Article
Endocrinology & Metabolism
Yijun Lin, Lingling Chen, Xue You, Zixuan Li, Chenchen Li, Yan Chen
Summary: The study demonstrated the regulatory role of PAQR9 in hepatic ketogenesis and showed that deletion of PAQR9 attenuated ketogenesis and fatty acid oxidation during fasting by decreasing PPARa protein stability and competing with HUWE1 for interaction with PPAR alpha.
MOLECULAR METABOLISM
(2021)
Review
Immunology
Wanjin Li, Junying Yuan
Summary: RIPK1 acts as a crucial regulator in TNFR1 signaling, controlling cell death, survival, and inflammation. The activation of RIPK1 kinase not only promotes necroptosis and apoptosis, but also induces the transcription of inflammatory cytokines, leading to inflammation. Moreover, activated RIPK1 translocates to the nucleus to interact with the BAF complex, facilitating chromatin remodeling and transcription. This review highlights the proinflammatory role of RIPK1 kinase in human neurodegenerative diseases and discusses the potential of targeting RIPK1 kinase for the treatment of inflammatory pathology in human diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Chuanliang Chu, Renyan Huang, Liping Liu, Guilin Tang, Jinghua Xiao, Heejin Yoo, Meng Yuan
Summary: The OsNRAMP1 gene plays an important role in regulating metal ion and reactive oxygen species homeostasis in rice. Removal of this gene leads to enhanced broad-spectrum disease resistance and safety against toxic heavy metals.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Wen-Bo Li, Shuang-Wei Song, Meng-Meng Zhong, Lan-Gong Liu, Lei Su, Li-Bo Han, Gui-Xian Xia, Yong-Duo Sun, Hai-Yun Wang
Summary: This study demonstrates the important role of the actin-binding protein GhVLN2 in host defense against the soilborne fungus Verticillium dahliae in cotton plants. The regulated expression and dynamic remodeling of the actin cytoskeleton contribute to the modulation of cotton immune responses against V. dahliae.
Article
Plant Sciences
Bingsen Wang, Mengshu Huang, Wenfeng He, Yuqi Wang, Liu Yu, Dan Zhou, Chengzhen Meng, Dong Cheng, Huishan Qiu, Xiaodan Tan, Botao Song, Huilan Chen
Summary: Knock down of StTOPP6 enhances resistance to bacterial wilt in potato by activating the MAPK3-mediated pathway and inducing accumulation of reactive oxygen species.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Immunology
Lisa Cucolo, Qingzhou Chen, Jingya Qiu, Yongjun Yu, Max Klapholz, Krista A. Budinich, Zhaojun Zhang, Yue Shao, Igor E. Brodsky, Martha S. Jordan, D. Gary Gilliland, Nancy R. Zhang, Junwei Shi, Andy J. Minn
Summary: Interferon-gamma has various effects on cancer immune checkpoint blockade, including its role in resistance. The study found that the expression of Ripk1 gene is strongly associated with interferon-mediated resistance. RIPK1 diverts TNF signaling in cancer cells, leading to the production of immunosuppressive chemokines and decreased expression of TNF superfamily ligands in T and NK cells.
Article
Plant Sciences
Peng Zhang, Xiaoding Ma, Lina Liu, Chanjuan Mao, Yongkang Hu, Bingxiao Yan, Jia Guo, Xinyu Liu, Jinxia Shi, Gang-Seob Lee, Xiaowu Pan, Yiwen Deng, Zhengguang Zhang, Zhensheng Kang, Yongli Qiao
Summary: In this study, a lesion mimic mutant (LMM) called spl38 was identified in rice, which is essential for plant defense and cell death. The spl38 mutant showed enhanced resistance to rice pathogens and delayed flowering, while overexpression of OsMED16 increased susceptibility. OsMED16 interacts with OsPR3 to negatively regulate cell death and immunity in rice, possibly through the chitin signaling pathway.
Article
Multidisciplinary Sciences
Murat Kirtay, Josefine Sell, Christian Marx, Holger Haselmann, Mihai Ceanga, Zhong-Wei Zhou, Vahid Rahmati, Joanna Kirkpatrick, Katrin Buder, Paulius Grigaravicius, Alessandro Ori, Christian Geis, Zhao-Qi Wang
Summary: ATR, a key regulator of DNA damage response and replication stress, also plays a role in regulating neuronal activity beyond its known functions. Deletion of ATR in neurons leads to increased intrinsic activity, aberrant firing, and heightened epileptiform activity, potentially increasing susceptibility to ataxia and epilepsy.
