNA-Seq and functional analysis revealed that IA regulated the adipogenesis of preadipocytes through stimulate the phosphorylation of STAT1. CONCLUSIONS Taken together, IA has been identified as a potent metabolite for the prevention or treatment of obesity.
Collapse
Affiliation(s)
- Ling Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China
| | - Jing Zhao
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China
| | - Zhou Peng
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China
| | - Zhongxiao Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China
| | - Shan Huang
- Endocrinology Department, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaohua Dong
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China
| | - Jianfang Gao
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China.
| | - Xirong Guo
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, 1111 XianXia Road, Shanghai, 200336, People's Republic of China.
| |
Collapse
|
2
|
Cirinciani M, Da Pozzo E, Trincavelli ML, Milazzo P, Martini C. Drug Mechanism: A bioinformatic update. Biochem Pharmacol 2024:116078. [PMID: 38402909 DOI: 10.1016/j.bcp.2024.116078] [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: 12/13/2023] [Revised: 02/01/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
A drug Mechanism of Action (MoA) is a complex biological phenomenon that describes how a bioactive compound produces a pharmacological effect. The complete knowledge of MoA is fundamental to fully understanding the drug activity. Over the years, many experimental methods have been developed and a huge quantity of data has been produced. Nowadays, considering the increasing omics data availability and the improvement of the accessible computational resources, the study of a drug MoA is conducted by integrating experimental and bioinformatics approaches. The development of new in silico solutions for this type of analysis is continuously ongoing; herein, an updating review on such bioinformatic methods is presented. The methodologies cited are based on multi-omics data integration in biochemical networks and Machine Learning (ML). The multiple types of usable input data and the advantages and disadvantages of each method have been analyzed, with a focus on their applications. Three specific research areas (i.e. cancer drug development, antibiotics discovery, and drug repurposing) have been chosen for their importance in the drug discovery fields in which the study of drug MoA, through novel bioinformatics approaches, is particularly productive.
Collapse
Affiliation(s)
- Martina Cirinciani
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Eleonora Da Pozzo
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy; Center for Instrument Sharing University of Pisa (CISUP), Lungarno Pacinotti, 43/44, 56126 Pisa, Italy
| | - Maria Letizia Trincavelli
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy; Center for Instrument Sharing University of Pisa (CISUP), Lungarno Pacinotti, 43/44, 56126 Pisa, Italy
| | - Paolo Milazzo
- Center for Instrument Sharing University of Pisa (CISUP), Lungarno Pacinotti, 43/44, 56126 Pisa, Italy; Department of Computer Science, University of Pisa, Largo Pontecorvo, 3, 56127 Pisa, Italy
| | - Claudia Martini
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy; Center for Instrument Sharing University of Pisa (CISUP), Lungarno Pacinotti, 43/44, 56126 Pisa, Italy.
| |
Collapse
|
3
|
Wang L, Lu Y, Li D, Zhou Y, Yu L, Mesa Eguiagaray I, Campbell H, Li X, Theodoratou E. The landscape of the methodology in drug repurposing using human genomic data: a systematic review. Brief Bioinform 2024; 25:bbad527. [PMID: 38279645 PMCID: PMC10818097 DOI: 10.1093/bib/bbad527] [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: 07/17/2023] [Revised: 11/24/2023] [Accepted: 12/19/2023] [Indexed: 01/28/2024] Open
Abstract
The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.
Collapse
Affiliation(s)
- Lijuan Wang
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Doudou Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yajing Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lili Yu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ines Mesa Eguiagaray
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh MRC Institute of Genetics and Cancer, Edinburgh, UK
| |
Collapse
|
4
|
Sanni O, Fasemore T, Nkomozepi P. Non-Genetic-Induced Zebrafish Model for Type 2 Diabetes with Emphasis on Tools in Model Validation. Int J Mol Sci 2023; 25:240. [PMID: 38203409 PMCID: PMC10778736 DOI: 10.3390/ijms25010240] [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: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The unrelenting increase in the incidence of type 2 diabetes (T2D) necessitates the urgent need for effective animal models to mimic its pathophysiology. Zebrafish possess human-like metabolic traits and share significant genetic similarities, making them valuable candidates for studying metabolic disorders, including T2D. This review emphasizes the critical role of animal models in diabetes research, especially focusing on zebrafish as an alternative model organism. Different approaches to a non-genetic model of T2D in zebrafish, such as the glucose solution, diet-induced, chemical-induced, and combined diet-induced and glucose solution methods, with an emphasis on model validation using indicators of T2D, were highlighted. However, a significant drawback lies in the validation of these models. Some of these models have not extensively demonstrated persistent hyperglycemia or response to insulin resistance and glucose tolerance tests, depicted the morphology of the pancreatic β-cell, or showed their response to antidiabetic drugs. These tools are crucial in T2D pathology. Future research on non-genetic models of T2D in zebrafish must extensively focus on validating the metabolic deficits existing in the model with the same metabolic defects in humans and improve on the existing models for a better understanding of the molecular mechanisms underlying T2D and exploring potential therapeutic interventions.
Collapse
Affiliation(s)
- Olakunle Sanni
- Department of Human Anatomy and Physiology, University of Johannesburg, Doornfontein 2028, South Africa; (T.F.); (P.N.)
| | | | | |
Collapse
|
5
|
Gao J, Zhang Z, Dong X, Zhao J, Peng Z, Zhang L, Xu Z, Xu L, Wang X, Guo X. Traumatic acid inhibits ACSL4 associated lipid accumulation in adipocytes to attenuate high-fat diet-induced obesity. FASEB J 2023; 37:e23278. [PMID: 37902573 DOI: 10.1096/fj.202301166r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/25/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Obesity is a major health concern that lacks effective intervention strategies. Traumatic acid (TA) is a potent wound-healing agent in plants, considered an antioxidant food ingredient. This study demonstrated that TA treatment significantly reduced lipid accumulation in human adipocytes and prevented high-fat diet induced obesity in zebrafish. Transcriptome sequencing revealed TA-activated fatty acid (FA) degradation and FA metabolism signaling pathways. Moreover, western blotting and quantitative polymerase chain reaction showed that TA inhibited the expression of long-chain acyl-CoA synthetase-4 (ACSL4). Overexpression of ACSL4 resulted in the reversal of TA beneficiary effects, indicating that the attenuated lipid accumulation of TA was regulated by ACSL4 expression. Limited proteolysis-mass spectrometry and microscale thermophoresis were then used to confirm hexokinase 2 (HK2) as a direct molecular target of TA. Thus, we demonstrated the molecular basis of TA in regulating lipid accumulation and gave the first evidence that TA may function through the HK2-ACSL4 axis.
Collapse
Affiliation(s)
- Jianfang Gao
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongxiao Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohua Dong
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhao
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhou Peng
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ling Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongqing Xu
- Department of General Practice, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liling Xu
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingyun Wang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xirong Guo
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
6
|
Chang C, Li H, Zhang R. Zebrafish facilitate non-alcoholic fatty liver disease research: Tools, models and applications. Liver Int 2023; 43:1385-1398. [PMID: 37122203 DOI: 10.1111/liv.15601] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has become an increasingly epidemic metabolic disease worldwide. NAFLD can gradually deteriorate from simple liver steatosis, inflammation and fibrosis to liver cirrhosis and/or hepatocellular carcinoma. Zebrafish are vertebrate animal models that are genetically and metabolically conserved with mammals and have unique advantages such as high fecundity, rapid development ex utero and optical transparency. These features have rendered zebrafish an emerging model system for liver diseases and metabolic diseases favoured by many researchers in recent years. In the present review, we summarize a series of tools for zebrafish NAFLD research and the models established through different dietary feeding, hepatotoxic chemical treatments and genetic manipulations via transgenic or genome editing technologies. We also discuss how zebrafish models facilitate NAFLD studies by providing novel insights into NAFLD pathogenesis, toxicology research, and drug evaluation and discovery.
Collapse
Affiliation(s)
- Cheng Chang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Huicong Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Ruilin Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
| |
Collapse
|
7
|
Sun Y, Heng J, Liu F, Zhang S, Liu P. Isolation and proteomic study of fish liver lipid droplets. BIOPHYSICS REPORTS 2023; 9:120-133. [PMID: 38028150 PMCID: PMC10648235 DOI: 10.52601/bpr.2023.230004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/02/2023] [Indexed: 12/01/2023] Open
Abstract
Lipid droplets (LDs) are a neutral lipid storage organelle that is conserved in almost all species. Excessive storage of neutral lipids in LDs is directly associated with many metabolic syndromes. Zebrafish is a better model animal for the study of LD biology due to its transparent embryonic stage compared to other organisms. However, the study of LDs in fish has been difficult due to the lack of specific LD marker proteins and the limitation of purification technology. In this paper, the purification and proteomic analysis of liver LDs of fish including zebrafish and Carassius auratus were performed for the first time. 259 and 267 proteins were identified respectively. Besides most of the identified proteins were reported in previous LD proteomes of mammals, indicating the similarity between mammal and fish LDs. We also identified many unique proteins of liver LDs in fish that are involved in the regulation of LD dynamics. Through morphological and biochemical analysis, we found that the marker protein Plin2 of zebrafish LD was located on LDs in Huh7 cells. These results will facilitate further study of LDs in fish and liver metabolic diseases using fish as a model animal.
