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| 1 | Biomarkers and subtypes of deranged lipid metabolism in nonalcoholic fatty liver disease显示文摘Nonalcoholic fatty liver disease(NAFLD)is a heterogeneous and complex disease that is imprecisely diagnosed by liver biopsy.NAFLD covers a spectrum that ranges from simple steatosis,nonalcoholic steatohepatitis(NASH)with varying degrees of fibrosis,to cirrhosis,which is a major risk factor for hepatocellular carcinoma.Lifestyle and eating habit changes during the last century have made NAFLD the most common liver disease linked to obesity,type 2 diabetes mellitus and dyslipidemia,with a global prevalence of 25%.NAFLD arises when the uptake of fatty acids(FA)and triglycerides(TG)from circulation and de novo lipogenesis saturate the rate of FAβ-oxidation and verylow density lipoprotein(VLDL)-TG export.Deranged lipid metabolism is also associated with NAFLD progression from steatosis to NASH,and therefore,alterations in liver and serum lipidomic signatures are good indicators of the disease’s development and progression.This review focuses on the importance of the classification of NAFLD patients into different subtypes,corresponding to the main alteration(s)in the major pathways that regulate FA homeostasis leading,in each case,to the initiation and progression of NASH.This concept also supports the targeted intervention as a key approach to maximize therapeutic efficacy and opens the door to the development of precise NASH treatments. | José M Mato Cristina Alonso Mazen Noureddin Shelly C Lu | 2019 | World Journal of Gastroenterology2019，25，24： | 19 |
| 2 | Role of gut microbiota in identification of novel TCM-derived active metabolites显示文摘Traditional Chinese Medicine(TCM)has been extensively used to ameliorate diseases in Asia for over thousands of years.However,owing to a lack of formal scientific validation,the absence of information regarding the mechanisms underlying TCMs restricts their application.After oral administration,TCM herbal ingredients frequently are not directly absorbed by the host,but rather enter the intestine to be transformed by gut microbiota.The gut microbiota is a microbial community living in animal intestines,and functions to maintain host homeostasis and health.Increasing evidences indicate that TCM herbs closely affect gut microbiota composition,which is associated with the conversion of herbal components into active metabolites.These may significantly affect the therapeutic activity of TCMs.Microbiota analyses,in conjunction with modern multiomics platforms,can together identify novel functional metabolites and form the basis of future TCM research. | Tzu-Lung Lin Chia-Chen Lu Wei-Fan Lai Ting-Shu Wu Jang-Jih Lu Young-Mao Chen Chi-Meng Tzeng Hong-Tao Liu Hong Wei Hsin-Chih Lai | 2021 | Protein & Cell2021，12，5： | 16 |
| 3 | Time-resolved multiomics analysis of the genetic regulation of maize kernel moisture显示文摘Maize kernel moisture content(KMC)at harvest greatly affects mechanical harvesting,transport and storage.KMC is correlated with kernel dehydration rate(KDR)before and after physiological maturity.KMC and KDR are complex traits governed by multiple quantitative trait loci(QTL).Their genetic architecture is incompletely understood.We used a multiomics integration approach with an association panel to identify genes influencing KMC and KDR.A genome-wide association study using time-series KMC data from 7 to 70 days after pollination and their transformed KDR data revealed respectively 98and 279 loci significantly associated with KMC and KDR.Time-series transcriptome and proteome datasets were generated to construct KMC correlation networks,from which respectively 3111 and 759 module genes and proteins were identified as highly associated with KMC.Integrating multiomics analysis,several promising candidate genes for KMC and KDR,including Zm00001d047799 and Zm00001d035920,were identified.Further mutant experiments showed that Zm00001d047799,a gene encoding heat shock 70 kDa protein 5,reduced KMC in the late stage of kernel development.Our study provides resources for the identification of candidate genes influencing maize KMC and KDR,shedding light on the genetic architecture of dynamic changes in maize KMC. | Jianzhou Qu Shutu Xu Xiaonan Gou Hao Zhang Qian Cheng Xiaoyue Wang Chuang Ma Jiquan Xue | 2023 | The Crop Journal2023，11，1： | 1 |