NATURE COMMUNICATIONS
(2021)
Editorial Material
Immunology
Michelle A. Kelliher, Katherine A. Fitzgerald
Summary: Resistance mechanisms have hindered the effectiveness of immune checkpoint blockade therapies, but inhibition of TBK1 can restore their efficacy by sensitizing tumors to RIPK1 kinase-dependent cell death.
TRENDS IN IMMUNOLOGY
(2023)
Review
Microbiology
Michael Hemkemeyer, Sanja A. Schwalb, Stefanie Heinze, Rainer Georg Joergensen, Florian Wichern
Summary: While research has primarily focused on the cycling of carbon, nitrogen, and phosphorus in soil microbial communities, it is known that other elements play a significant role in microbial functioning. This knowledge has yet to be fully synthesized for soil microorganisms.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Hailin Tu, Weihang Xiong, Jie Zhang, Xueqiang Zhao, Xin Lin
Summary: The phosphorylation of RIPK1 at tyrosine residue is crucial for regulating cell death and inflammation, and its dysregulation can lead to systemic inflammation and disturbed hematopoiesis.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Si-wei Wang, Qing Zhang, Dan Lu, You-chen Fang, Xiao-ci Yan, Jing Chen, Zhi-kan Xia, Qian-ting Yuan, Lin-hai Chen, Yang-ming Zhang, Fa-jun Nan, Xin Xie
Summary: Acute lung injury (ALI) is a severe condition that can lead to acute respiratory distress syndrome (ARDS) with high mortality rate. Inflammation, particularly involving neutrophils, is believed to be a major factor in the development of ALI. The discovery of the role of GPR84, a medium chain fatty acid receptor, in regulating neutrophil functions in ALI provides new insights and potential drug targets for treatment.
ACTA PHARMACOLOGICA SINICA
(2023)
Article
Plant Sciences
Suren Deng, Jingyi Li, Zezhen Du, Zixuan Wu, Jian Yang, Hongmei Cai, Gaobing Wu, Fangsen Xu, Yichao Huang, Sheliang Wang, Chuang Wang
Summary: Intracellular phosphate homeostasis is crucial for cell metabolism and growth. Under short-term phosphate starvation, plants induce the expression of acid phosphatase OsACP1 to recycle phosphate from organic phosphate, impacting plant growth and productivity under both sufficient and deficient phosphate conditions. OsACP1 plays a key role in regulating rice growth by recycling phosphate from organic sources in the endoplasmic reticulum and Golgi apparatus.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Meng-Qi Feng, Meng-Di Lu, Jian-Mei Long, Zhao-Ping Yin, Nan Jiang, Peng-Bo Wang, Yue Liu, Wen-Wu Guo, Xiao-Meng Wu
Summary: This study reveals the regulatory pathway of miR156-SPLs and miR172-TOEs in somatic embryogenesis (SE) in citrus callus. CsAGL15 and CsFUS3 activate csi-miR156a, which represses CsSPL genes and further regulates csi-miR172d and CsTOEs. This leads to alterations in starch accumulation in callus cells and affects SE efficiency in citrus.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Cell Biology
Lei Luo, Yanna Dang, Yan Shi, Panpan Zhao, Yunhai Zhang, Kun Zhang
Summary: SIN3A is a central scaffold protein involved in the regulation of HDAC1 expression during early embryonic development in mammals. The maternal origin of SIN3A was confirmed in pigs, cattle, mice, and humans, with its depletion causing developmental arrest in pigs but not in bovines. Furthermore, SIN3A affects CCNB1 expression, which is crucial for embryonic development, and can be partially rescued by exogenous CCNB1 mRNA injection.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Xiaotao Shen, Si Wu, Liang Liang, Songjie Chen, Kevin Contrepois, Zheng-Jiang Zhu, Michael Snyder
Summary: Accurate and efficient compound annotation has been a challenge for LC-MS-based data, but efforts to overcome this obstacle have been limited by the sources of spectral information used. The metID R package aims to address this issue by combining information from major databases for streamlined compound annotation, making the process automatic and reproducible across platforms.