Collapse
Affiliation(s)
- Yuwei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Heng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
8
|
Liang S, Liu D, Xiao Z, Greenbaum J, Shen H, Xiao H, Deng H. Repurposing Approved Drugs for Sarcopenia Based on Transcriptomics Data in Humans. Pharmaceuticals (Basel) 2023; 16:ph16040607. [PMID: 37111364 PMCID: PMC10145476 DOI: 10.3390/ph16040607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Sarcopenia, characterized by age-related loss of muscle mass, strength, and decreased physical performance, is a growing public health challenge amid the rapidly ageing population. As there are no approved drugs that target sarcopenia, it has become increasingly urgent to identify promising pharmacological interventions. In this study, we conducted an integrative drug repurposing analysis utilizing three distinct approaches. Firstly, we analyzed skeletal muscle transcriptomic sequencing data in humans and mice using gene differential expression analysis, weighted gene co-expression analysis, and gene set enrichment analysis. Subsequently, we employed gene expression profile similarity assessment, hub gene expression reversal, and disease-related pathway enrichment to identify and repurpose candidate drugs, followed by the integration of findings with rank aggregation algorithms. Vorinostat, the top-ranking drug, was also validated in an in vitro study, which demonstrated its efficacy in promoting muscle fiber formation. Although still requiring further validation in animal models and human clinical trials, these results suggest a promising drug repurposing prospect in the treatment and prevention of sarcopenia.
Collapse
Affiliation(s)
- Shuang Liang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Danyang Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410013, China
| | - Zhengwu Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
| | - Hongmei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Hongwen Deng
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 999039, USA
| |
Collapse
|
9
|
Qin D, Lei Y, Xie W, Zheng Q, Peng Z, Liu Y, Dai B, Ma T, Wei P, Gao C, Guo X, Gao J, Zhao J, Du J, Zeng Q, Zhang Z, Dong X, Shen H. Methionine sulfoxide suppresses adipogenic differentiation by regulating the mitogen-activated protein kinase signaling pathway. Cell Biol Int 2023; 47:648-659. [PMID: 36448374 DOI: 10.1002/cbin.11964] [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: 04/14/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 12/02/2022]
Abstract
In this study, methionine sulfoxide (MetO) was identified as an active metabolite that suppresses adipogenesis after screening obese individuals versus the normal population. MetO suppressed the gene and protein expression of CCAAT/enhancer binding protein (C/EBP) α, adipocyte fatty acid binding protein 4 (FABP4), and the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) during human preadipocyte (HPA) differentiation. Adipogenesis decreased following MetO treatment; however, the preadipocyte number, proliferation, and apoptosis were unaffected. The activity of phosphorylated extracellular signal-related kinase (P-ERK) of the mitogen-activated protein kinase (MAPK) pathway was significantly inhibited in HPA after MetO treatment. Furthermore, treatment of preadipocytes with the selective P-ERK1/2 agonist Ro 67-7476 abolished the effect of MetO against adipogenesis suggesting that MetO function is dependent on the MAPK pathway. The mechanistic insights of adipogenesis suppression by MetO presented in this study shows its potential as an antiobesity drug.
Collapse
Affiliation(s)
- Dani Qin
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Yong Lei
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Wen Xie
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Qiuju Zheng
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Zhou Peng
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwen Liu
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Biao Dai
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Tieliang Ma
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Ping Wei
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| | - Chunlin Gao
- Department of Pediatrics, Jinling Hospital, Nanjing, China
| | - Xirong Guo
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfang Gao
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhao
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Juan Du
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qianyi Zeng
- Shenzhen Bay Laboratory, Bayray Innovation Center, Shenzhen, China
| | - Zhongxiao Zhang
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohua Dong
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiping Shen
- Department of Pediatrics, Yixing People's Hospital, Yixing, China
| |
Collapse
|
10
|
Qin S, Li W, Yu H, Xu M, Li C, Fu L, Sun S, He Y, Lv J, He W, Chen L. Guiding Drug Repositioning for Cancers Based on Drug Similarity Networks. Int J Mol Sci 2023; 24:ijms24032244. [PMID: 36768566 PMCID: PMC9917231 DOI: 10.3390/ijms24032244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Drug repositioning aims to discover novel clinical benefits of existing drugs, is an effective way to develop drugs for complex diseases such as cancer and may facilitate the process of traditional drug development. Meanwhile, network-based computational biology approaches, which allow the integration of information from different aspects to understand the relationships between biomolecules, has been successfully applied to drug repurposing. In this work, we developed a new strategy for network-based drug repositioning against cancer. Combining the mechanism of action and clinical efficacy of the drugs, a cancer-related drug similarity network was constructed, and the correlation score of each drug with a specific cancer was quantified. The top 5% of scoring drugs were reviewed for stability and druggable potential to identify potential repositionable drugs. Of the 11 potentially repurposable drugs for non-small cell lung cancer (NSCLC), 10 were confirmed by clinical trial articles and databases. The targets of these drugs were significantly enriched in cancer-related pathways and significantly associated with the prognosis of NSCLC. In light of the successful application of our approach to colorectal cancer as well, it provides an effective clue and valuable perspective for drug repurposing in cancer.
Collapse
Affiliation(s)
- Shimei Qin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Hongzheng Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Manyi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Chao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lei Fu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Shibin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuehan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Weiming He
- Institute of Opto-Electronics, Harbin Institute of Technology, Harbin 150001, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
- Correspondence: ; Tel.: +86-451-8667-4768
| |
Collapse
|
11
|
Esculetin Alleviates Nonalcoholic Fatty Liver Disease on High-Cholesterol-Diet-Induced Larval Zebrafish and FFA-Induced BRL-3A Hepatocyte. Int J Mol Sci 2023; 24:ijms24021593. [PMID: 36675107 PMCID: PMC9866237 DOI: 10.3390/ijms24021593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD), defined in recent years as metabolic-associated fatty liver disease (MAFLD), is one of the most common liver diseases in the world, with no drugs on market. Esculetin (ESC) is an active compound discovered in a variety of natural products that modulates a wide range of metabolic diseases and is a potential drug for the treatment of NAFLD. In this study, we used an HCD-induced NAFLD larval zebrafish model in vivo and an FFA-induced BRL-3A hepatocyte model in vitro to evaluate the anti-NAFLD effect of ESC. Lipid lowering, anti-oxidation and anti-inflammation effects were revealed on ESC and related gene changes were observed. This study provides a reference for further study and development of ESC as a potential anti-NAFLD/MAFLD drug.
Collapse
|
12
|
Parolo S, Mariotti F, Bora P, Carboni L, Domenici E. Single-cell-led drug repurposing for Alzheimer's disease. Sci Rep 2023; 13:222. [PMID: 36604493 PMCID: PMC9816180 DOI: 10.1038/s41598-023-27420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Alzheimer's disease is the most common form of dementia. Notwithstanding the huge investments in drug development, only one disease-modifying treatment has been recently approved. Here we present a single-cell-led systems biology pipeline for the identification of drug repurposing candidates. Using single-cell RNA sequencing data of brain tissues from patients with Alzheimer's disease, genome-wide association study results, and multiple gene annotation resources, we built a multi-cellular Alzheimer's disease molecular network that we leveraged for gaining cell-specific insights into Alzheimer's disease pathophysiology and for the identification of drug repurposing candidates. Our computational approach pointed out 54 candidate drugs, mainly targeting MAPK and IGF1R signaling pathways, which could be further evaluated for their potential as Alzheimer's disease therapy.
Collapse
Affiliation(s)
- Silvia Parolo
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), 38068, Rovereto, Italy.
| | - Federica Mariotti
- grid.491181.4Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), 38068 Rovereto, Italy
| | - Pranami Bora
- grid.491181.4Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), 38068 Rovereto, Italy
| | - Lucia Carboni
- grid.6292.f0000 0004 1757 1758Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy
| | - Enrico Domenici
- grid.491181.4Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), 38068 Rovereto, Italy ,grid.11696.390000 0004 1937 0351Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| |
Collapse
|
13
|
Zhang JJ, Shen Y, Chen XY, Jiang ML, Yuan FH, Xie SL, Zhang J, Xu F. Integrative network-based analysis on multiple Gene Expression Omnibus datasets identifies novel immune molecular markers implicated in non-alcoholic steatohepatitis. Front Endocrinol (Lausanne) 2023; 14:1115890. [PMID: 37008925 PMCID: PMC10061151 DOI: 10.3389/fendo.2023.1115890] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
INTRODUCTION Non-alcoholic steatohepatitis (NASH), an advanced subtype of non-alcoholic fatty liver disease (NAFLD), has becoming the most important aetiology for end-stage liver disease, such as cirrhosis and hepatocellular carcinoma. This study were designed to explore novel genes associated with NASH. METHODS Here, five independent Gene Expression Omnibus (GEO) datasets were combined into a single cohort and analyzed using network biology approaches. RESULTS 11 modules identified by weighted gene co-expression network analysis (WGCNA) showed significant association with the status of NASH. Further characterization of four gene modules of interest demonstrated that molecular pathology of NASH involves the upregulation of hub genes related to immune response, cholesterol and lipid metabolic process, extracellular matrix organization, and the downregulation of hub genes related to cellular amino acid catabolic, respectively. After DEGs enrichment analysis and module preservation analysis, the Turquoise module associated with immune response displayed a remarkably correlation with NASH status. Hub genes with high degree of connectivity in the module, including CD53, LCP1, LAPTM5, NCKAP1L, C3AR1, PLEK, FCER1G, HLA-DRA and SRGN were further verified in clinical samples and mouse model of NASH. Moreover, single-cell RNA-seq analysis showed that those key genes were expressed by distinct immune cells such as microphages, natural killer, dendritic, T and B cells. Finally, the potential transcription factors of Turquoise module were characterized, including NFKB1, STAT3, RFX5, ILF3, ELF1, SPI1, ETS1 and CEBPA, the expression of which increased with NASH progression. DISCUSSION In conclusion, our integrative analysis will contribute to the understanding of NASH and may enable the development of potential biomarkers for NASH therapy.
