Article
Multidisciplinary Sciences
Jin Meng, Ling Fu, Keke Liu, Caiping Tian, Ziyun Wu, Youngeun Jung, Renan B. Ferreira, Kate S. Carroll, T. Keith Blackwell, Jing Yang
Summary: The study provides a comprehensive assessment of cysteine reactivity and oxidative modifications in C. elegans, shedding light on redox signaling at the organismal level.
NATURE COMMUNICATIONS
(2021)
Article
Energy & Fuels
Wenchang Yang, Yaxin Wang, Yongzhou Huang, Jiaxian Yu, Tao Wang, Chengguo Li, Lei Yang, Peng Zhang, Liang Shi, Yuping Yin, Kaixiong Tao, Ruidong Li
Summary: Cuproptosis, a new cell death pathway induced by copper, is associated with mitochondrial respiration and mediated by protein lipoylation. This study explores the role of cuproptosis in colorectal cancer progression. The results show that elesclomol-Cu inhibits cell viability and promotes apoptosis in colorectal cancer cells. Additionally, 4-Octyl itaconate (4-OI) enhances cuproptosis and inhibits aerobic glycolysis through GAPDH, leading to better anti-tumor effects in vivo.
Article
Biochemistry & Molecular Biology
Xiaoling Zhang, Hao Liu, Haidong Wang, Rongjie Zhao, Qian Lu, Yunlong Liu, Yicheng Han, Hongming Pan, Weidong Han
Summary: This study found that b3galt5 is highly expressed in hepatocellular carcinoma (HCC) and associated with poor prognosis. It promotes the proliferation and survival of HCC cells and activates the mTOR/p70s6k pathway to enhance glycolysis through O-linked glycosylation modification. Inhibition of p70s6k reduces glycolysis in b3galt5-overexpressing cells. This study uncovers a novel mechanism and potential therapy target for HCC.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Vipul Batra, Vanya Bhushan, Syed Azmal Ali, Parul Sarwalia, Ankit Pal, Seema Karanwal, Subhash Solanki, Arumugam Kumaresan, Rakesh Kumar, Tirtha Kumar Datta
Summary: The study identified over 300 proteins on the ejaculated buffalo sperm surface, most of which were extracellular and involved in immune or reproductive processes. Flow cytometry with six FITC-labelled lectins confirmed glycosylation of these proteins, and various beta-defensins including BuBD-129 and 126 were identified on the sperm surface. The findings suggest that buffalo spermatozoa are heavily glycosylated and that BuBDs may play a role in sperm function and male fertility regulation.
Article
Biochemistry & Molecular Biology
Matthew E. R. Maitland, Miljan Kuljanin, Xu Wang, Gilles A. Lajoie, Caroline Schild-Poulter
Summary: Ubiquitination is a crucial post-translational modification that controls protein stability and function. The study identified potential substrates of the CTLH complex and revealed that the complex inhibits glycolysis by non-degradative ubiquitination of PKM2 and LDHA, thus playing a key role in regulating cellular metabolism.
Article
Microbiology
Haiying Ma, Yujuan Niu
Summary: A study found that highly pathogenic fowl adenovirus serotype 4 (FAdV-4) infection can restore the metabolic networks in host cells, and host cell metabolism plays an important role in virus replication. Furthermore, the production of the virus was significantly reduced when the host cells were cultured in glucose or glutamine-deficient conditions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Oncology
Yan Li, Xinying Qian, Yiyun Lin, Lei Tao, Zeping Zuo, Huaqin Zhang, Shengyong Yang, Xiaobo Cen, Yinglan Zhao
Summary: The study demonstrates that LSD1 inhibitor ZY0511 significantly alters lipid metabolism in colorectal and cervical cancer cells, reducing levels of phosphatidylserine, phosphatidylethanolamine, phosphatidylcholine, and sphingomyelin. This suggests that LSD1 may regulate cancer progression by affecting lipid metabolism.
Article
Biochemistry & Molecular Biology
Shun Yao, Xiaoli Zhang, Xiuxiu Jin, Mingzhu Yang, Ya Li, Lin Yang, Jin Xu, Bo Lei
Summary: This study revealed the changes in molecular proteins, signaling pathways, and cellular activities in skin fibroblasts derived from LHON patients through proteomic analysis and functional studies. The results confirmed the increased glycolysis, decreased oxidoreductase activity, and metabolic disturbance of fatty acid in LHON fibroblasts, providing further evidence for the mechanisms of mitochondrial dysfunction mediated by the m.G11778A mutation.
