Article
Oncology
E. G. Garcia, A. Veloso, M. L. Oliveira, J. R. Allen, S. Loontiens, D. Brunson, D. Do, C. Yan, R. Morris, S. Iyer, S. P. Garcia, N. Iftimia, W. Van Loocke, F. Matthijssens, K. McCarthy, J. T. Barata, F. Speleman, T. Taghon, A. Gutierrez, P. Van Vlierberghe, W. Haas, J. S. Blackburn, D. M. Langenau
Summary: The study identifies PRL3 as a collaborating oncogenic driver in T-ALL, which synergizes with MYC to promote leukemia development and suppress apoptosis in cells. By suppressing downstream phosphorylation signaling pathways, PRL3's role in T-ALL is elucidated.
Article
Biochemistry & Molecular Biology
Nicholas K. K. Tonks
Summary: In October 2020, a celebration for Eddy Fischer's 100th birthday was held via ZOOM due to COVID restrictions. Eddy Fischer, along with Ed Krebs, made significant contributions to the field of signal transduction through their discovery of reversible protein phosphorylation. This work has had a profound impact on the biotechnology industry and the treatment of various cancers.
Article
Multidisciplinary Sciences
Samme Amena Tasmia, Md Kaderi Kibria, Khanis Farhana Tuly, Md Ariful Islam, Mst Shamima Khatun, Md Mehedi Hasan, Md Nurul Haque Mollah
Summary: In this study, a computational predictor was developed to predict serine phosphorylation sites in Schizosaccharomyces pombe. The proposed method achieved the highest scores in various performance measurements compared to other models, indicating its success. This research is of great importance for predicting serine phosphorylation sites in fungi.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yuri N. Chirgadze, Kevin P. Battaile, Ilya Likhachev, Nikolay K. Balabaev, Roni D. Gordon, Vladimir Romanov, Andres Lin, Robert Karisch, Robert Lam, Max Ruzanov, Evgeniy Brazhnikov, Emil F. Pai, Benjamin G. Neel, Nickolay Y. Chirgadze
Summary: In this study, crystal structures of PTP1B apo-enzyme and a complex with a newly identified allosteric inhibitor were presented. The inhibitor binding site is located 18A away from the active center, causing significant rearrangements in the enzyme's active center. Signals from the inhibitor were found to transfer to the catalytic area through dynamic fluctuations of protein structure.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Tony Hunter
Summary: Protein phosphorylation is a reversible post-translational modification involving various natural amino acids. While serine, threonine, and tyrosine phosphorylation have been extensively studied, less is known about non-canonical phosphorylations such as histidine phosphorylation. Recent advances in research tools have accelerated our understanding of the multifaceted functions of histidine phosphorylation in cellular processes.
Article
Oncology
Marie Schwarz, Sophie Rizzo, Walter Espinoza Paz, Anne Kresinsky, Damien Thevenin, Joerg P. Mueller
Summary: This study demonstrates that mutations in PTPRJ can increase its activity and impair FLT3 activity in acute myeloid leukemia cells, thereby restricting the transformation and proliferation abilities of leukemic cells.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Emily C. Suter, Eva M. Schmid, Andrew R. Harris, Erik Voets, Brian Francica, Daniel A. Fletcher
Summary: The study reveals that the phagocytic decisions of macrophages are regulated by the ratio of activating ligand to inhibitory ligand, and a ratio of at least 10:1 is required for promoting phagocytosis. Ratiometric signaling is crucial for phagocytosis of tumor cells and can be modified by blocking SIRP alpha.