Collapse
Affiliation(s)
- Jun-jie Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
- *Correspondence: Jun-jie Zhang, ; Fei Xu,
| | - Yan Shen
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Xiao-yuan Chen
- Department of Publication Health and Health Management, Gannan Medical University, Ganzhou, China
| | - Man-lei Jiang
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Feng-hua Yuan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Shui-lian Xie
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Jie Zhang
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Fei Xu
- Department of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
- *Correspondence: Jun-jie Zhang, ; Fei Xu,
| |
Collapse
|
14
|
Jiang Y, Zhang JX, Liu R. Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing. PLoS Comput Biol 2022; 18:e1010744. [PMID: 36534703 PMCID: PMC9810203 DOI: 10.1371/journal.pcbi.1010744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/03/2023] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
The synergy between human immunodeficiency virus (HIV) and Mycobacterium tuberculosis (MTB) could accelerate the deterioration of immunological functions. Previous studies have explored the pathogenic mechanisms of HIV mono-infection (HMI), MTB mono-infection (MMI) and MTB/HIV co-infection (MHCI), but their similarities and specificities remain to be profoundly investigated. We thus designed a computational framework named IDEN to identify gene pairs related to these states, which were then compared from different perspectives. MMI-related genes showed the highest enrichment level on a greater number of chromosomes. Genes shared by more states tended to be more evolutionarily conserved, posttranslationally modified and topologically important. At the expression level, HMI-specific gene pairs yielded higher correlations, while the overlapping pairs involved in MHCI had significantly lower correlations. The correlation changes of common gene pairs showed that MHCI shared more similarities with MMI. Moreover, MMI- and MHCI-related genes were enriched in more identical pathways and biological processes, further illustrating that MTB may play a dominant role in co-infection. Hub genes specific to each state could promote pathogen infections, while those shared by two states could enhance immune responses. Finally, we improved the network proximity measure for drug repurposing by considering the importance of gene pairs, and approximately ten drug candidates were identified for each disease state.
Collapse
Affiliation(s)
- Yao Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jia-Xuan Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail:
| |
Collapse
|
15
|
Six types of tea extracts attenuated high-fat diet-induced metabolic syndrome via modulating gut microbiota in rats. Food Res Int 2022; 161:111788. [DOI: 10.1016/j.foodres.2022.111788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/03/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
|
16
|
Nutrigenetic Interaction of Spontaneously Hypertensive Rat Chromosome 20 Segment and High-Sucrose Diet Sensitizes to Metabolic Syndrome. Nutrients 2022; 14:nu14163428. [PMID: 36014934 PMCID: PMC9416443 DOI: 10.3390/nu14163428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Several corresponding regions of human and mammalian genomes have been shown to affect sensitivity to the manifestation of metabolic syndrome via nutrigenetic interactions. In this study, we assessed the effect of sucrose administration in a newly established congenic strain BN.SHR20, in which a limited segment of rat chromosome 20 from a metabolic syndrome model, spontaneously hypertensive rat (SHR), was introgressed into Brown Norway (BN) genomic background. We mapped the extent of the differential segment and compared the genomic sequences of BN vs. SHR within the segment in silico. The differential segment of SHR origin in BN.SHR20 spans about 9 Mb of the telomeric portion of the short arm of chromosome 20. We identified non-synonymous mutations e.g., in ApoM, Notch4, Slc39a7, Smim29 genes and other variations in or near genes associated with metabolic syndrome in human genome-wide association studies. Male rats of BN and BN.SHR20 strains were fed a standard diet for 18 weeks (control groups) or 16 weeks of standard diet followed by 14 days of high-sucrose diet (HSD). We assessed the morphometric and metabolic profiles of all groups. Adiposity significantly increased only in BN.SHR20 after HSD. Fasting glycemia and the glucose levels during the oral glucose tolerance test were higher in BN.SHR20 than in BN groups, while insulin levels were comparable. The fasting levels of triacylglycerols were the highest in sucrose-fed BN.SHR20, both compared to the sucrose-fed BN and the control BN.SHR20. The non-esterified fatty acids and total cholesterol concentrations were higher in BN.SHR20 compared to their respective BN groups, and the HSD elicited an increase in non-esterified fatty acids only in BN.SHR20. In a new genetically defined model, we have isolated a limited genomic region involved in nutrigenetic sensitization to sucrose-induced metabolic disturbances.
Collapse
|
17
|
Niehues A, Bizzarri D, Reinders MJT, Slagboom PE, van Gool AJ, van den Akker EB, 't Hoen PAC. Metabolomic predictors of phenotypic traits can replace and complement measured clinical variables in population-scale expression profiling studies. BMC Genomics 2022; 23:546. [PMID: 35907790 PMCID: PMC9339202 DOI: 10.1186/s12864-022-08771-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Population-scale expression profiling studies can provide valuable insights into biological and disease-underlying mechanisms. The availability of phenotypic traits is essential for studying clinical effects. Therefore, missing, incomplete, or inaccurate phenotypic information can make analyses challenging and prevent RNA-seq or other omics data to be reused. A possible solution are predictors that infer clinical or behavioral phenotypic traits from molecular data. While such predictors have been developed based on different omics data types and are being applied in various studies, metabolomics-based surrogates are less commonly used than predictors based on DNA methylation profiles.In this study, we inferred 17 traits, including diabetes status and exposure to lipid medication, using previously trained metabolomic predictors. We evaluated whether these metabolomic surrogates can be used as an alternative to reported information for studying the respective phenotypes using expression profiling data of four population cohorts. For the majority of the 17 traits, the metabolomic surrogates performed similarly to the reported phenotypes in terms of effect sizes, number of significant associations, replication rates, and significantly enriched pathways.The application of metabolomics-derived surrogate outcomes opens new possibilities for reuse of multi-omics data sets. In studies where availability of clinical metadata is limited, missing or incomplete information can be complemented by these surrogates, thereby increasing the size of available data sets. Additionally, the availability of such surrogates could be used to correct for potential biological confounding. In the future, it would be interesting to further investigate the use of molecular predictors across different omics types and cohorts.
Collapse
Affiliation(s)
- Anna Niehues
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Geert Grooteplein Zuid 26-28, Nijmegen, 6525 GA, Netherlands.,Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud university medical center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, Netherlands
| | - Daniele Bizzarri
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Delft Bioinformatics Lab, TU Delft, Van Mourik Broekmanweg 6, Delft, 2628 XE, Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud university medical center, Geert Grooteplein Zuid 10, Nijmegen, 6525 GA, Netherlands
| | - Erik B van den Akker
- Molecular Epidemiology, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Leiden Computational Biology Center, LUMC, Einthovenweg 20, Leiden, 2333 ZC, Netherlands.,Delft Bioinformatics Lab, TU Delft, Van Mourik Broekmanweg 6, Delft, 2628 XE, Netherlands
| | | | | | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Geert Grooteplein Zuid 26-28, Nijmegen, 6525 GA, Netherlands.
| |
Collapse
|
18
|
Yang Z, Zhu X, Wen A, Ran J, Qin L, Zhu Y. Coix Seed-Based Milk Fermented With Limosilactobacillus reuteri Improves Lipid Metabolism and Gut Microbiota in Mice Fed With a High-Fat Diet. Front Nutr 2022; 9:921255. [PMID: 35903451 PMCID: PMC9320324 DOI: 10.3389/fnut.2022.921255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to investigate the effects of coix seed-based milk (CSM) fermented with Limosilactobacillus reuteri (L. reuteri) on dyslipidemia and the composition of the intestinal microbiota in high fat diet (HFD)-fed mice. Changes in the body weight, serum lipid levels, activities of hepatic oxidative stress factors, expression of lipid-related genes, and composition of the intestinal microbiota of HFD-fed mice after supplementation with CSM were determined. The results showed that intake of CSM reduced the body weight gain as well as serum total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) levels, and increased the high-density lipoprotein cholesterol (HDL-C) levels in the mice. Meanwhile, supplementation with CSM could relieve liver oxidative stress, down-regulate the expression of genes related to lipid synthesis, and prevent liver fat accumulation in mice fed with HFD. The 16S rRNA sequencing of the intestinal microbiota showed that CSM regulated the gut microbiota community structure at different taxonomic levels, and reversed gut dysbiosis induced by HFD. The relative abundance of Muribaculaceae, Lachnospiraceae, Dubosiella and Akkermansia which are negatively correlated with blood lipid levels were significantly increased by the intervention of CSM, while the relative abundance of Desulfovibrionaceae, Ruminococca-ceae_UCG-014, Psychrobacter, and Staphylococcus which have positive correlation with blood lipid levels were significantly decreased. These results indicated that CSM might serve as a novel and promising dietary supplement for ameliorating hyperlipidemia and intestinal microbiota disorders caused by HFDs.
