Review
Nutrition & Dietetics
Elena Marisol Cruz-Garcia, Maria E. Frigolet, Samuel Canizales-Quinteros, Ruth Gutierrez-Aguilar
Summary: The main roles of adipose tissue are to store triglycerides and secrete adipokines, which regulate energy balance and inflammation. In obesity, dysfunction of adipocytes leads to inflammation and insulin resistance. This systematic review aimed to identify differentially expressed genes in subcutaneous adipose tissue of lean, obese, and post-RYGB individuals. The results showed that both the lean state and post-RYGB are similar in terms of increased expression of insulin-sensitizing molecules, promoting lipogenesis over lipolysis, and downregulating factors that promote inflammation.
Article
Genetics & Heredity
Linghui Wang, Hao Gu, Tianci Liao, Yuhang Lei, Yanhao Qiu, Qiuyang Chen, Lei Chen, Shunhua Zhang, Jinyong Wang, Xiaoxia Hao, Dongmei Jiang, Ye Zhao, Lili Niu, Xuewei Li, Linyuan Shen, Mailin Gan, Li Zhu
Summary: By sequencing, identifying, and analyzing tsRNAs using pigs as animal models, this research reports the characteristics of tsRNAs in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT). A total of 474 tsRNAs, with differential expression in endocrine and immune systems, as well as lipid metabolism, were found in white adipose tissue (WAT). The study also discovered a connection between the activity of the host tRNA engaged in translation and the production of tsRNAs. Furthermore, tsRNAs and miRNAs were found to be involved in the regulation of fatty acid metabolism in adipose tissue.
Article
Agriculture, Dairy & Animal Science
Hao Gu, Mailin Gan, Linghui Wang, Yiting Yang, Jinyong Wang, Lei Chen, Shunhua Zhang, Ye Zhao, Lili Niu, Dongmei Jiang, Yiwu Chen, Anan Jiang, Linyuan Shen, Li Zhu
Summary: This study investigates the expression differences of tsRNA in subcutaneous adipose tissue of obese and lean pigs, and reveals that tsRNA may participate in the regulation of energy metabolism in porcine adipocytes by influencing MAPK, AMPK, and other signaling pathways, thus promoting lipid deposition and contributing to obesity development.
Article
Agriculture, Dairy & Animal Science
Jing Wang, Youbing Yang, Baosong Xing, Junfeng Chen, Qingxia Lu, Jiaqing Zhang, Qiaoling Ren, Qiang Ma, Hongxia Guo, Hai Cao
Summary: This study revealed the molecular mechanisms underlying the regulation of lipid metabolism after castration under the involvement of circular RNAs, involving pathways like TGF-beta, insulin, AMPK, and MAPK, as well as the functions of miRNAs such as miR-143a-3p, miR-378, and miR-195 in adipogenesis and lipid metabolism. In addition, the study demonstrated the regulatory effects of testosterone and miR-181a on circ_0005912 expression in porcine intramuscular adipocytes.
ANIMAL SCIENCE JOURNAL
(2021)
Article
Multidisciplinary Sciences
Wenyang Sun, Tinghuan Zhang, Silu Hu, Qianzi Tang, Xi Long, Xu Yang, Shuangbao Gun, Lei Chen
Summary: In this study, the differences in chromatin accessibility between SAT and VAT were characterized using DNase-seq, revealing their associations with metabolic and inflammatory processes. Moreover, two candidate genes, NR1D1 and CRYM, were identified using integrated epigenetic and transcriptomic data, suggesting their crucial roles in regulating distinct characteristics between SAT and VAT.
Article
Biology
Yan Gong, Jun He, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jianhua He, Haiming Ma
Summary: This study reveals the transcription profiles and functional networks in lncRNA and mRNA in subcutaneous adipose tissue of Ningxiang piglets at different developmental stages. Most DEmRNAs were up-regulated in piglets, while they were down-regulated in late fattening stages, with DElncRNAs being up-regulated in late fattening stages. Modules 2 and 5 exhibit similar transcription modes, mainly involved in steroid biosynthesis, glycosphingolipid biosynthesis, metabolic pathways, and glycerolipid metabolism.
