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metabolism 2

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Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Frontiers of Medicine doi: 10.1007/s11684-023-1020-z

Abstract: Retroperitoneal liposarcoma (RLPS) is the main subtype of retroperitoneal soft sarcoma (RSTS) and has a poor prognosis and few treatment options, except for surgery. The proteomic and metabolic profiles of RLPS have remained unclear. The aim of our study was to reveal the metabolic profile of RLPS. Here, we performed proteomic analysis (n = 10), metabolomic analysis (n = 51), and lipidomic analysis (n = 50) of retroperitoneal dedifferentiated liposarcoma (RDDLPS) and retroperitoneal well-differentiated liposarcoma (RWDLPS) tissue and paired adjacent adipose tissue obtained during surgery. Data analysis mainly revealed that glycolysis, purine metabolism, pyrimidine metabolism and phospholipid formation were upregulated in both RDDLPS and RWDLPS tissue compared with the adjacent adipose tissue, whereas the tricarboxylic acid (TCA) cycle, lipid absorption and synthesis, fatty acid degradation and biosynthesis, as well as glycine, serine, and threonine metabolism were downregulated. Of particular importance, the glycolytic inhibitor 2-deoxy-D-glucose and pentose phosphate pathway (PPP) inhibitor RRX-001 significantly promoted the antitumor effects of the MDM2 inhibitor RG7112 and CDK4 inhibitor abemaciclib. Our study not only describes the metabolic profiles of RDDLPS and RWDLPS, but also offers potential therapeutic targets and strategies for RLPS.

Keywords: RLPS     proteomics     metabolomics     lipidomics     metabolism    

Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Frontiers of Medicine 2014, Volume 8, Issue 1,   Pages 58-67 doi: 10.1007/s11684-014-0318-2

Abstract: Omics technologies allow high-throughput screening of sepsis biomarkers.This review paper serves as a reference for future studies that employ an integrated, multi-omics approach

Keywords: sepsis     biomarker     genomics     transcriptomics     proteomics     metabolomics    

Deciphering the pharmacological mechanism of Guan-Jie-Kang in treating rat adjuvant-induced arthritis using omics

Hudan Pan, Yanfang Zheng, Zhongqiu Liu, Zhongwen Yuan, Rutong Ren, Hua Zhou, Ying Xie, Liang Liu

Frontiers of Medicine 2019, Volume 13, Issue 5,   Pages 564-574 doi: 10.1007/s11684-018-0676-2

Abstract: Thus, this study establishes a new omics analytical method integrated with bioinformatics analysis for

Keywords: arthritis     traditional Chinese medicine     pharmacological mechanism     metabolism     adjuvant-induced arthritis     omics    

Innate immune checkpoint Siglec10 in cancers: mining of comprehensive omics data and validation in patient

Frontiers of Medicine 2022, Volume 16, Issue 4,   Pages 596-609 doi: 10.1007/s11684-021-0868-z

Abstract: Sialic acid binding Ig-like lectin 10 (Siglec10) is a member of innate immune checkpoints that inhibits the activation of immune cells through the interaction with its ligand CD24 on tumor cells. Here, by analyzing public databases containing 64 517 patients of 33 cancer types, we found that the expression of Siglec10 was altered in 18 types of cancers and was associated with the clinical outcomes of 11 cancer types. In particular, Siglec10 was upregulated in patients with kidney renal clear cell carcinoma (KIRC) and was inversely associated with the prognosis of the patients. In 131 KIRC patients of our settings, Siglec10 was elevated in the tumor tissues of 83 (63.4%) patients compared with that in their counterpart normal kidney tissues. Moreover, higher level of Siglec10 was associated with advanced disease (stages III and IV) and worse prognosis. Silencing of CD24 in KIRC cells significantly increased the number of Siglec10-expressing macrophages phagocytosing KIRC cells. In addition, luciferase activity assays suggested that Siglec10 was a potential target of the transcription factors c-FOS and GATA1, which were identified by data mining. These results demonstrate that Siglec10 may have important oncogenic functions in KIRC, and represents a novel target for the development of immunotherapies.