Collapse
Affiliation(s)
- Zhoujie Yang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, China
| | - Xiaoli Zhu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Anyan Wen
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Jingqi Ran
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Likang Qin
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
- *Correspondence: Likang Qin
| | - Yi Zhu
- Plant Protection and Plant Quarantine Station of Guizhou Province, Guiyang, China
| |
Collapse
|
19
|
Araújo MC, Soczek SHS, Pontes JP, Marques LAC, Santos GS, Simão G, Bueno LR, Maria-Ferreira D, Muscará MN, Fernandes ES. An Overview of the TRP-Oxidative Stress Axis in Metabolic Syndrome: Insights for Novel Therapeutic Approaches. Cells 2022; 11:cells11081292. [PMID: 35455971 PMCID: PMC9030853 DOI: 10.3390/cells11081292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/19/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
Metabolic syndrome (MS) is a complex pathology characterized by visceral adiposity, insulin resistance, arterial hypertension, and dyslipidaemia. It has become a global epidemic associated with increased consumption of high-calorie, low-fibre food and sedentary habits. Some of its underlying mechanisms have been identified, with hypoadiponectinemia, inflammation and oxidative stress as important factors for MS establishment and progression. Alterations in adipokine levels may favour glucotoxicity and lipotoxicity which, in turn, contribute to inflammation and cellular stress responses within the adipose, pancreatic and liver tissues, in addition to hepatic steatosis. The multiple mechanisms of MS make its clinical management difficult, involving both non-pharmacological and pharmacological interventions. Transient receptor potential (TRP) channels are non-selective calcium channels involved in a plethora of physiological events, including energy balance, inflammation and oxidative stress. Evidence from animal models of disease has contributed to identify their specific contributions to MS and may help to tailor clinical trials for the disease. In this context, the oxidative stress sensors TRPV1, TRPA1 and TRPC5, play major roles in regulating inflammatory responses, thermogenesis and energy expenditure. Here, the interplay between these TRP channels and oxidative stress in MS is discussed in the light of novel therapies to treat this syndrome.
Collapse
Affiliation(s)
- Mizael C. Araújo
- Programa de Pós-Graduação, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (M.C.A.); (G.S.S.)
| | - Suzany H. S. Soczek
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba 80250-060, PR, Brazil; (S.H.S.S.); (G.S.); (L.R.B.); (D.M.-F.)
- Programa de Pós-Graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba 80230-020, PR, Brazil
| | - Jaqueline P. Pontes
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal do Maranhão, São Luís 565085-080, MA, Brazil;
| | - Leonardo A. C. Marques
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.A.C.M.); (M.N.M.)
| | - Gabriela S. Santos
- Programa de Pós-Graduação, Universidade CEUMA, São Luís 65075-120, MA, Brazil; (M.C.A.); (G.S.S.)
| | - Gisele Simão
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba 80250-060, PR, Brazil; (S.H.S.S.); (G.S.); (L.R.B.); (D.M.-F.)
- Programa de Pós-Graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba 80230-020, PR, Brazil
| | - Laryssa R. Bueno
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba 80250-060, PR, Brazil; (S.H.S.S.); (G.S.); (L.R.B.); (D.M.-F.)
- Programa de Pós-Graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba 80230-020, PR, Brazil
| | - Daniele Maria-Ferreira
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba 80250-060, PR, Brazil; (S.H.S.S.); (G.S.); (L.R.B.); (D.M.-F.)
- Programa de Pós-Graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba 80230-020, PR, Brazil
| | - Marcelo N. Muscará
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; (L.A.C.M.); (M.N.M.)
| | - Elizabeth S. Fernandes
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba 80250-060, PR, Brazil; (S.H.S.S.); (G.S.); (L.R.B.); (D.M.-F.)
- Programa de Pós-Graduação em Biotecnologia Aplicada à Saúde da Criança e do Adolescente, Faculdades Pequeno Príncipe, Curitiba 80230-020, PR, Brazil
- Correspondence:
| |
Collapse
|
20
|
Fisher JL, Jones EF, Flanary VL, Williams AS, Ramsey EJ, Lasseigne BN. Considerations and challenges for sex-aware drug repurposing. Biol Sex Differ 2022; 13:13. [PMID: 35337371 PMCID: PMC8949654 DOI: 10.1186/s13293-022-00420-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/06/2022] [Indexed: 01/09/2023] Open
Abstract
Sex differences are essential factors in disease etiology and manifestation in many diseases such as cardiovascular disease, cancer, and neurodegeneration [33]. The biological influence of sex differences (including genomic, epigenetic, hormonal, immunological, and metabolic differences between males and females) and the lack of biomedical studies considering sex differences in their study design has led to several policies. For example, the National Institute of Health's (NIH) sex as a biological variable (SABV) and Sex and Gender Equity in Research (SAGER) policies to motivate researchers to consider sex differences [204]. However, drug repurposing, a promising alternative to traditional drug discovery by identifying novel uses for FDA-approved drugs, lacks sex-aware methods that can improve the identification of drugs that have sex-specific responses [7, 11, 14, 33]. Sex-aware drug repurposing methods either select drug candidates that are more efficacious in one sex or deprioritize drug candidates based on if they are predicted to cause a sex-bias adverse event (SBAE), unintended therapeutic effects that are more likely to occur in one sex. Computational drug repurposing methods are encouraging approaches to develop for sex-aware drug repurposing because they can prioritize sex-specific drug candidates or SBAEs at lower cost and time than traditional drug discovery. Sex-aware methods currently exist for clinical, genomic, and transcriptomic information [1, 7, 155]. They have not expanded to other data types, such as DNA variation, which has been beneficial in other drug repurposing methods that do not consider sex [114]. Additionally, some sex-aware methods suffer from poorer performance because a disproportionate number of male and female samples are available to train computational methods [7]. However, there is development potential for several different categories (i.e., data mining, ligand binding predictions, molecular associations, and networks). Low-dimensional representations of molecular association and network approaches are also especially promising candidates for future sex-aware drug repurposing methodologies because they reduce the multiple hypothesis testing burden and capture sex-specific variation better than the other methods [151, 159]. Here we review how sex influences drug response, the current state of drug repurposing including with respect to sex-bias drug response, and how model organism study design choices influence drug repurposing validation.
Collapse
Affiliation(s)
- Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Avery S. Williams
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Elizabeth J. Ramsey
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| |
Collapse
|
21
|
Guru A, Velayutham M, Arockiaraj J. Lipid-Lowering and Antioxidant Activity of RF13 Peptide From Vacuolar Protein Sorting-Associated Protein 26B (VPS26B) by Modulating Lipid Metabolism and Oxidative Stress in HFD Induced Obesity in Zebrafish Larvae. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10376-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
22
|
Ren T, Guo X, Zhang J, Liu Z. Pyroptosis-Related Signatures for Predicting Prognosis in Breast Cancer. Front Surg 2022; 9:788437. [PMID: 35211500 PMCID: PMC8861281 DOI: 10.3389/fsurg.2022.788437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundFemale breast cancer (BC) has become the most common cancer in the world, and its mortality was considerably higher in transitioning vs. transitioned countries. Pyroptosis, an inflammation-dependent programmed cell death mediated by inflammasomes, has been observed in human colorectal tumors and gliomas. However, the characteristics of pyrolysis-related genes and their influence and mechanism on the tumorigenesis and progress of BC were unknown.MethodsBased on the global public database, we used comprehensive bioinformatics analysis to systematically analyze the expression of pyroptosis-related genes in BC and their relationship in tumor progression. In addition, BC patients were divided into two groups, and the clinical features and outcomes could be better predicted by the consistent clustering of pyroptosis-related genes. Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was used to establish a risk score. Then, we further explored the prognostic value and clinical features of pyroptosis genes. Finally, we used the Human Protein Atlas (HPA) platform to identify the expression at protein levels of the key genes.ResultsWe confirmed that the expression of pyroptosis-related genes was different in BC and normal breast tissues. A high frequency of somatic mutations occurred in BC. In addition, 33 pyroptosis-related proteins interacted frequently. Based on univariate analysis and the LASSO Cox model, five pyroptosis-related genes [including GADMA, interleukin-6 (IL-6), NLR pyrin domain-containing protein 6 (NLRP6), caspase-1 (CASP1), and caspase-9 (CASP9)], were obtained to calculate a risk score. The risk score was identified as an independent risk factor for the prognosis of BC and might play an auxiliary role in clinical classification. The HPA platform confirmed that the expression trends of the key genes were consistent with our previous studies.ConclusionPyroptosis had an important effect on the progression of BC. And the pyroptosis-related genes could be used as new prognostic biomarkers and therapeutic targets for BC.