Article
Agriculture, Multidisciplinary
Nazrul Islam, Hari B. Krishnan, Janet Slovin, Savithiry Natarajan
Summary: A total of 718 metabolites were identified in the leaves and seeds of a soybean mutant, which contains 21 deleted genes and exhibits higher protein content in seeds. Among these metabolites, 164 were found only in seeds, 89 only in leaves, and 465 in both tissues. The mutant showed higher abundance of certain flavonoids and other metabolites in leaves compared to the wild type, as well as increased cysteine content in both leaves and seeds. This study provides valuable insights into the metabolic effects of gene deletions in soybean and their potential application in breeding improved nutritional traits.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yao Shen, Mao Sun, Jun Zhu, Mengying Wei, Huichen Li, Pan Zhao, Jiajia Wang, Ruikai Li, Lianlian Tian, Yanyan Tao, Peng Shen, Jian Zhang
Summary: Metabolic reprogramming in colorectal cancer was characterized through metabolomics analysis, revealing important metabolic changes and their correlation with the prognosis of colorectal cancer patients.
Article
Biotechnology & Applied Microbiology
Mu-En Chen, Mong-Hsun Tsai, Hsiang-Ting Huang, Ching-Chu Tsai, Mei-Ju Chen, Da-Syuan Yang, Teng-Zhi Yang, John Wang, Rong-Nan Huang
Summary: This study focused on the egg transcriptome of Forcipomyia taiwana, a biting midge, revealing that the down-regulation of key genes laccase2 and DCE/yellow in the melanin synthesis pathway may be responsible for the NaCl-induced inhibition of egg melanization.
Article
Cell Biology
Yue Gong, Peng Ji, Yun-Song Yang, Shao Xie, Tian-Jian Yu, Yi Xiao, Ming-Liang Jin, Ding Ma, Lin-Wei Guo, Yu-Chen Pei, Wen-Jun Chai, Da-Qiang Li, Fan Bai, Francois Bertucci, Xin Hu, Yi-Zhou Jiang, Zhi-Ming Shao
Summary: This study investigated metabolic dysregulation in TNBCs using a multi-omics database, identifying three heterogeneous metabolic-pathway-based subtypes with distinct metabolic features. These subtypes had different prognoses, molecular subtype distributions, and genomic alterations, as well as varying sensitivities to metabolic inhibitors targeting fatty acid synthesis and glycolysis. Additionally, inhibition of lactate dehydrogenase could enhance tumor response to anti-PD-1 immunotherapy in specific TNBC subtypes.
Article
Plant Sciences
Xinqiao Zhan, Yingpeng Tong
Summary: In this study, comparative transcriptome analyses revealed significant enrichment of terpenoid biosynthesis and cytochrome P450 pathways in Sinocalycanthus chinensis. Phylogenetic analysis showed high sequence similarity of terpene synthases between S. chinensis and Arabidopsis, classified into three subfamilies. Most phytohormone pathway-related genes were upregulated in flowers and downregulated in leaves.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Lulu Jiang, Sixiu Liu, Xinglong Jia, Qinting Gong, Xin Wen, Weiwei Lu, Jintong Yang, Xinyuan Wu, Xuan Wang, Yanrui Suo, Yilin Li, Motonari Uesugi, Zhi-bei Qu, Minjia Tan, Xiaojie Lu, Lu Zhou
Summary: DNA-encoded chemical library (DEL) is a widely used method for lead compound discovery. This study focuses on the design and utility of tyrosine-targeting DELs and successfully identifies tyrosine-targetable proteins as models for covalent inhibitors. The strategy of combining activity-based proteome profiling and covalent DEL enrichment shows the potential use of this methodology in further covalent drug discovery.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Cell Biology
Kerui Fan, Kun Chen, Xinyan Zan, Ying Zhi, Xue Zhang, Xinyue Zhang, Jinghuan Qiu, Gang Liu, Longjiang Li, Li Tang, Kai Hu, Jingyuan Wan, Xianqiong Gong, Yongqiang Yang, Li Zhang
Summary: Accumulating evidence suggests that metabolic responses are closely related to signal transduction, providing new opportunities for controlling various disorders. This study investigated the molecular mechanisms of IRG1/itaconate in regulating apoptosis in mice with LPS/D-Gal-induced liver injury. The findings showed that IRG1 deletion increased hepatocyte apoptosis and liver injury, and impaired the Nrf2 signaling and enhanced the activation of the AMPK/JNK pathway. Furthermore, supplementation with 4-octyl itaconate resulted in beneficial outcomes in fulminant liver injury. Therefore, IRG1/itaconate might function as a negative regulator of AMPK-induced hepatocyte apoptosis in LPS/D-Gal-induced liver injury.