Article
Nutrition & Dietetics
Li Liu, Yuansi Chen, Jiaxin Chen, Ming Lu, Rui Guo, Jiajia Han, Yu Zhang, Xiaoting Pei, Zhiguang Ping
Summary: The methylation levels of PRDM16 gene promoter in abdominal subcutaneous adipose tissue (SAT) and omental adipose tissue (OAT) have complex relationships with overweight/obesity, with differences in methylation levels between different weight groups and different adipose tissue types. The variation of methylation haplotypes combination of multiple sites may play some roles in influencing obesity.
CLINICAL NUTRITION
(2021)
Article
Endocrinology & Metabolism
Pavel Hruska, Jan Kucera, Matej Pekar, Pavol Holeczy, Miloslav Mazur, Marek Buzga, Daniela Kuruczova, Peter Lenart, Jana Fialova Kucerova, David Potesil, Zbynek Zdrahal, Julie Bienertova-Vasku
Summary: The study compared the proteomic profiles of mature adipocytes from different adipose tissue depots, with findings showing that subcutaneous adipocytes are more active in vesicular transport, secretion, and lipid metabolism, while visceral adipocytes have higher protein expression related to mitochondrial energy metabolism and translational or biosynthetic activity.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Cell Biology
Seoyoung Jun, Anthony R. Angueira, Ethan C. Fein, Josephine M. E. Tan, Angela H. Weller, Lan Cheng, Kirill Batmanov, Jeff Ishibashi, Alexander P. Sakers, Rachel R. Stine, Patrick Seale
Summary: This study reveals the cell types involved in brown adipose tissue (BAT) development and identifies GATA6 as a crucial transcription factor in BAT development.
DEVELOPMENTAL CELL
(2023)
Article
Cell Biology
Hai P. Nguyen, Frances Lin, Danielle Yi, Ying Xie, Jennie Dinh, Pengya Xue, Hei Sook Sul
Summary: Adipose tissue mass and adiposity change throughout lifespan, with visceral adipose tissue (VAT) increasing and subcutaneous adipose tissue (SAT) decreasing with aging. A regulatory cell population called ARCs emerges in aging SAT, expressing progenitor markers but lacking adipogenic capacity, inhibiting proliferation and differentiation of neighboring adipose precursors. Pu.1 is identified as a driving factor for ARC development, correlating with aging-associated loss of SAT.
DEVELOPMENTAL CELL
(2021)
Article
Medicine, General & Internal
Florian Flenkenthaler, Erik Laendstroem, Bachuki Shashikadze, Mattias Backman, Andreas Blutke, Julia Philippou-Massier, Simone Renner, Martin Hrabe de Angelis, Ruediger Wanke, Helmut Blum, Georg J. Arnold, Eckhard Wolf, Thomas Froehlich
Summary: Adipose tissue is no longer just for energy storage, it is also an important endocrine organ involved in regulating energy balance. Adipokines are found to regulate blood glucose levels and improve metabolic balance. Lack of understanding exists regarding how different adipose tissue types are affected by insulin deficiency in diseases like type 1 diabetes.