Collapse
|
23
|
Network-Based Approach to Repurpose Approved Drugs for COVID-19 by Integrating GWAS and Text Mining Data. Processes (Basel) 2022. [DOI: 10.3390/pr10020326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has a rapidly increasing prevalence and has caused significant morbidity/mortality. Despite the availability of many vaccines that can offer widespread immunization, it is also important to reach effective treatment for COVID-19 patients. However, the development of novel drug therapeutics is usually a time-consuming and costly process, and therefore, repositioning drugs that were previously approved for other purposes could have a major impact on the fight against COVID-19. Here, we first identified lung-specific gene regulatory/interaction subnetworks (COVID-19-related genes modules) enriched for COVID-19-associated genes obtained from GWAS and text mining. We then screened the targets of 220 approved drugs from DrugBank, obtained their drug-induced gene expression profiles in the LINCS database, and constructed lung-specific drug-related gene modules. By applying an integrated network-based approach to quantify the interactions of the COVID-19-related gene modules and drug-related gene modules, we prioritized 13 approved drugs (e.g., alitretinoin, clocortolone, terazosin, doconexent, and pergolide) that could potentially be repurposed for the treatment of COVID-19. These findings provide important and timely insights into alternative therapeutic options that should be further explored as COVID-19 continues to spread.
Collapse
|
24
|
Popescu VB, Kanhaiya K, Năstac DI, Czeizler E, Petre I. Network controllability solutions for computational drug repurposing using genetic algorithms. Sci Rep 2022; 12:1437. [PMID: 35082323 PMCID: PMC8791995 DOI: 10.1038/s41598-022-05335-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/29/2021] [Indexed: 12/22/2022] Open
Abstract
Control theory has seen recently impactful applications in network science, especially in connections with applications in network medicine. A key topic of research is that of finding minimal external interventions that offer control over the dynamics of a given network, a problem known as network controllability. We propose in this article a new solution for this problem based on genetic algorithms. We tailor our solution for applications in computational drug repurposing, seeking to maximize its use of FDA-approved drug targets in a given disease-specific protein-protein interaction network. We demonstrate our algorithm on several cancer networks and on several random networks with their edges distributed according to the Erdős-Rényi, the Scale-Free, and the Small World properties. Overall, we show that our new algorithm is more efficient in identifying relevant drug targets in a disease network, advancing the computational solutions needed for new therapeutic and drug repurposing approaches.
Collapse
Affiliation(s)
| | | | - Dumitru Iulian Năstac
- POLITEHNICA University of Bucharest, Faculty of Electronics, Telecommunications and Information Technology, 061071, Bucharest, Romania
| | - Eugen Czeizler
- Computer Science, Åbo Akademi University, 20500, Turku, Finland
- National Institute for Research and Development in Biological Sciences, 060031, Bucharest, Romania
| | - Ion Petre
- Department of Mathematics and Statistics, University of Turku, 20014, Turku, Finland.
- National Institute for Research and Development in Biological Sciences, 060031, Bucharest, Romania.
| |
Collapse
|
25
|
Diversity: current and prospective secondary metabolites for nutrition and medicine. Curr Opin Biotechnol 2021; 74:164-170. [PMID: 34942505 DOI: 10.1016/j.copbio.2021.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/28/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022]
Abstract
Plants have been used as sources of food, feed and medicine for millennia. The ever-increasing population has, however, dramatically increased the burden on our arable land to meet nutritional demand. Concomitantly, and in part due to poor nutrition, we are faced with massive increases in chronic diseases, meaning the need for medicine has also increased. Here, we look back on research in these areas, surveying the polyphenols as a case study for health-conferring metabolites. We conclude that the tools that will allow us to breed more nutritious crops are all at hand. We stress that collaboration between plant and medical research needs to be intensified in order to improve our understanding of the bioactivities. In doing so, we attempt to draw a roadmap for the use of plants for mid-21st Century human health.
Collapse
|
26
|
Hung JC, Wu JL, Li HC, Chiu HW, Hong JR. The Proapoptotic Gene Bad Regulates Brain Development via p53-Mediated Stress Signals in Zebrafish. Cells 2021; 10:cells10112820. [PMID: 34831043 PMCID: PMC8616466 DOI: 10.3390/cells10112820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 01/01/2023] Open
Abstract
Studies have shown that the BH3-only domain Bad regulates brain development via the control of programmed cell death (PCD), but very few studies have addressed its effect on the molecular signaling of brain development in the system. In this work, we examined the novel role of zebrafish Bad in initial programmed cell death for brain morphogenesis through the priming of p53-mediated stress signaling. In a biological function study on the knockdown of Bad by morpholino oligonucleotides, at 24 h post-fertilization (hpf) Bad defects induced abnormal hindbrain development, as determined in a tissue section by means of HE staining which traced the damaged hindbrain. Then, genome-wide approaches for monitoring either the upregulation of apoptotic-related genes (11.8%) or the downregulation of brain development-related genes (29%) at the 24 hpf stage were implemented. The p53/caspase-8-mediated apoptotic death pathway was strongly involved, with the pathway being strongly reversed in a p53 mutant (p53M214K) line during Bad knockdown. Furthermore, we propose the involvement of a p53-mediated stress signal which is correlated with regulating Bad loss-mediated brain defects. We found that some major genes in brain development, such as crybb1, pva1b5, irx4a, pax7a, and fabp7a, were dramatically restored in the p53M214K line, and brain development recovered to return movement behavior to normal. Our findings suggest that Bad is required for (PCD) control, exerting a p53 stress signal on caspase-8/tBid-mediated death signaling and brain development-related gene regulation.
Collapse
Affiliation(s)
- Jo-Chi Hung
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; (J.-C.H.); (H.-C.L.); (H.-W.C.)
| | - Jen-Leih Wu
- Laboratory of Marine Molecular Biology and Biotechnology, Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei 115, Taiwan;
| | - Huei-Ching Li
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; (J.-C.H.); (H.-C.L.); (H.-W.C.)
| | - Hsuan-Wen Chiu
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; (J.-C.H.); (H.-C.L.); (H.-W.C.)
| | - Jiann-Ruey Hong
- Laboratory of Molecular Virology and Biotechnology, Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan; (J.-C.H.); (H.-C.L.); (H.-W.C.)
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Correspondence: ; Tel.: +886-6-2003082; Fax: +886-6-2766505
| |
Collapse
|
27
|
Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
Collapse
Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| |
Collapse
|
28
|
Pan Y, Lei X, Zhang Y. Association predictions of genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, radiomics, drug, symptoms, environment factor, and disease networks: A comprehensive approach. Med Res Rev 2021; 42:441-461. [PMID: 34346083 DOI: 10.1002/med.21847] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 05/22/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Currently, the research of multi-omics, such as genomics, proteinomics, transcriptomics, microbiome, metabolomics, pathomics, and radiomics, are hot spots. The relationship between multi-omics data, drugs, and diseases has received extensive attention from researchers. At the same time, multi-omics can effectively predict the diagnosis, prognosis, and treatment of diseases. In essence, these research entities, such as genes, RNAs, proteins, microbes, metabolites, pathways as well as pathological and medical imaging data, can all be represented by the network at different levels. And some computer and biology scholars have tried to use computational methods to explore the potential relationships between biological entities. We summary a comprehensive research strategy, that is to build a multi-omics heterogeneous network, covering multimodal data, and use the current popular computational methods to make predictions. In this study, we first introduce the calculation method of the similarity of biological entities at the data level, second discuss multimodal data fusion and methods of feature extraction. Finally, the challenges and opportunities at this stage are summarized. Some scholars have used such a framework to calculate and predict. We also summarize them and discuss the challenges. We hope that our review could help scholars who are interested in the field of bioinformatics, biomedical image, and computer research.
Collapse
Affiliation(s)
- Yi Pan
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yuchen Zhang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| |
Collapse
|
29
|
Rao B, Li J, Ren T, Yang J, Zhang G, Liu L, Wang H, Huang M, Ren Z, Yu Z. RPL19 Is a Prognostic Biomarker and Promotes Tumor Progression in Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:686547. [PMID: 34350180 PMCID: PMC8327752 DOI: 10.3389/fcell.2021.686547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/30/2021] [Indexed: 01/07/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignancies, and the therapeutic outcome remains undesirable due to its recurrence and metastasis. Gene dysregulation plays a pivotal role in the occurrence and progression of cancer, and the molecular mechanisms are largely unknown. Methods The differentially expressed genes of HCC screened from the GSE39791 dataset were used to conduct weighted gene co-expression network analysis. The selected hub genes were validated in The Cancer Genome Atlas (TCGA) database and 11 HCC datasets from the Gene Expression Omnibus (GEO) database. Then, a tissue microarray comprising 90 HCC specimens and 90 adjacent normal specimens was used to validate the hub genes. Moreover, the Hallmark, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to identify enriched pathways. Then, we conducted the immune infiltration analysis. Results A total of 17 co-expression modules were obtained by weighted gene co-expression network analysis. The green, blue, and purple modules were the most relevant to HCC samples. Four hub genes, RPL19, RPL35A, RPL27A, and RPS12, were identified. Interestingly, we found that all four genes were highly expressed in HCC and that their high expression was related to a poor prognosis by analyzing the TCGA and GEO databases. Furthermore, we investigated RPL19 in HCC tissue microarrays and demonstrated that RPL19 was overexpressed in tumor tissues compared with non-tumor tissues (p = 0.016). Moreover, overexpression of RPL19 predicted a poor prognosis in hepatocellular carcinoma (p < 0.0007). Then, enrichment analysis revealed that cell cycle pathways were significantly enriched, and bile acid metabolism-related pathways were significantly down-regulated when RPL19 was highly expressed. Furthermore, immune infiltration analysis showed that immune response was suppressed. Conclusion Our study demonstrates that RPL19 may play an important role in promoting tumor progression and is correlated with a poor prognosis in HCC. RPL19 may serve as a promising biomarker and therapeutic target for the precise diagnosis and treatment of HCC in the future.