Article
Chemistry, Analytical
Xi Chen, Yandong Yin, Mingdu Luo, Zhiwei Zhou, Yuping Cai, Zheng-Jiang Zhu
Summary: Lipids play important roles in physiological and pathological processes in living organisms. However, high-coverage and high-accuracy lipidomic analysis of complex biological samples remains challenging due to the structural diversity and isomer and isobaric features of lipids. In this study, a four-dimensional untargeted lipidomics approach based on trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) was developed to improve lipid identification and quantification. The results showed that TIMS-based multi-dimensional separation improved the differentiation of isomeric and isobaric lipids and increased the quality of MS/MS spectra.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Jingshu Li, Ye Cao, Kongyan Niu, Jiaqian Qiu, Han Wang, Yingnag You, Dean Li, Yu Luo, Zhengjiang Zhu, Yaoyang Zhang, Nan Liu
Summary: Lysine acetylation is an important post-translational modification involved in regulating various cellular processes, including aging. However, the acetylome-wide analysis in mammalian tissues during aging is limited. This study combines antibody enrichment and label-free quantitative acetylomic analysis to investigate the changes in protein acetylation during natural aging and upon the treatment of NMN. The results identify previously unknown acetylation sites and highlight the potential of protein acetylation events as aging biomarkers. Furthermore, the study demonstrates the beneficial effects of NMN on age-related protein acetylation. These findings lay a critical foundation for understanding the functional role of protein post-translational modifications in healthy aging and disease conditions.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Ruohong Wang, Yandong Yin, Jingshu Li, Hongmiao Wang, Wanting Lv, Yang Gao, Tangci Wang, Yedan Zhong, Zhiwei Zhou, Yuping Cai, Xiaoyang Su, Nan Liu, Zheng-Jiang Zhu
Summary: The authors develop a global isotope tracing technology with metabolome-wide coverage to measure labeled metabolites. Using fruit flies as a model organism, they investigate metabolic activities during aging and reveal the importance of metabolic coordination and metabolic shifts.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Jingyao Wang, Shaoqing Zhou, Yan Cheng, Lin Cheng, Ying Qin, Zhenfeng Zhang, Aiwei Bi, Huaijiang Xiang, Xinheng He, Xiaoxu Tian, Wenbin Liu, Jian Zhang, Chao Peng, Zhengjiang Zhu, Min Huang, Ying Li, Guanglei Zhuang, Li Tan
Summary: There is increasing interest in covalent targeted inhibitors for drug discovery against previously undruggable sites and targets. Novel arsenous warheads are characterized for their unique features in reacting with thiol species in a reversible manner. The development of selective and potent inhibitors using organoarsenic probes proves effective in targeting pyruvate kinase M2 (PKM2) and inhibiting tumor growth.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Kongyan Niu, Jinyang Zhang, Shuwen Ge, Dean Li, Kunfeng Sun, Yingnan You, Jiaqian Qiu, Kun Wang, Xueting Wang, Rui Liu, Yandong Liu, Bing Li, Zheng-Jiang Zhu, Lefeng Qu, Hong Jiang, Nan Liu
Summary: The researchers introduced the ONE-seq method to identify RNA transcripts containing NAD cap. They discovered over a thousand previously unknown NAD-RNAs and revealed the overall dynamics of NAD-RNAs with age. This method facilitates the functional investigation of NAD-capped RNAs.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Chemistry, Analytical
Yuping Cai, Zhiwei Zhou, Zheng-Jiang Zhu
Summary: Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics faces challenges in annotating large-scale and unambiguous metabolites in complex biological matrices due to the diversity of metabolome. Recent advancements in metabolite annotation strategies include spectral match algorithms, in-silico MS/MS spectral prediction, and network-based approaches. Analytical dimensions such as retention time and collision cross-section have been expanded to support multidimensional metabolite annotation. Stable-isotope labeling is also highlighted for aiding structural verification of metabolites. This review summarizes the state-of-the-art approaches in annotating metabolites for LC-MS-based untargeted metabolomics, with the aim of discovering novel functional metabolites.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Hongmiao Wang, Yandong Yin, Zheng-Jiang Zhu
Summary: In this study, a method called MetImage was developed to encode LC-MS-based untargeted metabolomics data into multi-channel digital images, which were then used for developing deep learning-based AI models for clinical diagnosis. MetImage was successfully applied in the clinical screening of ESCC, achieving superior performances. This method encoding raw data into images improved the interpretability of the AI models.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Mingdu Luo, Yandong Yin, Zhiwei Zhou, Haosong Zhang, Xi Chen, Hongmiao Wang, Zheng-Jiang Zhu