FRONTIERS IN MEDICINE
(2021)
Article
Multidisciplinary Sciences
Pan Zhang, Qinggang Li, Yijing Wu, Yawen Zhang, Bo Zhang, Hao Zhang
Summary: This study used RNA-Seq and proteomics techniques to investigate the key pathways and genes involved in subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. The results showed that the metabolic pathways differed between the backfat group and the IMF group. We identified candidate genes that may be associated with tissue-specific lipid deposition.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Lijun Shi, Huihui Li, Xiaoyu Huang, Ze Shu, Jingna Li, Ligang Wang, Hua Yan, Lixian Wang
Summary: Understanding the molecular mechanisms of sow pregnancy development is crucial for genetic improvement of pig breeding traits and provides resources for biomedical research on human pregnancy diseases. However, there is a lack of transcriptome and metabolome data across different stages of sow pregnancy. In this study, we analyzed 84 RNA sequencing and 42 metabolome datasets from pig blood samples across six developmental stages. The findings revealed the sequence features, stage-specific molecules, expression patterns, regulatory mechanisms, and important pregnancy-related metabolites in both pigs and humans. These results are expected to contribute essential resources for pig breeding and biomedical research on human pregnancy diseases.
Article
Biology
Yifeng Zhang, Yingchun Sun, Zhongzi Wu, Xinwei Xiong, Junjie Zhang, Junwu Ma, Shijun Xiao, Lusheng Huang, Bin Yang
Summary: The study analyzed RNA sequence data for subcutaneous fat (SCF), intramuscular fat (IMF), and longissimus dorsi muscle (LDM) samples from 155 F-6 pigs to investigate gene expression levels and network connectivity. Results showed significant differences in gene expression and network connectivity between SCF and IMF, with tissue-specific genes and network modules associated with fat deposition.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Agriculture, Dairy & Animal Science
Mao Ning, Yihan Zhao, Dongmei Dai, Chang Yao, Huatao Liu, Lingzhao Fang, Bo Wang, Yi Zhang, Jie Cao
Summary: Ketosis is a common metabolic disease in dairy cows. This study analyzed the transcriptome of subcutaneous white adipose tissue in cows with and without type II ketosis and identified neurotrophic tyrosine kinase receptor type 2 (NTRK2) as a key gene associated with the disease. The downregulation of NTRK2 in the adipose tissue suggests a potential involvement of impaired central nervous system regulation in abnormal lipid mobilization during type II ketosis in cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Zoology
Yi Wang, Chen Wang, Wei Hong, Shilin Tian, Qin Lu, Bing-Jun Wang, Huaiming Jin, Nima Zhuoma, Xin Lu, Huabin Zhao
Summary: This study investigates the molecular adaptations associated with cooperative breeding in Tibetan ground tits by resequencing the whole genome of wild populations. It identifies candidate genes and functional ontologies related to hormonal regulation, such as oxytocin signaling, estrogen signaling, and insulin secretion. These findings provide important insights into the genetic roles in the evolution of cooperative breeding.
Article
Biology
Ying-Hui Li, Chao Qin, Li Wang, Chengzhi Jiao, Huilong Hong, Yu Tian, Yanfei Li, Guangnan Xing, Jun Wang, Yongzhe Gu, Xingpeng Gao, Delin Li, Hongyu Li, Zhangxiong Liu, Xin Jing, Beibei Feng, Tao Zhao, Rongxia Guan, Yong Guo, Jun Liu, Zhe Yan, Lijuan Zhang, Tianli Ge, Xiangkong Li, Xiaobo Wang, Hongmei Qiu, Wanhai Zhang, Xiaoyan Luan, Yingpeng Han, Dezhi Han, Ruzhen Chang, Yalong Guo, Jochen C. Reif, Scott A. Jackson, Bin Liu, Shilin Tian, Li-juan Qiu
Summary: This study analyzed the genome sequences of soybeans and revealed the evolutionary history and domestication process of soybean. The expansion and breeding of soybean were accompanied by positive selection of flowering time genes, and genetic introgression in soybean landraces mostly derived from sympatric wild populations.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Agriculture, Multidisciplinary
Lin-zhen Zhang, Li He, Ning Wang, Jia-hua An, Gen Zhang, Jin Chai, Yu-jie Wu, Chang-jiu Dai, Xiao-han Li, Ting Lian, Ming-zhou Li, Long Jin
Summary: This study identified a natural antisense transcript, APMAP-AS, which is associated with lipid synthesis and positively regulates adipogenic differentiation. APMAP-AS forms an RNA-RNA duplex with APMAP, increasing its stability and promoting lipid metabolism while inhibiting the expression of inflammatory factors.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Genetics & Heredity
Zhiming Wang, Jin Chai, Yuhao Wang, Yiren Gu, Keren Long, Mingzhou Li, Long Jin
Summary: Animal fat deposition has a significant impact on meat flavor and texture. In this study, we investigated the regulatory role of lncPLAAT3-AS in promoting preadipocyte proliferation and adipocyte differentiation. Our findings suggest that lncPLAAT3-AS upregulates PLAAT3 expression through a sponge-like mechanism involving miR-503-5p binding.