Collapse
Affiliation(s)
- Benchen Rao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianhao Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Ren
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guizhen Zhang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liwen Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Maoxin Huang
- Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
30
|
Wang G, Miao Y, Kim N, Sweren E, Kang S, Hu Z, Garza LA. Association of the Psoriatic Microenvironment With Treatment Response. JAMA Dermatol 2021; 156:1057-1065. [PMID: 32876657 DOI: 10.1001/jamadermatol.2020.2118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance The ability to predict the efficacy of systemic psoriasis therapy based on immune profiles in skin biopsies could reduce the use of inappropriate treatment and its associated costs and adverse events. It could considerably decrease drug development trial costs as well. Objective To develop a bioinformatic gene signature score derived from skin mRNA to predict psoriasis treatment outcomes for a variety of therapies. Design, Setting, and Participants In this decision analytical model using 1145 skin samples from different cohorts of 12 retrospective psoriasis studies, samples were analyzed using the CIBERSORT algorithm to define the immune landscape of psoriasis lesions and controls. Random forest classification and principal component analysis algorithms were used to estimate psoriatic microenvironment (PME) signature genes and construct a PME score. Overall, 85 and 421 psoriasis lesions from 1 and 4 independent cohorts were used as discovery and validation studies, respectively. Among them, 157, 71, 89, and 90 psoriasis lesions were treated with etanercept, tofacitinib, adalimumab, and methotrexate, respectively. Main Outcomes and Measures Number of weeks after treatment initiation when responders and nonresponders could be predicted. Results Overall, 22 immune cell subtypes formed infiltration patterns that differentiated psoriasis lesions from healthy skin. In psoriasis lesions, the expression of 33 PME signature genes defined 2 immune phenotypes and in aggregate could be simplified to a numerical PME score. A high PME score, characterized by keratinocyte differentiation, correlated with a better treatment response (Psoriasis Area and Severity Index [PASI] reduction, 75.8%; 95% CI, 69.4% to 82.2%; P = .03), whereas a low PME score exhibited an immune activation signature and was associated with a worse response (PASI reduction, 53.5%; 95% CI, 45.3% to 61.7%; P = .03). The PME score at week 4 after treatment initiation correlated with future responder vs nonresponder to treatment status 8 to 12 weeks earlier than PASI reduction for etanercept, methotrexate plus adalimumab, and tofacitinib. Conclusions and Relevance The PME score is a biometric score that may predict clinical efficacy of systemic psoriasis therapy in advance of clinical responses. As an application of personalized medicine, it may reduce the exposure of patients with psoriasis to ineffective and expensive therapies.
Collapse
Affiliation(s)
- Gaofeng Wang
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China.,Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Yong Miao
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Noori Kim
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Evan Sweren
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Zhiqi Hu
- Department of Plastic and Aesthetic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Luis A Garza
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| |
Collapse
|
31
|
Pokhilko A, Handel AE, Curion F, Volpato V, Whiteley ES, Bøstrand S, Newey SE, Akerman CJ, Webber C, Clark MB, Bowden R, Cader MZ. Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories. Genome Res 2021; 31:1069-1081. [PMID: 34011578 PMCID: PMC8168586 DOI: 10.1101/gr.273961.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterogeneous samples, but it is limited in its detection and quantification of lowly expressed genes. This results in missing important biological signals, such as the expression of key transcription factors (TFs) driving cellular differentiation. We show that targeted sequencing of ∼1000 TFs (scCapture-seq) in iPSC-derived neuronal cultures greatly improves the biological information garnered from scRNA-seq. Increased TF resolution enhanced cell type identification, developmental trajectories, and gene regulatory networks. This allowed us to resolve differences among neuronal populations, which were generated in two different laboratories using the same differentiation protocol. ScCapture-seq improved TF-gene regulatory network inference and thus identified divergent patterns of neurogenesis into either excitatory cortical neurons or inhibitory interneurons. Furthermore, scCapture-seq revealed a role for of retinoic acid signaling in the developmental divergence between these different neuronal populations. Our results show that TF targeting improves the characterization of human cellular models and allows identification of the essential differences between cellular populations, which would otherwise be missed in traditional scRNA-seq. scCapture-seq TF targeting represents a cost-effective enhancement of scRNA-seq, which could be broadly applied to improve scRNA-seq resolution.
Collapse
Affiliation(s)
- Alexandra Pokhilko
- Translational Molecular Neuroscience Group, Weatherall Institute of Molecular Medicine, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Adam E Handel
- Translational Molecular Neuroscience Group, Weatherall Institute of Molecular Medicine, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Fabiola Curion
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Viola Volpato
- UK Dementia Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
| | - Emma S Whiteley
- Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - Sunniva Bøstrand
- Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - Sarah E Newey
- Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - Colin J Akerman
- Department of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - Caleb Webber
- UK Dementia Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
| | - Michael B Clark
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, OX3 7JX, United Kingdom.,Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom.,The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,University of Melbourne, Department of Medical Biology, Parkville, Victoria 3052, Australia
| | - M Zameel Cader
- Translational Molecular Neuroscience Group, Weatherall Institute of Molecular Medicine, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DS, United Kingdom
| |
Collapse
|
32
|
Saydmohammed M, Jha A, Mahajan V, Gavlock D, Shun TY, DeBiasio R, Lefever D, Li X, Reese C, Kershaw EE, Yechoor V, Behari J, Soto-Gutierrez A, Vernetti L, Stern A, Gough A, Miedel MT, Lansing Taylor D. Quantifying the progression of non-alcoholic fatty liver disease in human biomimetic liver microphysiology systems with fluorescent protein biosensors. Exp Biol Med (Maywood) 2021; 246:2420-2441. [PMID: 33957803 PMCID: PMC8606957 DOI: 10.1177/15353702211009228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metabolic syndrome is a complex disease that involves multiple organ systems including a critical role for the liver. Non-alcoholic fatty liver disease (NAFLD) is a key component of the metabolic syndrome and fatty liver is linked to a range of metabolic dysfunctions that occur in approximately 25% of the population. A panel of experts recently agreed that the acronym, NAFLD, did not properly characterize this heterogeneous disease given the associated metabolic abnormalities such as type 2 diabetes mellitus (T2D), obesity, and hypertension. Therefore, metabolic dysfunction-associated fatty liver disease (MAFLD) has been proposed as the new term to cover the heterogeneity identified in the NAFLD patient population. Although many rodent models of NAFLD/NASH have been developed, they do not recapitulate the full disease spectrum in patients. Therefore, a platform has evolved initially focused on human biomimetic liver microphysiology systems that integrates fluorescent protein biosensors along with other key metrics, the microphysiology systems database, and quantitative systems pharmacology. Quantitative systems pharmacology is being applied to investigate the mechanisms of NAFLD/MAFLD progression to select molecular targets for fluorescent protein biosensors, to integrate computational and experimental methods to predict drugs for repurposing, and to facilitate novel drug development. Fluorescent protein biosensors are critical components of the platform since they enable monitoring of the pathophysiology of disease progression by defining and quantifying the temporal and spatial dynamics of protein functions in the biosensor cells, and serve as minimally invasive biomarkers of the physiological state of the microphysiology system experimental disease models. Here, we summarize the progress in developing human microphysiology system disease models of NAFLD/MAFLD from several laboratories, developing fluorescent protein biosensors to monitor and to measure NAFLD/MAFLD disease progression and implementation of quantitative systems pharmacology with the goal of repurposing drugs and guiding the creation of novel therapeutics.