CELL DEATH & DISEASE
(2023)
Article
Chemistry, Physical
Qianqian Guo, Dongshan Wu, Lei Gao, Yingjie Bai, Yuan Liu, Nianxin Guo, Xiaoxia Du, Jun Yang, Xiaoming Wang, Xiaoguang Lei
Article
Chemistry, Multidisciplinary
Nan Chen, Yuan Liu, Yuanpei Li, Chu Wang
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Chemistry, Multidisciplinary
Wei Qin, Yanling Zhang, Huan Tang, Dongyang Liu, Ying Chen, Yuan Liu, Chu Wang
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Review
Biochemical Research Methods
Wei Qin, Kelvin F. Cho, Peter E. Cavanagh, Alice Y. Ting
Summary: This article introduces the proximity labeling technology for studying and applying molecular interactions. By fusing baits with promiscuous enzymes, endogenous molecules interacting with them can be tagged and identified by mass spectrometry or nucleic acid sequencing. PL technology has been used to map protein-protein, protein-RNA, and protein-DNA interactions.
Article
Oncology
Kezhong Chen, Yuntao Nie, Samina Park, Kai Zhang, Yangming Zhang, Yuan Liu, Bengang Hui, Lixin Zhou, Xun Wang, Qingyi Qi, Hao Li, Guannan Kang, Yuqing Huang, Yingtai Chen, Jiabao Liu, Jian Cui, Mingru Li, In Kyu Park, Chang Hyun Kang, Haifeng Shen, Yingshun Yang, Tian Guan, Yaxiao Zhang, Fan Yang, Young Tae Kim, Jun Wang
Summary: The study developed and validated a machine learning-based model for estimating the malignant probability of multiple pulmonary nodules, demonstrating excellent discrimination and calibration in the development cohort. External validation and prospective comparison showed higher AUC values and increased sensitivity and specificity. The model outperformed traditional models, clinicians, and a computer-aided diagnosis system, presenting solid performance as a convenient reference for decision-making.
CLINICAL CANCER RESEARCH
(2021)
Article
Microbiology
Hejun Liu, Meng Yuan, Deli Huang, Sandhya Bangaru, Fangzhu Zhao, Chang-Chun D. Lee, Linghang Peng, Shawn Barman, Xueyong Zhu, David Nemazee, Dennis R. Burton, Marit J. van Gils, Rogier W. Sanders, Hans-Christian Kornau, S. Momsen Reincke, Harald Pruss, Jakob Kreye, Nicholas C. Wu, Andrew B. Ward, Ian A. Wilson
Summary: This study presents a cross-neutralizing antibody, CV38-142, which can accommodate antigenic variation in SARS-related viruses, providing valuable information for addressing current and future antigenic drift in SARS-CoV-2 and protecting against zoonotic SARS-related coronaviruses.
CELL HOST & MICROBE
(2021)
Article
Immunology
Deli Huang, Jenny Tuyet Tran, Linghang Peng, Linlin Yang, Raymond T. Suhandynata, Melissa A. Hoffman, Fangzhu Zhao, Ge Song, Wan-Ting He, Oliver Limbo, Sean Callaghan, Elise Landais, Raiees Andrabi, Devin Sok, Joseph G. Jardine, Dennis R. Burton, James E. Voss, Robert L. Fitzgerald, David Nemazee
Summary: This study introduces a rapid and accurate assay for detecting receptor binding domain nAbs, utilizing a proximity-based luciferase assay. The method was validated and shown to be particularly useful in HIV patients, offering a cost-effective and real-time alternative for evaluating the potency of SARS-CoV-2 nAbs induced by infection or vaccines.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Cell Biology
Hyeseon Cho, Kristina Kay Gonzales-Wartz, Deli Huang, Meng Yuan, Mary Peterson, Janie Liang, Nathan Beutler, Jonathan L. Torres, Yu Cong, Elena Postnikova, Sandhya Bangaru, Chloe Adrienna Talana, Wei Shi, Eun Sung Yang, Yi Zhang, Kwanyee Leung, Lingshu Wang, Linghang Peng, Jeff Skinner, Shanping Li, Nicholas C. Wu, Hejun Liu, Cherrelle Dacon, Thomas Moyer, Melanie Cohen, Ming Zhao, Frances Eun-Hyung Lee, Rona S. Weinberg, Iyadh Douagi, Robin Gross, Connie Schmaljohn, Amarendra Pegu, John R. Mascola, Michael Holbrook, David Nemazee, Thomas F. Rogers, Andrew B. Ward, Ian A. Wilson, Peter D. Crompton, Joshua Tan