Article
Biochemistry & Molecular Biology
Xiaokai Li, Zhining Zhong, Ruowei Zhang, Jiaman Zhang, Yu Zhang, Sha Zeng, Qinjiao Du, Haoming Wang, Songling Zhang, Lu Lu, Mingzhou Li, Keren Long
Summary: In this study, a muscular dystrophy mouse model was created by Ptrf knockout, and single-nucleus RNA sequencing was used to investigate the transcriptional changes in skeletal muscle. The study revealed significant alterations in the transcriptome of different types of muscle fibers and mononuclear cells in response to muscular dystrophy, providing valuable insights into the molecular mechanisms of muscular dystrophy.
Article
Multidisciplinary Sciences
Long Jin, Danyang Wang, Jiaman Zhang, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang, Mingzhou Li
Summary: Using a pig model, the study investigates how chromatin architecture in adipose tissue is regulated in relation to obesity. Analysis of the data reveals similarities and differences in chromatin architecture between humans and pigs, providing valuable insights into the regulation of obesity-related genes.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Yujie Wang, Xun Wang, Yi Luo, Jiaman Zhang, Yu Lin, Jie Wu, Bo Zeng, Lei Liu, Peiqi Yan, Jiyuan Liang, Hongrui Guo, Long Jin, Qianzi Tang, Keren Long, Mingzhou Li
Summary: This study generated a de novo pigeon genome assembly and conducted a high resolution spatio-temporal transcriptomic analysis of the crop epithelium in pigeons. The study identified "lactation"-related genes involved in lipid and protein metabolism and revealed extensive reorganization of promoter-enhancer interactions linked to the expression of these genes. The spatial localization of gene expression in specific epithelial layers was correlated with phenotypic changes in the crop.
Article
Biology
Qin Zou, Rong Yuan, Yu Zhang, Yifei Wang, Ting Zheng, Rui Shi, Mei Zhang, Yujing Li, Kaixin Fei, Ran Feng, Binyun Pan, Xinyue Zhang, Zhengyin Gong, Li Zhu, Guoqing Tang, Mingzhou Li, Xuewei Li, Yanzhi Jiang
Summary: Studying cellular specialization in different anatomical regions of pig skin can enhance our understanding of skin information and provide insights for human skin research.
Article
Geriatrics & Gerontology
Linyuan Shen, Tianci Liao, Qiuyang Chen, Yuhang Lei, Linghui Wang, Hao Gu, Yanhao Qiu, Ting Zheng, Yiting Yang, Chenggang Wei, Lei Chen, Ye Zhao, Lili Niu, Shunhua Zhang, Yan Zhu, Mingzhou Li, Jinyong Wang, Xuewei Li, Mailin Gan, Li Zhu
Summary: This study explores the role of tRNA-derived small RNAs (tsRNAs), specifically 5'tiRNA-Gly, in skeletal muscle regeneration. It is found that 5'tiRNA-Gly is significantly up-regulated after muscle injury and promotes inflammation through the TGF-beta signaling pathway. These findings provide a new potential target for skeletal muscle regeneration treatment.
JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE
(2023)
Article
Physiology
Jinwei Zhang, Yang Shen, Guitao Yang, Jing Sun, Chuang Tang, Hao Liang, Jideng Ma, Xiaoqian Wu, Haoran Cao, Meng Wu, Yuchun Ding, Mingzhou Li, Zuohua Liu, Liangpeng Ge
Summary: This study analyzed the impact of commensal microbiota on the host's mucosal immunity. It found that the absence of commensal microbiota led to smaller Peyer's patches in the gastrointestinal tract, particularly regarding B and T cells. Gene expression analysis revealed that commensal microbiota plays an important role in the development of mucosal immunity in the intestine. Overall, this study revealed the regulatory mechanisms of commensal microbiota in the host's Peyer's patches and emphasized the importance of early microbial colonization for mucosal immunity development.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Weiqiang Liu, Pingfen Zhu, Meng Li, Zihao Li, Yang Yu, Gaoming Liu, Juan Du, Xiao Wang, Jing Yang, Ran Tian, Inge Seim, Alaattin Kaya, Mingzhou Li, Ming Li, Vadim N. Gladyshev, Xuming Zhou
Summary: The variation in lifespan among mammals is significant, and the study aims to uncover the evolutionary forces and molecular features related to longevity. Comparative transcriptomics analysis of liver, kidney, and brain tissues of 103 mammalian species revealed that only a few genes have common expression patterns with longevity. However, pathways related to translation fidelity and methionine restriction showed correlation with lifespan. The study suggests that lifespan regulation through gene expression is driven by polygenic and indirect natural selection.
Article
Biochemistry & Molecular Biology
Jingyi Bai, Yu Lin, Jiaman Zhang, Ziyu Chen, Yujie Wang, Mingzhou Li, Jing Li
Summary: The study used ATAC-seq and rRNA-depleted RNA-seq to analyze the chromatin accessibility and transcriptional features in multiple tissues of newborn pigs and during porcine liver development. The researchers obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage, and found that tissue-specific accessible promoters were associated with active transcription and tissue-specific functions. Additionally, they observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. This study expands our understanding of epigenetic regulation in mammalian tissues and organ development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jing Yang, Xingxing Zhu, Rui Wang, Mingzhou Li, Qianzi Tang
Summary: In this study, we comprehensively evaluated the performance of 24 popular state-of-the-art methods for complete end-to-end Hi-C data analysis using manually curated or experimentally validated benchmark datasets. Our results indicate that HiC-Pro, DomainCaller, and Fit-Hi-C2 showed relatively balanced performances in different aspects, providing a reference for researchers to choose suitable Hi-C analysis tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Huan Liu, Dengke Pan, Pu Li, Dandan Wang, Bo Xia, Ruixin Zhang, Junfeng Lu, Xiangyang Xing, Jiaxiang Du, Xiao Zhang, Long Jin, Lin Jiang, Linong Yao, Mingzhou Li, Jiangwei Wu
Summary: A novel sepsis pig model is created by modifying the surgical strategy of cecal ligation and puncture (CLP), which for the first time recapitulates the whole course of sepsis in humans. Increased levels of ZBED6 in skeletal muscle are shown in this model and sepsis patients, and protection against sepsis-induced muscle wasting is demonstrated in ZBED6-deficient pigs. The direct target of ZBED6 is revealed to be DOCK3, and septic ZBED6-deficient pigs show increased DOCK3 expression in skeletal muscle and myocytes, activating the RAC1/PI3K/AKT pathway and protecting against sepsis-induced muscle wasting.
Article
Multidisciplinary Sciences
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Yan Li, Rui Liu, Mingzhou Li
Summary: The storage of lipids as energy in adipose tissue is conserved, but there are substantial differences in the physiological activities of adipose tissues among species. This study characterized the transcriptional and lipidomic profiles of subcutaneous and visceral adipose tissues across 15 vertebrate species, spanning more than 300 million years of evolution. The data revealed greater variation in AT transcriptome and lipidome among species than within the same species, providing a resource for future studies on functional differences among adipose tissues in vertebrate species.