Article
Biochemistry & Molecular Biology
Jannis Ulke, Christian Schwedler, Janine Krueger, Vanessa Stein, Peter Geserick, Andre Kleinridders, Kai Kappert
Summary: This study characterized the glycosylation pattern of PTPRJ in the liver and found that high-fat diet-induced obesity altered the glycosylation pattern of PTPRJ. These findings provide new insights into the role of glycosylation in metabolic disorders.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2024)
Review
Biochemistry & Molecular Biology
Kalle Gehring, Guennadi Kozlov, Meng Yang, Rayan Fakih
Summary: Phosphatases of regenerating liver (PRLs) are protein phosphatases involved in the control of cell growth and migration. Recent studies have shown that PRLs have dual functions as both catalytically active enzymes and pseudophosphatases, contributing to their unique properties.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jeffery T. T. Jolly, Ty C. C. Cheatham, Jessica S. S. Blackburn
Summary: Phosphatase of regenerating liver 3 (PRL-3) is associated with cancer metastasis and interacts with the CNNM family of proteins to regulate intracellular metal concentration. However, the factors that regulate PRL-3's activity and its interactions with CNNM proteins are unknown.
Article
Biochemistry & Molecular Biology
Kyoko Nakajima, Shota Araki, Masahiro Kawahara
Summary: In this study, minimal synthetic receptors were engineered by incorporating multiple tyrosine motifs to reconstitute signaling properties. These receptors, activated by synthetic small-molecule ligands, were able to recruit and activate up to four signaling molecules of interest, offering potential for analyzing and controlling cell fate.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Louise Pinet, Nadine Assrir, Carine van Heijenoort
Summary: ErbBs are receptor tyrosine kinases involved in development and diseases, with their C-terminal tails (CTs) shown to be intrinsically disordered and involved in phosphorylation and interaction processes. Recent studies reveal active roles of CT in regulating kinase activity, modulating phosphorylation events, and the importance of prolines in structural dynamics and regulatory interactions.
Article
Biology
Mohammad Arefian, N. Bhagya, T. S. Keshava Prasad
Summary: Protein phosphorylation plays a critical role in regulating plant growth, especially during the morphogenesis at flowering stage. Further research on the phosphorylation regulation mechanisms during flowering is needed, which may have a positive impact on increasing crop productivity.
BIOLOGICAL REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Jesse Stoop, Erik H. Douma, Marc van Der Vlag, Marten P. Smidt, Lars P. van Der Heide
Summary: Our study provides detailed insights into the regulation of dopamine synthesis, revealing that Ser40 phosphorylation serves as the crucial switch controlling tyrosine hydroxylase activity.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Cell Biology
Chen Gao, Nancy Cao, Yibin Wang
Summary: Protein phosphorylation and dephosphorylation play crucial roles in various aspects of cellular function, with metal dependent protein phosphatases being recognized as important components in the signal transduction network. Individual PPM isoforms have been found to have specific functions in signaling and cellular processes, and abnormal PPM expression and activity are implicated in major human diseases. Inhibitors targeting PPM members have been developed as potential therapeutic strategies for human diseases.
CELLULAR SIGNALLING
(2021)
Article
Cell Biology
Yunpeng Bai, Guimei Yu, Hong-Ming Zhou, Ovini Amarasinghe, Yuan Zhou, Peipei Zhu, Qinglin Li, Lujuan Zhang, Frederick Nguele Meke, Yiming Miao, Eli Chapman, W. Andy Tao, Zhong-Yin Zhang
Summary: Overexpression of PTP4A phosphatases is associated with advanced cancers and their biological functions are not fully understood. In this study, we identified VCP/p97 as a substrate of PTP4A2. PTP4A2 dephosphorylates VCP at Tyr805, allowing the association of VCP with its cofactors in the ELDR complex, which is involved in lysophagy and lysosomal homeostasis. Deletion of Ptp4a2 disrupts lysosomal homeostasis and impairs recovery from acute kidney injury.