Summary: Research isolated 216 monoclonal antibodies from patients with COVID-19, with three potent antibodies neutralizing the Alpha and Beta variants of SARS-CoV-2. Bispecific antibodies designed through distinct mechanisms showed high efficacy in inhibiting virus infection, with one exhibiting over 100-fold higher potency than a monoclonal antibody cocktail and protecting against disease in hamster models.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Wei Qin, Samuel A. Myers, Dominique K. Carey, Steven A. Carr, Alice Y. Ting
Summary: Proximity labeling combined with organic-aqueous phase separation is a versatile approach for mapping and discovering proteins with novel functions in specific subcellular compartments. The method enables the identification of RNA binding proteins in the nucleus, nucleolus, and outer mitochondrial membrane.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Panpan Zhou, Meng Yuan, Ge Song, Nathan Beutler, Namir Shaabani, Deli Huang, Wan-Ting He, Xueyong Zhu, Sean Callaghan, Peter Yong, Fabio Anzanello, Linghang Peng, James Ricketts, Mara Parren, Elijah Garcia, Stephen A. Rawlings, Davey M. Smith, David Nemazee, John R. Teijaro, Thomas F. Rogers, Ian A. Wilson, Dennis R. Burton, Raiees Andrabi
Summary: This study describes a broadly neutralizing antibody CC40.8 that targets the spike fusion machinery of coronaviruses and demonstrates its protective efficacy against SARS-CoV-2 in animal models, indicating its potential for the development of pan-coronavirus vaccines.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Cherrelle Dacon, Courtney Tucker, Linghang Peng, Chang-Chun D. Lee, Ting-Hui Lin, Meng Yuan, Yu Cong, Lingshu Wang, Lauren Purser, Jazmean K. Williams, Chul-Woo Pyo, Ivan Kosik, Zhe Hu, Ming Zhao, Divya Mohan, Andrew J. R. Cooper, Mary Peterson, Jeff Skinner, Saurabh Dixit, Erin Kollins, Louis Huzella, Donna Perry, Russell Byrum, Sanae Lembirik, David Drawbaugh, Brett Eaton, Yi Zhang, Eun Sung Yang, Man Chen, Kwanyee Leung, Rona S. Weinberg, Amarendra Pegu, Daniel E. Geraghty, Edgar Davidson, Iyadh Douagi, Susan Moir, Jonathan W. Yewdell, Connie Schmaljohn, Peter D. Crompton, Michael R. Holbrook, David Nemazee, John R. Mascola, Ian A. Wilson, Joshua Tan
Summary: This study identified six monoclonal antibodies that bind to spike proteins from all seven human-infecting coronaviruses. Two of these antibodies, COV44-62 and COV44-79, showed broad neutralizing activity against alpha- and betacoronaviruses, including the Omicron subvariants of SARS-CoV-2. The fusion peptide region in the spike protein was found to be a potential candidate epitope for next-generation coronavirus vaccine development.
Article
Microbiology
Cherrelle Dacon, Linghang Peng, Ting-Hui Lin, Courtney Tucker, Chang-Chun D. Lee, Yu Cong, Lingshu Wang, Lauren Purser, Andrew J. R. Cooper, Jazmean K. Williams, Chul-Woo Pyo, Meng Yuan, Ivan Kosik, Zhe Hu, Ming Zhao, Divya Mohan, Mary Peterson, Jeff Skinner, Saurabh Dixit, Erin Kollins, Louis Huzella, Donna Perry, Russell Byrum, Sanae Lembirik, Michael Murphy, Yi Zhang, Eun Sung Yang, Man Chen, Kwanyee Leung, Rona S. Weinberg, Amarendra Pegu, Daniel E. Geraghty, Edgar Davidson, Benjamin J. Doranz, Iyadh Douagi, Susan Moir, Jonathan W. Yewdell, Connie Schmaljohn, Peter D. Crompton, John R. Mascola, Michael R. Holbrook, David Nemazee, Ian A. Wilson, Joshua Tan
Summary: In this study, 55 monoclonal antibodies were identified from COVID-19 convalescent donors that can bind diverse betacoronavirus spike proteins. Most antibodies targeted a non-neutralizing S2 epitope, but 11 antibodies targeting the stem helix showed neutralizing activity against different betacoronavirus lineages. These findings revealed a class of IGHV1-46/IGKV3-20 antibodies that can broadly neutralize betacoronaviruses by targeting the stem helix.
CELL HOST & MICROBE
(2023)
Article
Mathematical & Computational Biology
Peng Bai, Yang Zhou, Yuan Liu, Gang Li, Zhengqian Li, Tao Wang, Xiangyang Guo
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE
(2020)