| 4 | Unveiling E2F4,TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis显示文摘Senescence,a stable state of growth arrest,affects many physiological and pathophysiological processes,especially aging.Previous work has indicated that transcription factors(TFs)play a role in regulating senescence.However,a systematic study of regulatory TFs during replicative senescence(RS)using multiomics analysis is still lacking.Here,we generated timeresolved RNA-seq,reduced representation bisulfite sequencing(RRBS)and ATAC-seq datasets during RS of mouse skin fibroblasts,which demonstrated that an enhanced inflammatory response and reduced proliferative capacity were the main characteristics of RS in both the transcriptome and epigenome.Through integrative analysis and genetic manipulations,we found that transcription factors E2F4,TEAD1 and AP-1 are key regulators of RS.Overexpression of E2f4 improved cellular proliferative capacity,attenuated SA-β-Gal activity and changed RS-associated differentially methylated sites(DMSs).Moreover,knockdown of Tead1 attenuated SA-β-Gal activity and partially altered the RS-associated transcriptome.In addition,knockdown of Atf3,one member of AP-1 superfamily TFs,reduced Cdkn2a(p16)expression in pre-senescent fibroblasts.Taken together,the results of this study identified transcription factors regulating the senescence program through multi-omics analysis,providing potential therapeutic targets for anti-aging. | Yuting Wang Liping Liu Yifan Song Xiaojie Yu Hongkui Deng | 2022 | Protein & Cell2022，13，10： | 1 |
| 5 | Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens显示文摘Background Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying hens.Methods Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic steatosis.Results The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins(DEPs) interacted with differentially acetylated proteins(DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group(P < 0.05). Lipidomics detected a variety of sphingolipids(SPs) and glycerophospholipids(GPs) were negatively correlated with hepatic steatosis(r ≤-0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol transport.Conclusions In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of acetylation in hepatic steatosis and depict the changes in hepatic cholesterol metabolism. The findings provides a wealth of information to facilitate a deeper understanding of the pathophysiology of fatty liver and contributes to the development of therapeutic strategies. | Xiaoli Guo Qianqian Zhou Jiaming Jin Fangren Lan Chaoliang Wen Junying Li Ning Yang Congjiao Sun | 2024 | Journal of Animal Science and Biotechnology2024，15，1： | 0 |
| 6 | Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology显示文摘There is great heterogeneity among inflammatory bowel disease(IBD)patients in terms of pathogenesis,clinical manifestation,response to treatment,and prognosis,which requires the individualized and precision management of patients.Many studies have focused on prediction biomarkers and models for assessing IBD disease type,activity,severity,and prognosis.During the era of biologics,how to predict the response and side effects of patients to different treatments and how to quickly recognize the loss of response have also become important topics.Multiomics is a promising area for investigating the complex network of IBD pathogenesis.Integrating numerous amounts of data requires the use of artificial intelligence. | Xin-Yu Liu Hao Tang Qing-Yang Zhou Yan-Lin Zeng Dan Chen Hui Xu Yue Li Bei Tan Jia-Ming Qian | 2023 | World Journal of Gastroenterology2023，29，2： | 0 |
| 7 | Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease显示文摘Inflammatory bowel disease(IBD)is a complex disease with variability in genetic,environmental,and lifestyle factors affecting disease presentation and course.Precision medicine has the potential to play a crucial role in managing IBD by tailoring treatment plans based on the heterogeneity of clinical and temporal variability of patients.Precision medicine is a population-based approach to managing IBD by integrating environmental,genomic,epigenomic,transcriptomic,proteomic,and metabolomic factors.It is a recent and rapidly developing medicine.The widespread adoption of precision medicine worldwide has the potential to result in the early detection of diseases,optimal utilization of healthcare resources,enhanced patient outcomes,and,ultimately,improved quality of life for individuals with IBD.Though precision medicine is promising in terms of better quality of patient care,inadequacies exist in the ongoing research.There is discordance in study conduct,and data collection,utilization,interpretation,and analysis.This review aims to describe the current literature on precision medicine,its multiomics approach,and future directions for its application in IBD. | Gowthami Sai Kogilathota Jagirdhar Jose Andres Perez Andrea Belen Perez Salim Surani | 2023 | World Journal of Gastroenterology2023，29，36： | 0 |