Article
Chemistry, Analytical
Xin Feng, Anton Iliuk, Xiaoye Zhang, Shengnan Jia, Ao Shen, Wenke Zhang, Lianghai Hu, W. Andy Tao
Summary: In this study, an amphiphile-dendrimer supramolecular probe (ADSP) was developed for efficient capture and high-throughput analysis of exosomes, allowing the detection of marker proteins. The ADSP forms a supramolecular complex with exosomes by interacting with their phospholipid bilayers, and can be easily coated onto magnetic beads or nitrocellulose membranes for capture. This new strategy exhibits excellent extraction capability, superior sensitivity, good quantitation ability, and high throughput using clinical samples.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Jie Sun, Qing Li, Yajie Ding, Dong Wei, Marco Hadisurya, Zhuojun Luo, Zhongze Gu, Bobin Chen, W. Andy Tao
Summary: Researchers introduced a functionally tunable material and strategy, extracellular vesicles to phosphoproteins (EVTOP), for monitoring disease-relevant phosphorylation events in circulating biofluids. EVs were efficiently isolated by magnetic beads and enriched for phosphopeptides for phosphoproteomic analyses. This platform enables the quantitative detection of a large number of EV phosphopeptides in a small volume of biofluids, presenting broad clinical applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Oncology
Xiaoqing Cheng, Yirui Sun, Maureen Highkin, Nagalaxmi Vemalapally, Xiaohua Jin, Brandon Zhou, Julie L. Prior, Ashley R. Tipton, Shunqiang Li, Anton Iliuk, Samuel Achilefu, Ian S. Hagemann, John R. Edwards, Ron Bose
Summary: In HER2-mutated breast cancer, PIK3CA mutation activates p21-CDK4/6-cyclin D1 signaling to drive resistance to HER2-targeted therapies, which can be overcome using CDK4/6 inhibitors.
Article
Biochemical Research Methods
Xin Feng, Shengnan Jia, Muhammad Mujahid Ali, Guiyuan Zhang, Dejun Li, W. Andy Tao, Lianghai Hu
Summary: This study analyzed the urinary exosomal proteome and performed high-throughput downstream validation using a supramolecular probe-based capture and in situ detection. The technology efficiently enriched exosomes from urine samples with high concentration (5.5 x 1010 particles/mL) and high purity (2.607 x 1010 particles/mg). Proteomic analysis revealed 68 up-regulated proteins in patients with hepatocellular carcinoma, and three of them were validated using the supramolecular probe-based array.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Marco Hadisurya, Zheng-Chi Lee, Zhuojun Luo, Guiyuan Zhang, Yajie Ding, Hao Zhang, Anton B. Iliuk, Roberto Pili, Ronald S. Boris, W. Andy Tao
Summary: The translation of cancer signaling research into clinical application has been slow and ineffective. However, extracellular vesicles (EVs) show promise as a source for developing disease phosphoprotein markers. This study focuses on using mass spectrometry to profile urinary EV phosphoproteomics for renal cell cancer (RCC) differentiation. By optimizing the process of EV isolation, phosphopeptide enrichment, and DIA method, this study provides a powerful tool for future clinical applications.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Correction
Biochemistry & Molecular Biology
Ammara Abdullah, Saeed Salehin Akhand, Juan Sebastian Paez Paez, Wells Brown, Li Pan, Sarah Libring, Michael Badamy, Emily Dykuizen, Luis Solorio, W. Andy Tao, Michael K. Wendt
Review
Chemistry, Analytical
Xiaofeng Wu, Yi-Kai Liu, Anton B. Iliuk, W. Andy Tao
Summary: Protein phosphorylation is crucial for cellular physiology and dysregulation of phosphorylation events can lead to diseases. Clinical analysis of disease-related phosphoproteins provides unique information for precision medicine. Mass spectrometry (MS) is a powerful tool for identifying and studying phosphorylation events, and recent advances in sample preparation and instrument technology have contributed to its clinical applications. Data-independent acquisition method in MS and biofluid-derived extracellular vesicles are promising directions for future research and liquid biopsy.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Guochen Qin, Menghuan Qu, Bei Jia, Wei Wang, Zhuojun Luo, Chun-Peng Song, W. Andy Tao, Pengcheng Wang