Keywords: innate immune checkpoint     Siglec10     kidney renal clear cell carcinoma    

Applying TCM Constitution Theory to Infertility via Omics

Qi Wang

Engineering 2023, Volume 30, Issue 11,   Pages 30-31 doi: 10.1016/j.eng.2023.05.005

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction networks

Hong LI,Ziding ZHANG

Frontiers of Agricultural Science and Engineering 2016, Volume 3, Issue 2,   Pages 102-112 doi: 10.15302/J-FASE-2016100

Abstract: Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics)

Keywords: plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

Technology and Equipment of Big Data on Crop Phenomics

Wen Weiliang , Guo Xinyu, Zhang Ying , Gu Shenghao, Zhao Chunjiang

Strategic Study of CAE 2023, Volume 25, Issue 4,   Pages 227-238 doi: 10.15302/J-SSCAE-2023.04.015

Abstract:

Automatic equipment and information technologies make it possible to acquire multi-scale and multi-source heterogeneous data of crops under different growth conditions, forming big data on crop phenomics. This will greatly promote the research progress of crop functional genomics, digital breeding, and smart cultivation. In this paper, the demand for and industrial development of technology and equipment of big data on crop phenomics are analyzed. Then, the current situation of research and development in this area is summarized from five aspects: data acquisition hardware, data transmission, data analysis, knowledge formation, and applications. The problems and developmental trends of relevant technologies, equipment, and industrial application in China are analyzed from the perspectives of high-throughput acquisition and intelligent analysis of big data on crop phenomics. At last, the following suggestions are proposed: achieving breakthroughs regarding key crop phenotyping sensor technologies from the underlying chip level, forming an autonomous phenotyping extraction technology system on the basis of controllable open source, strengthening the standards system construction for big data on crop phenomics, creating a new model of genotype‒phenotype‒environment big data-driven digital breeding and smart cultivation, and building a talent pool and collaborative network for crop phenomics.

Keywords: crop phenomics     phenotyping big data     technology and equipment for phenotyping     multi-omics    

The Application of Artificial Intelligence Accelerates G Protein-Coupled Receptor Ligand Discovery Review

Wei Chen,Chi Song,Liang Leng,Sanyin Zhang,Shilin Chen

Engineering 2024, Volume 32, Issue 1,   Pages 19-29 doi: 10.1016/j.eng.2023.09.011

Abstract: Furthermore, an AI-driven multi-omics integration strategy for GPCR ligand discovery that combines informationfrom various omics disciplines was proposed.

Keywords: G protein-coupled receptor     Ligand     Artificial intelligence     Multi-omics     Drug discovery    

MiR-516a-3p is a Novel Mediator of Hepatocellular Carcinoma Oncogenic Activity and Cellular Metabolism

Tao Rui,Xueyou Zhang,Shi Feng,Haitao Huang,Shaowei Zhan,Haiyang Xie,Lin Zhou,Shusen Zheng,Qi Ling,

Engineering 2022, Volume 16, Issue 9,   Pages 162-175 doi: 10.1016/j.eng.2021.07.020

Abstract: The integrated multi-omics and co-enriched pathway analysis showed that miR-516a-3p regulates the metabolic

Keywords: Hepatocellular carcinoma     miRNA cluster     Exosome     Multi-omics    

Expanding the Scope of Multivariate Regression Approaches in Cross-Omics Research Article

Xiaoxi Hu, Yue Ma, Yakun Xu, Peiyao Zhao, Jun Wang

Engineering 2021, Volume 7, Issue 12,   Pages 1725-1731 doi: 10.1016/j.eng.2020.05.028

Abstract: Our method extensions provide valuable guidelines for future omics research, especially with respect

Keywords: Multivariate regression methods     Reduced rank regression     Sparsity     Dimensionality reduction     Variable selection    

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp. 1647: Pseudo-Tetrapeptides Article

Hongmin Sun, Xingxing Li, Minghua Chen, Ming Zhong, Yihua Li, Kun Wang, Yu Du, Xin Zhen, Rongmei Gao, Yexiang Wu, Yuanyuan Shi, Liyan Yu, Yongsheng Che, Yuhuan Li, Jian-Dong Jiang, Bin Hong, Shuyi Si

Engineering 2022, Volume 16, Issue 9,   Pages 176-186 doi: 10.1016/j.eng.2021.05.010

Abstract: We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete.By integrating multi-omics data, we discovered a number of novel antiviral pseudo-tetrapeptides produced

Keywords: Multi-omics     Anti-influenza A virus     Anti-coronavirus     Streptomyces sp. 1647     Pseudo-tetrapeptides    

Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats Article

Yifan Liu, Jing Chen, Zhonglin Liu, Zhaowei Hou, Bo Liang, Liying Wang, Lei Zhou, Libin Shou, Dandan Lin, Shizhong Yang, Jinfeng Liu, Xiaolin Wu, Jidong Gu, Bozhong Mu

Engineering 2023, Volume 24, Issue 5,   Pages 265-276 doi: 10.1016/j.eng.2021.08.027