Collapse
Affiliation(s)
- Manush Saydmohammed
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Anupma Jha
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vineet Mahajan
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dillon Gavlock
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Richard DeBiasio
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniel Lefever
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiang Li
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Celeste Reese
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erin E Kershaw
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vijay Yechoor
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jaideep Behari
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Pittsburgh, PA 15261, USA
- UPMC Liver Clinic, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alejandro Soto-Gutierrez
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Larry Vernetti
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Andrew Stern
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Albert Gough
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mark T Miedel
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| |
Collapse
|
33
|
Liu DY, Liu JC, Liang S, Meng XH, Greenbaum J, Xiao HM, Tan LJ, Deng HW. Drug Repurposing for COVID-19 Treatment by Integrating Network Pharmacology and Transcriptomics. Pharmaceutics 2021; 13:545. [PMID: 33919660 PMCID: PMC8069812 DOI: 10.3390/pharmaceutics13040545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Since coronavirus disease 2019 (COVID-19) is a serious new worldwide public health crisis with significant morbidity and mortality, effective therapeutic treatments are urgently needed. Drug repurposing is an efficient and cost-effective strategy with minimum risk for identifying novel potential treatment options by repositioning therapies that were previously approved for other clinical outcomes. Here, we used an integrated network-based pharmacologic and transcriptomic approach to screen drug candidates novel for COVID-19 treatment. Network-based proximity scores were calculated to identify the drug-disease pharmacological effect between drug-target relationship modules and COVID-19 related genes. Gene set enrichment analysis (GSEA) was then performed to determine whether drug candidates influence the expression of COVID-19 related genes and examine the sensitivity of the repurposing drug treatment to peripheral immune cell types. Moreover, we used the complementary exposure model to recommend potential synergistic drug combinations. We identified 18 individual drug candidates including nicardipine, orantinib, tipifarnib and promethazine which have not previously been proposed as possible treatments for COVID-19. Additionally, 30 synergistic drug pairs were ultimately recommended including fostamatinib plus tretinoin and orantinib plus valproic acid. Differential expression genes of most repurposing drugs were enriched significantly in B cells. The findings may potentially accelerate the discovery and establishment of an effective therapeutic treatment plan for COVID-19 patients.
Collapse
Affiliation(s)
- Dan-Yang Liu
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China;
| | - Jia-Chen Liu
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (J.-C.L.); (S.L.); (X.-H.M.); (H.-M.X.)
| | - Shuang Liang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (J.-C.L.); (S.L.); (X.-H.M.); (H.-M.X.)
| | - Xiang-He Meng
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (J.-C.L.); (S.L.); (X.-H.M.); (H.-M.X.)
| | - Jonathan Greenbaum
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (J.-C.L.); (S.L.); (X.-H.M.); (H.-M.X.)
| | - Li-Jun Tan
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China;
| | - Hong-Wen Deng
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha 410081, China;
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (J.-C.L.); (S.L.); (X.-H.M.); (H.-M.X.)
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA;
| |
Collapse
|
34
|
Sarno F, Benincasa G, List M, Barabasi AL, Baumbach J, Ciardiello F, Filetti S, Glass K, Loscalzo J, Marchese C, Maron BA, Paci P, Parini P, Petrillo E, Silverman EK, Verrienti A, Altucci L, Napoli C. Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside. Clin Epigenetics 2021; 13:66. [PMID: 33785068 PMCID: PMC8010949 DOI: 10.1186/s13148-021-01047-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Despite impressive efforts invested in epigenetic research in the last 50 years, clinical applications are still lacking. Only a few university hospital centers currently use epigenetic biomarkers at the bedside. Moreover, the overall concept of precision medicine is not widely recognized in routine medical practice and the reductionist approach remains predominant in treating patients affected by major diseases such as cancer and cardiovascular diseases. By its' very nature, epigenetics is integrative of genetic networks. The study of epigenetic biomarkers has led to the identification of numerous drugs with an increasingly significant role in clinical therapy especially of cancer patients. Here, we provide an overview of clinical epigenetics within the context of network analysis. We illustrate achievements to date and discuss how we can move from traditional medicine into the era of network medicine (NM), where pathway-informed molecular diagnostics will allow treatment selection following the paradigm of precision medicine.
Collapse
Affiliation(s)
- Federica Sarno
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Giuditta Benincasa
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Albert-Lazlo Barabasi
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
- Chair of Computational Systems Biology, University of Hamburg, Notkestrasse 9, Hamburg, Germany
| | - Fortunato Ciardiello
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy
| | | | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Bradley A Maron
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paola Paci
- Department of Computer, Control, and Management Engineering, Sapienza University, Rome, Italy
| | - Paolo Parini
- Department of Laboratory Medicine and Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Enrico Petrillo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonella Verrienti
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Napoli, Italy.
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Department of Internal Medicine and Specialistic Units, AOU, University of Campania "Luigi Vanvitelli", Naples, Italy
| |
Collapse
|
35
|
Zebrafish as an animal model for biomedical research. Exp Mol Med 2021; 53:310-317. [PMID: 33649498 PMCID: PMC8080808 DOI: 10.1038/s12276-021-00571-5] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Zebrafish have several advantages compared to other vertebrate models used in modeling human diseases, particularly for large-scale genetic mutant and therapeutic compound screenings, and other biomedical research applications. With the impactful developments of CRISPR and next-generation sequencing technology, disease modeling in zebrafish is accelerating the understanding of the molecular mechanisms of human genetic diseases. These efforts are fundamental for the future of precision medicine because they provide new diagnostic and therapeutic solutions. This review focuses on zebrafish disease models for biomedical research, mainly in developmental disorders, mental disorders, and metabolic diseases.
Collapse
|
36
|
Gimenez N, Tripathi R, Giró A, Rosich L, López-Guerra M, López-Oreja I, Playa-Albinyana H, Arenas F, Mas JM, Pérez-Galán P, Delgado J, Campo E, Farrés J, Colomer D. Systems biology drug screening identifies statins as enhancers of current therapies in chronic lymphocytic leukemia. Sci Rep 2020; 10:22153. [PMID: 33335123 PMCID: PMC7746765 DOI: 10.1038/s41598-020-78315-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a B lymphoid malignancy highly dependent on the microenvironment. Despite new targeted therapies such as ibrutinib and venetoclax, disease progression and relapse remain an issue. CLL cell interactions with the supportive tissue microenvironment play a critical role in disease pathogenesis. We used a platform for drug discovery based on systems biology and artificial intelligence, to identify drugs targeting key proteins described to have a role in the microenvironment. The selected compounds were screened in CLL cell lines in the presence of stromal cells to mimic the microenvironment and validated the best candidates in primary CLL cells. Our results showed that the commercial drug simvastatin was the most effective and selective out of the tested compounds. Simvastatin decreased CLL cell survival and proliferation as well as cell adhesion. Importantly, this drug enhanced the antitumor effect of venetoclax and ibrutinib. We proposed that systems biology approaches combined with pharmacological screening could help to find new drugs for CLL treatment and to predict new combinations with current therapies. Our results highlight the possibility of repurposing widely used drugs such as statins to target the microenvironment and to improve the efficacy of ibrutinib or venetoclax in CLL cells.
Collapse
Affiliation(s)
- Neus Gimenez
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Anaxomics Biotech, Barcelona, Spain
| | - Rupal Tripathi
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ariadna Giró
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Laia Rosich
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Mònica López-Guerra
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Irene López-Oreja
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Fabian Arenas
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | | | - Patricia Pérez-Galán
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Microenvironment in Lymphoma Pathogenesis and Therapy Group, IDIBAPS, Barcelona, Spain
| | - Julio Delgado
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Department of Hematology, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Elias Campo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain.,University of Barcelona, Barcelona, Spain
| | | | - Dolors Colomer
- Experimental Therapeutics in Lymphoid Malignancies Group, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain. .,Hematopathology Unit, Department of Pathology, Hospital Clinic, IDIBAPS, Barcelona, Spain. .,University of Barcelona, Barcelona, Spain.
| |
Collapse
|
37
|
Liu Y, Jin J, Chen Y, Chen C, Chen Z, Xu L. Integrative analyses of biomarkers and pathways for adipose tissue after bariatric surgery. Adipocyte 2020; 9:384-400. [PMID: 32684073 PMCID: PMC7469525 DOI: 10.1080/21623945.2020.1795434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We explored potential biomarkers and molecular mechanisms regarding multiple benefits after bariatric surgery. Differentially expressed genes (DEGs) for subcutaneous adipose tissue (AT) after bariatric surgery were identified by analyzing two expression profiles from the GEO. Subsequently, enrichment analysis, GSEA, PPI network, and gene-microRNAs and gene-TFs networks were interrogated to identify hub genes and associated pathways. Co-expressed DEGs included one that was up-regulated and 22 that were down-regulated genes. The enrichment analyses indicated that down-regulated DEGs were significantly involved in inflammatory responses. GSEA provided comprehensive evidence that most genes enriched in pro-inflammation pathways, while gene-sets after surgery enriched in metabolism. We identified nine hub genes in the PPI network, most of which were validated as highly expressed and hypomethylated in obesity by Attie Lab Diabetes and DiseaseMeth databases, respectively. DGIdb was also applied to predict potential therapeutic agents that might reverse abnormally high hub gene expression. Bariatric surgery induces a significant shift from an obese pro-inflammatory state to an anti-inflammatory state, with improvement in adipocyte metabolic function – representing key mechanisms whereby AT function improves after bariatric surgery. Our study deepens a mechanistic understanding of the benefits of bariatric surgery and provides potential biomarkers or treatment targets for further research.