| 8 | Multiomics metabolic and epigenetics regulatory network in cancer:A systems biology perspective显示文摘Genetic,epigenetic,and metabolic alterations are all hallmarks of cancer.However,the epigenome and metabolome are both highly complex and dynamic biological networks in vivo.The interplay between the epigenome and metabolome contributes to a biological system that is responsive to the tumor microenvironment and possesses a wealth of unknown biomarkers and targets of cancer therapy.From this perspective,we first review the state of high-throughput biological data acquisition(i.e.multiomics data)and analysis(i.e.computational tools)and then propose a conceptual in silico metabolic and epigenetic regulatory network(MER-Net)that is based on these current high-throughput methods.The conceptual MER-Net is aimed at linking metabolomic and epigenomic networks through observation of biological processes,omics data acquisition,analysis of network information,and integration with validated database knowledge.Thus,MER-Net could be used to reveal new potential biomarkers and therapeutic targets using deep learning models to integrate and analyze large multiomics networks.We propose that MER-Net can serve as a tool to guide integrated metabolomics and epigenomics research or can be modified to answer other complex biological and clinical questions using multiomics data. | Xuezhu Wang Yucheng Dong Yongchang Zheng Yang Chen | 2021 | Journal of Genetics and Genomics2021，48，7： | 0 |
| 9 | Phylogenomic,morphological,and niche differentiation analyses unveil species delimitation and evolutionary history of endangered maples in Acer series Campestria(Sapindaceae)显示文摘Accurate species delimitation is crucial for biodiversity conservation.The Acer series Campestria comprises four species,A.campestre L.,A.miyabei Maxim.,A.miaotaiense P.C.Tsoong,and A.yangjuechi Fang&P.L.Chiu.To clarify controversies over the taxonomic status of the latter three endangered species,we undertook phylogenomic,morphological,and niche differentiation analyses in series Campestria.Our coalescent species tree of 544 and 77 single-copy nuclear genes supported series Campestria as monophyletic,with A.yangjuechi having the closest relationship with A.miaotaiense.However,in the plastome-derived tree based on 64 protein coding sequences,the four species did not cluster together,and each of them grouped with some other sympatric Acer species.Given this nuclear-cytoplasmic conflict,we hypothesize that A.yangjuechi have been subject to nuclear gene introgression and plastid(pt)capture involving another sympatric maple,that is,A.amplum Rehder.Principal component analysis and machine learning based on morphological data could not separate A.yangjuechi and A.miaotaiense,but they both could be clearly distinguished from A.miyabei.Moreover,the niche overlap tests of the two more widespread species,A.miyabei and A.miaotaiense,showed they clearly occupy distinct niches.Overall,we conclude that A.miyabei and A.miaotaiense are distinct species,while A.yangjuechi(endemic to Mt.Tianmu/East China)should be treated as a subspecies of A.miaotaiense.Our study points out that multiple lines of phylogenomic,morphological,and ecological evidence prove highly useful in species delimitation.Additionally,our results should help to inform conservation measures for endangered species of the genus Acer/series Campestria in East Asia. | Xiao-Kai Fan Jing Wu Hans Peter Comes Yu Feng Ting Wang Shu-Zhen Yang Takaya Iwasaki Hong Zhu Yun Jiang Joongku Lee Pan Li | 2023 | Journal of Systematics and Evolution2023，61，2： | 0 |
| 10 | Precision Medicine in Cardiovascular Diseases显示文摘Since President Obama announced the Precision Medicine Initiative in the United States,more and more attention has been paid to precision medicine.However,clinicians have already used it to treat conditions such as cancer.Many cardiovascular diseases have a familial presentation,and genetic variants are associated with the prevention,diagnosis,and treatment of cardiovascular diseases,which are the basis for providing precise care to patients with cardiovascular diseases.Large-scale cohorts and multiomics are critical components of precision medicine.Here we summarize the application of precision medicine to cardiovascular diseases based on cohort and omic studies,and hope to elicit discussion about future health care. | Yan Liu Jie Du | 2017 | Cardiovascular Innovations and Applications2017，，B02： | 0 |
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