Abstract:

The microbial conversion of alkanes to methane in hydrocarbon contaminated environments is an intrinsic bioremediation strategy under anoxic conditions. However, the mechanism of microbial methanogenic alkane degradation is currently unclear. Under ten-years of continuous efforts, we obtained a methanogenic n-alkane-degrading (C15–C20) enrichment culture that exhibited sustained improvements in the kinetic properties of methane production. The integrated metagenomic and metatranscriptomic analyses revealed that n-alkanes were mainly attacked by members of Desulfosarcinaceae, Firmicutes, and Synergistetes using the fumarate addition strategy, and were then further degraded in a common effort by Tepidiphilus members. Meanwhile, the abundant members of Anaerolineaceae were mainly responsible for cell debris recycling. However, according to the metatranscriptomic analyses, methane was predicted to be produced mainly via H2-dependent methylotrophic methanogenesis, primarily from necromass-derived trimethylamine mediated by Methanomethyliaceae within the candidate phylum Verstraetearchaeota. These findings reveal that H2-dependent methylotrophic methanogens, as well as methylotrophic methanogens, may play important ecological roles in the carbon cycle of hydrocarbon enriched subsurface ecosystems.

Keywords: Methanogenic hydrocarbon degradation     Oily sludge     Bioremediation     Alkanes    

Temporal Integrative Omics Reveals an Increase in Nondegradative Ubiquitylation during Primary Hepatocyte Article

Zhengyi Jiang, Zeyu Sun, Xiaoxi Ouyang, Yalei Zhao, Menghao Zhou, Baohong Wang, Qirui Li, Linxiao Fan, Sainan Zhang, Lanjuan Li

Engineering 2020, Volume 6, Issue 11,   Pages 1302-1314 doi: 10.1016/j.eng.2020.02.011

Abstract:

Primary hepatocytes (PHCs) are widely used in various fields, but the progressive deterioration of liver-specific features in vitro significantly limits their application. While the transcriptional regulation and whole cell proteome (WCP) of PHCs have been extensively studied, only a small number of studies have addressed the role of posttranslational modifications in this process. To elucidate the underlying mechanisms that induce dedifferentiation, we carried out parallel quantifications of the transcriptome, WCP, ubiquitinome, and phosphoproteome of rat PHCs after 0, 6, 12, 24, and 48 h of in vitro culture. Our data constitute a detailed proteomic analysis of dedifferentiated PHCs including 2196 proteins, 2056 ubiquitinated sites, and 4932 phosphorylated peptides. We revealed a low correlation between the transcriptome and WCP during dedifferentiation. A combined analysis of the ubiquitinome with the corresponding WCP indicated that the dedifferentiation of PHCs led to an increase in nondegradative K27 ubiquitination. Functional analysis of the altered phosphoproteins suggested a significant enrichment in ferroptosis. In all, 404 proteins with both ubiquitination and phosphorylation were identified to be involved in critical metabolic events. Furthermore, Ptbp1, Hnrpd, Hnrnpu, and Srrm2 were identified as hub genes. Taken together, our data provide new insights into proteome dynamics during PHC dedifferentiation and potential targets to inhibit the dedifferentiation process.

Keywords: Ubiquitination     Phosphoproteome     Proteome     Dedifferentiation     Primary hepatocytes    

Multi-Omics Analysis Provides Insight into the Possible Molecular Mechanism of Hay Fever Based on Gut Article

Pei Han, Li-Sha Li, Zi-Xi Wang, Lin Xi, Hang Yu, Lin Cong, Zheng-Wei Zhang, Jie Fu, Ran Peng, Li-Bin Pan, Shu-Rong Ma, Xue-Yan Wang, Hong-Tian Wang, Xiang-Dong Wang, Yan Wang, Jin-Lyu Sun, Jian-Dong Jiang

Engineering 2022, Volume 15, Issue 8,   Pages 115-125 doi: 10.1016/j.eng.2021.03.013

Abstract:

Due to the worldwide epidemic of allergic disease and a cure nowhere in sight, there is a crucial need to explore its pathophysiological mechanisms. As allergic disease has been associated with gut dysbiosis, we searched for a possible mechanism from the perspective of the molecular interface between host and microbiota with concurrent metabolomics and microbiome composition analysis. Sprague-Dawley rats were injected with Artemisia pollen extract to stimulate a hyper reaction to pollen. This hyper reaction decreased the circulation of valine, isoleucine, aspartate, glutamate, glutamine, indole-propionate (IPA), and myo-inositol, and reduced short-chain fatty acids (SCFAs) in feces. Several beneficial genera belonging to Ruminococcaceae, Lachnospiraceae, and Clostridiales declined in the model group, whereas Helicobacter and Akkermansia were only expressed in the model group. Furthermore, the expression of intestinal claudin-3 and liver fatty acid binding protein was downregulated in the model group and associated with metabolic changes and bacteria. Our results suggest that alterations in amino acids as well as their derivatives (especially valine, and IPA which is the reductive product of tryptophan) , SCFAs, and the gut microbiome (specifically Akkermansia and Helicobacter) may disrupt the intestinal barrier function by inhibiting the expression of claudin proteins and affecting the mucus layer, which further results in hay fever.

Keywords: Metabolome     Gut microbiota     Hay fever     Allergic diseases     Intestinal barrier dysfunction    

Title Author Date Type Operation

Multi-omics joint analysis revealed the metabolic profile of retroperitoneal liposarcoma

Journal Article

Sepsis biomarkers: an omics perspective

Xiao Liu, Hui Ren, Daizhi Peng

Journal Article

Deciphering the pharmacological mechanism of Guan-Jie-Kang in treating rat adjuvant-induced arthritis using omics

Hudan Pan, Yanfang Zheng, Zhongqiu Liu, Zhongwen Yuan, Rutong Ren, Hua Zhou, Ying Xie, Liang Liu

Journal Article

Innate immune checkpoint Siglec10 in cancers: mining of comprehensive omics data and validation in patient

Journal Article

Applying TCM Constitution Theory to Infertility via Omics

Qi Wang

Journal Article

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction networks

Hong LI,Ziding ZHANG

Journal Article

Technology and Equipment of Big Data on Crop Phenomics

Wen Weiliang , Guo Xinyu, Zhang Ying , Gu Shenghao, Zhao Chunjiang

Journal Article

The Application of Artificial Intelligence Accelerates G Protein-Coupled Receptor Ligand Discovery

Wei Chen,Chi Song,Liang Leng,Sanyin Zhang,Shilin Chen

Journal Article

MiR-516a-3p is a Novel Mediator of Hepatocellular Carcinoma Oncogenic Activity and Cellular Metabolism

Tao Rui,Xueyou Zhang,Shi Feng,Haitao Huang,Shaowei Zhan,Haiyang Xie,Lin Zhou,Shusen Zheng,Qi Ling,

Journal Article

Expanding the Scope of Multivariate Regression Approaches in Cross-Omics Research

Xiaoxi Hu, Yue Ma, Yakun Xu, Peiyao Zhao, Jun Wang

Journal Article

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp. 1647: Pseudo-Tetrapeptides

Hongmin Sun, Xingxing Li, Minghua Chen, Ming Zhong, Yihua Li, Kun Wang, Yu Du, Xin Zhen, Rongmei Gao, Yexiang Wu, Yuanyuan Shi, Liyan Yu, Yongsheng Che, Yuhuan Li, Jian-Dong Jiang, Bin Hong, Shuyi Si

Journal Article

Pan Hudan: Discovery of Anti-Arthritis Mechanism of Traditional Chinese Medicine Compound based on Omics

23 Oct 2021

Conference Videos

Long-Term Cultivation and Meta-Omics Reveal Methylotrophic Methanogenesis in Hydrocarbon-Impacted Habitats

Yifan Liu, Jing Chen, Zhonglin Liu, Zhaowei Hou, Bo Liang, Liying Wang, Lei Zhou, Libin Shou, Dandan Lin, Shizhong Yang, Jinfeng Liu, Xiaolin Wu, Jidong Gu, Bozhong Mu

Journal Article

Temporal Integrative Omics Reveals an Increase in Nondegradative Ubiquitylation during Primary Hepatocyte

Zhengyi Jiang, Zeyu Sun, Xiaoxi Ouyang, Yalei Zhao, Menghao Zhou, Baohong Wang, Qirui Li, Linxiao Fan, Sainan Zhang, Lanjuan Li

Journal Article

Multi-Omics Analysis Provides Insight into the Possible Molecular Mechanism of Hay Fever Based on Gut

Pei Han, Li-Sha Li, Zi-Xi Wang, Lin Xi, Hang Yu, Lin Cong, Zheng-Wei Zhang, Jie Fu, Ran Peng, Li-Bin Pan, Shu-Rong Ma, Xue-Yan Wang, Hong-Tian Wang, Xiang-Dong Wang, Yan Wang, Jin-Lyu Sun, Jian-Dong Jiang

Journal Article