Summary: This study developed a highly sensitive method for detecting S-nitrosylation peptides, allowing for quantitative identification of S-nitrosylated proteins and revealing a key role of GSNOR1 in regulating endoplasmic reticulum functions in Arabidopsis.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yi-Kai Liu, Xiaofeng Wu, Marco Hadisurya, Li Li, Hristos Kaimakliotis, Anton Iliuk, W. Andy Tao
Summary: Extracellular vesicle proteomics is a useful tool for discovering biomarkers for disease diagnosis and treatment. However, the current workflow for analyzing EV proteomes using mass spectrometry is not suitable for clinical settings. In this study, we developed a one-pot analytical pipeline that combines a robust EV isolation method and in situ protein sample preparation to detect urinary EV proteomes. This streamlined pipeline enabled the analysis of the entire EV proteome in one day and yielded better results compared to existing methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Zheng-Chi Lee, Marco Hadisurya, Zhuojun Luo, Li Li, W. Andy Tao
Summary: Extracellular vesicles (EVs) have been identified as a promising source of disease biomarkers. However, the current methods for processing EV samples have limitations in terms of yield, integrity, speed, capacity, and recovery efficiency. In this study, we developed a high-throughput automated workflow that enables efficient isolation, lysis, and extraction of proteins from EVs in clinical samples. The automated protocol shows reproducible and robust proteomic quantitation, and has been successfully applied to identify upregulated proteins in kidney cancer patients compared to healthy controls. This hands-free workflow has the potential to streamline biomarker discovery, tumor monitoring, and early cancer diagnoses in both clinical and research settings.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Analytical
Yuanyuan Deng, Qing Li, Jie Sun, Leyao Ma, Yajie Ding, Yuhan Cai, Anton Iliuk, Bobin Chen, Zhuoying Xie, W. Andy Tao
Summary: Primary central nervous system lymphoma (PCNSL) is a rare and aggressive type of non-Hodgkin's lymphoma, posing challenges in diagnosis and treatment. This study introduces a method called EVTRAP for efficient isolation of extracellular vesicles (EVs) from cerebrospinal fluid (CSF) and applies it to analyze phosphoproteomics in PCNSL patients. The results demonstrate the feasibility of EVTRAP-based strategy in detecting molecular markers for PCNSL.
Article
Medicine, Research & Experimental
Marco Hadisurya, Li Li, Kananart Kuwaranancharoen, Xiaofeng Wu, Zheng-Chi Lee, Roy N. Alcalay, Shalini Padmanabhan, W. Andy Tao, Anton Iliuk
Summary: Using urine extracellular vesicles (EVs), researchers identified potential diagnostic biomarkers for Parkinson's disease (PD) through proteomics and phosphoproteomics analysis.
COMMUNICATIONS MEDICINE
(2023)
Article
Biochemical Research Methods
Zheng-Chi Lee, Marco Hadisurya, Zhuojun Luo, Li Li, W. Andy Tao
Summary: This study developed an automated workflow for efficient and reproducible isolation and protein analysis of extracellular vesicles (EVs), overcoming the bottleneck in EV sample processing. The method identified a large number of potential biomarkers in kidney cancer patients compared to healthy controls, demonstrating its potential for biomarker discovery and early cancer diagnoses.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Jinmin Miao, Jiajun Dong, Yiming Miao, Yunpeng Bai, Zihan Qu, Brenson A. Jassim, Bo Huang, Quyen Nguyen, Yuan Ma, Allison A. Murray, Jinyue Li, Philip S. Low, Zhong-Yin Zhang
Summary: In this study, researchers discovered the first highly potent and selective TC-PTP degrader called TP1L, which can induce degradation of TC-PTP and enhance T-cell signaling and tumor killing efficacy.