Collapse
Affiliation(s)
- Yingshan Liu
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jing Jin
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yanshan Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chuna Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhenguo Chen
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Lingling Xu
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| |
Collapse
|
38
|
Rivas-Barragan D, Mubeen S, Guim Bernat F, Hofmann-Apitius M, Domingo-Fernández D. Drug2ways: Reasoning over causal paths in biological networks for drug discovery. PLoS Comput Biol 2020; 16:e1008464. [PMID: 33264280 PMCID: PMC7735677 DOI: 10.1371/journal.pcbi.1008464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 12/14/2020] [Accepted: 10/23/2020] [Indexed: 12/24/2022] Open
Abstract
Elucidating the causal mechanisms responsible for disease can reveal potential therapeutic targets for pharmacological intervention and, accordingly, guide drug repositioning and discovery. In essence, the topology of a network can reveal the impact a drug candidate may have on a given biological state, leading the way for enhanced disease characterization and the design of advanced therapies. Network-based approaches, in particular, are highly suited for these purposes as they hold the capacity to identify the molecular mechanisms underlying disease. Here, we present drug2ways, a novel methodology that leverages multimodal causal networks for predicting drug candidates. Drug2ways implements an efficient algorithm which reasons over causal paths in large-scale biological networks to propose drug candidates for a given disease. We validate our approach using clinical trial information and demonstrate how drug2ways can be used for multiple applications to identify: i) single-target drug candidates, ii) candidates with polypharmacological properties that can optimize multiple targets, and iii) candidates for combination therapy. Finally, we make drug2ways available to the scientific community as a Python package that enables conducting these applications on multiple standard network formats.
Collapse
Affiliation(s)
- Daniel Rivas-Barragan
- Barcelona Supercomputing Center, Barcelona, Spain
- Computer Architecture Department, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sarah Mubeen
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Fraunhofer Center for Machine Learning, Germany
| | | | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
- Fraunhofer Center for Machine Learning, Germany
| |
Collapse
|
39
|
Serrablo-Torrejon I, Lopez-Valenciano A, Ayuso M, Horton E, Mayo X, Medina-Gomez G, Liguori G, Jimenez A. High intensity interval training exercise-induced physiological changes and their potential influence on metabolic syndrome clinical biomarkers: a meta-analysis. BMC Endocr Disord 2020; 20:167. [PMID: 33172413 PMCID: PMC7653723 DOI: 10.1186/s12902-020-00640-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/20/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Despite the current debate about the effects of high intensity interval training (HIIT), HIIT elicits big morpho-physiological benefit on Metabolic Syndrome (MetS) treatment. However, no review or meta-analysis has compared the effects of HIIT to non-exercising controls in MetS variables. The aim of this study was to determine through a systematic review, the effectiveness of HIIT on MetS clinical variables in adults. METHODS Studies had to be randomised controlled trials, lasting at least 3 weeks, and compare the effects of HIIT on at least one of the MetS clinical variables [fasting blood glucose (BG), high-density lipoprotein (HDL-C) triglyceride (TG), systolic (SBP) or diastolic blood pressure (DBP) and waist circumference (WC)] compared to a control group. The methodological quality of the studies selected was evaluated using the PEDro scale. RESULTS Ten articles fulfilled the selection criteria, with a mean quality score on the PEDro scale of 6.7. Compared with controls, HIIT groups showed significant and relevant reductions in BG (- 0.11 mmol/L), SBP (- 4.44 mmHg), DBP (- 3.60 mmHg), and WC (- 2.26 cm). Otherwise, a slight increase was observed in HDL-C (+ 0.02 mmol/L). HIIT did not produce any significant changes in TG (- 1.29 mmol/L). CONCLUSIONS HIIT improves certain clinical aspects in people with MetS (BG, SBP, DBP and WC) compared to people with MetS who do not perform physical exercise. Plausible physiological changes of HIIT interventions might be related with large skeletal muscle mass implication, improvements in the vasomotor control, better baroreflex control, reduction of the total peripheral resistance, increases in excess post-exercise oxygen consumption, and changes in appetite and satiety mechanisms.
Collapse
Affiliation(s)
- I Serrablo-Torrejon
- Faculty Research Centre for Sport, Exercise & Life Sciences, School of Health and Life Sciences, Coventry University, Coventry, UK.
- GO fit LAB, Av. Islas de Filipinas, 7, 28003, Madrid, Spain.
| | - A Lopez-Valenciano
- GO fit LAB, Av. Islas de Filipinas, 7, 28003, Madrid, Spain
- Observatory of Healthy & Active Living, Spain Active Foundation, Centre for Sport Studies, King Juan Carlos University, Madrid, Spain
| | - M Ayuso
- GO fit LAB, Av. Islas de Filipinas, 7, 28003, Madrid, Spain
| | - E Horton
- Faculty Research Centre for Sport, Exercise & Life Sciences, School of Health and Life Sciences, Coventry University, Coventry, UK
| | - X Mayo
- GO fit LAB, Av. Islas de Filipinas, 7, 28003, Madrid, Spain
- Observatory of Healthy & Active Living, Spain Active Foundation, Centre for Sport Studies, King Juan Carlos University, Madrid, Spain
| | - G Medina-Gomez
- Observatory of Healthy & Active Living, Spain Active Foundation, Centre for Sport Studies, King Juan Carlos University, Madrid, Spain
| | - G Liguori
- University of Rhode Island, Kingston, RI, USA
| | - A Jimenez
- GO fit LAB, Av. Islas de Filipinas, 7, 28003, Madrid, Spain
- Observatory of Healthy & Active Living, Spain Active Foundation, Centre for Sport Studies, King Juan Carlos University, Madrid, Spain
- Advanced Wellbeing Research Centre, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield, UK
| |
Collapse
|
40
|
Priami C. Computational approaches to understanding nutrient metabolism and metabolic disorders. Curr Opin Biotechnol 2020; 70:7-14. [PMID: 33038781 DOI: 10.1016/j.copbio.2020.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/01/2020] [Accepted: 09/06/2020] [Indexed: 10/23/2022]
Abstract
Computational methods are becoming more and more essential to elucidate biological systems. Many different approaches exist with pros and cons. This paper reviews the most useful technologies focusing on nutrient metabolism and metabolic disorders. Space limitation prevents from exploring the examples in details, but pointers to the relevant papers are reported.
Collapse
Affiliation(s)
- Corrado Priami
- Dipartimento di Informatica, Università di Pisa, Largo Pontecorvo, 56124 Pisa, Italy.
| |
Collapse
|
41
|
Molica S, Lentini M, Zappalà D, Levato L. Effects of ibrutinib on glucose-lipid metabolism in patients with chronic lymphocytic leukemia (CLL). Leuk Lymphoma 2020; 61:2778-2780. [PMID: 32543252 DOI: 10.1080/10428194.2020.1779258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Stefano Molica
- Department Haematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - Mirella Lentini
- Department Haematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - Daniela Zappalà
- Department Haematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - Luciano Levato
- Department Haematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| |
Collapse
|
42
|
Wang D, Tian L, Shi C, Wei YX, Wang H, Liu TT, Gong M, Zhang YW, Yu RG, Wu XH. Network pharmacology-based prediction of the active ingredients and mechanism of Shen Gui capsule for application to coronary heart disease. Comput Biol Med 2020; 122:103825. [PMID: 32658730 DOI: 10.1016/j.compbiomed.2020.103825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Shen Gui capsule (SGC) is a new national drug in China that is widely used in clinical practice and has significant therapeutic effects on coronary heart disease (CHD). However, its active ingredients and mechanism of action for treating coronary heart disease remain unknown. Therefore, the purpose of this paper is to systematically explore the mechanism and efficacy of SGC in the "multicomponent-multitarget- multipathway" treatment for CHD using network pharmacology technology. METHODS The potential active ingredients of SGC were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and screened by pharmacokinetic parameters. Their possible targets were predicted using the TCMSP and DrugBank database. The CHD-related targets were identified from Comparative Toxicogenomics Database (CTD), UniProt, and PharmGKB database. The compound-target-disease network was constructed using Cytoscape for visualization. Additionally, the protein functional annotation and identification of signaling pathways of potential targets were performed by Gene Ontology (GO) and KEGG enrichment analysis using the Metascape platform. RESULTS The 61 active ingredients of SGC were found to regulate neuroactive ligand-receptor interaction, fluid shear stress and atherosclerosis, estrogen signaling pathway and other pathways through 62 targets. SGC is involved in regulating the circulatory system, nervous system and immune system and other aspects of the body, and thus plays a significant role in the treatment of CHD and its complications, showing the mechanism of SGC's "multicomponent, multitarget, and multipathway" prevention and treatment of CHD. In addition, three predictive components were first found to have potential biological activity by this method. CONCLUSION The studies we have performed successfully predict the effective components and potential targets of SGC in the prevention and treatment of CHD, which helped to systematically clarify its mechanism of action and provided a direction for future research on the modern mechanism of SGC in the treatment of CHD.
Collapse
Affiliation(s)
- Dan Wang
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Li Tian
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Chang Shi
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yu-Xi Wei
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Han Wang
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China; Department of Pharmacy, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300381, China
| | - Tian-Tian Liu
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Ming Gong
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Yan-Wen Zhang
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Rong-Guo Yu
- Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, 300384, China.
| | - Xiao-Hui Wu
- College of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| |
Collapse
|
43
|
Beneficial effects of flaxseed polysaccharides on metabolic syndrome via gut microbiota in high-fat diet fed mice. Food Res Int 2020; 131:108994. [DOI: 10.1016/j.foodres.2020.108994] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/03/2019] [Accepted: 01/07/2020] [Indexed: 12/23/2022]
|