Summary: The study develops a mass spectrum-oriented bottom-up assembly algorithm and a computational framework called Met4DX for ion mobility (IM)-resolved metabolomics, which addresses the challenge of high dimensionality in data processing. Met4DX outperforms existing tools in terms of coverage, sensitivity, peak fidelity, and quantification precision, and successfully detects and differentiates co-eluted metabolite isomers.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tao Zhang, Na Zhang, Jing Xing, Shuhua Zhang, Yulu Chen, Daichao Xu, Jinyang Gu
Summary: Hepatocyte apoptosis plays a crucial role in the progression of nonalcoholic steatohepatitis (NASH), but the molecular mechanisms underlying it are not well understood. In this study, the researchers identify UGDH and its product UDP-glucuronate as suppressors of NASH-associated liver damage by inhibiting RIPK1-dependent hepatocyte apoptosis. Through its conversion of UDP-glucose to UDP-glucuronate, UGDH suppresses RIPK1 activation by directly binding to its kinase domain. Restoring UDP-glucuronate levels improves liver damage even after the onset of NASH. These findings suggest UDP-glucuronate metabolism as a potential target for the specific treatment of NASH-associated liver damage.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Haosong Zhang, Mingdu Luo, Hongmiao Wang, Fandong Ren, Yandong Yin, Zheng-Jiang Zhu
Summary: The development of IM-MS has revolutionized the analysis of small molecules. The curation of comprehensive CCS databases plays a pivotal role in the successful application of IM-MS. AllCCS2, an enhanced version, achieved exceptional prediction accuracy and compatibility with different instrument platforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Tao Zhang, Daichao Xu, Jianping Liu, Min Wang, Li-Juan Duan, Min Liu, Huyan Meng, Yuan Zhuang, Huibing Wang, Yingnan Wang, Mingming Lv, Zhengyi Zhang, Jia Hu, Linyu Shi, Rui Guo, Xingxing Xie, Hui Liu, Emily Erickson, Yaru Wang, Wenyu Yu, Fabin Dang, Dongxian Guan, Cong Jiang, Xiaoming Dai, Hiroyuki Inuzuka, Peiqiang Yan, Jingchao Wang, Mrigya Babuta, Gewei Lian, Zhenbo Tu, Ji Miao, Gyongyi Szabo, Guo-Hua Fong, Antoine E. Karnoub, Yu-Ru Lee, Lifeng Pan, William G. Kaelin, Junying Yuan, Wenyi Wei
Summary: Zhang, Xu, Liu, Wang et al. have discovered that the EGLN1/pVHL-mediated proline hydroxylation inhibits the activity of RIPK1 kinase, but this mechanism is disrupted during prolonged hypoxia, leading to the activation of RIPK1 and consequent cell death and inflammation. The proline hydroxylation of HIF-1α mediated by the EGLN-pVHL pathway is a well-known mechanism for cellular adaptation to hypoxia. The study also reveals that RIPK1, a regulator of TNFR1-mediated cell death, is a target of EGLN1-pVHL, and its proline hydroxylation by EGLN1 suppresses its activation under normoxic conditions.
NATURE CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Youqi Tao, Wencheng Xia, Qinyue Zhao, Huaijiang Xiang, Chao Han, Shenqing Zhang, Wei Gu, Wenjun Tang, Ying Li, Li Tan, Dan Li, Cong Liu
Summary: Here we used cryoelectron microscopy to investigate the interaction mechanism between a series of compounds and α-synuclein fibrils. The ligand-fibril interaction was found to exhibit remarkable difference from the canonical ligand-protein interaction. We also identified a druggable pocket that is conserved in the ex vivo α-synuclein fibrils from multiple system atrophy.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Weimin Sun, Guowei Wu, Xinyu Tian, Chunting Qi, Jingli Liu, Yilun Tong, Mengmeng Zhang, Jiayang Gao, Ze Cao, Yuchao Zhang, Zhijun Liu, Xiaoxu Tian, Ping Wu, Chao Peng, Jingwen Li, Li Tan, Bing Shan, Jianping Liu, Ying Li, Junying Yuan
Summary: The study reveals that R406/R788 can promote sustained activation of TAK1, enhancing TNF-mediated necroptosis and RIPK1-dependent apoptosis. By directly binding to TAK1, R406 treatment activates TAK1 and promotes the interaction between TAK1 and RIPK1. Additionally, R406/R788 has been found to enhance the anticancer activities of TRAIL.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Tao Zhang, Daichao Xu, Elijah Trefts, Mingming Lv, Hiroyuki Inuzuka, Guobin Song, Min Liu, Jianlin Lu, Jianping Liu, Chen Chu, Min Wang, Huibing Wang, Huyan Meng, Hui Liu, Yuan Zhuang, Xingxing Xie, Fabin Dang, Dongxian Guan, Yuqin Men, Shuwen Jiang, Cong Jiang, Xiaoming Dai, Jing Liu, Zhen Wang, Peiqiang Yan, Jingchao Wang, Zhenbo Tu, Mrigya Babuta, Emily Erickson, Alissandra L. Hillis, Christian C. Dibble, John M. Asara, Gyongy Szabo, Piotr Sicinski, Ji Miao, Yu-Ru Lee, Lifeng Pan, Reuben J. Shaw, Junying Yuan, Wenyi Wei
Summary: This study reveals that AMPK phosphorylation of RIPK1 is a crucial metabolic checkpoint dictating cell fate response to metabolic stress, and highlights the previously unappreciated role of the AMPK-RIPK1 axis in integrating metabolism, cell death, and inflammation.
