Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H. A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: The 2021 Metrics of the HUPO Human Proteome Project (HPP) reveal significant progress in detecting protein expression in the human genome. The number of missing proteins has decreased, and the utilization of proteomics in biological and clinical research continues to expand and integrate effectively with other omics platforms. This represents a promising advancement in understanding the human proteome and its potential applications in healthcare.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Article
Plant Sciences
Liangqian Yu, Sidra Iqbal, Yuting Zhang, Guofang Zhang, Usman Ali, Shaoping Lu, Xuan Yao, Liang Guo
Summary: The study found that a large number of proteins in Brassica napus undergo sulphenylation during salt stress, with many proteins localizing to chloroplasts and cytoplasm and enzyme activity affected. Differential sulphenylated proteins indicate that metabolic processes such as photosynthesis and glycolysis play important roles in the response.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Pharmacology & Pharmacy
Zi Ye, Ke Wang, Lianguo Chen, Xiaofeng Jin, Hao Chen, Guanghui Tang, Shao Q. Yao, Zhiqiang Feng, Chong-Jing Zhang
Summary: A new type of TCIs (FL-18) with proteome-wide selectivity for p97 is reported. FL-18 showed potent inhibition towards U87MG tumor cells and selectively modified endogenous p97 as confirmed by various validation methods. FL-18 selectively modified cysteine residues located within the D2 ATP site of p97. This study provides a promising scaffold for cancer therapy.
ACTA PHARMACEUTICA SINICA B
(2022)
Article
Multidisciplinary Sciences
Philip To, Yingzi Xia, Sea On Lee, Taylor Devlin, Karen G. Fleming, Stephen D. Fried
Summary: The process of protein folding is complex and important, involving cellular factors and processes. Researchers have developed a new method to monitor the structural changes of Escherichia coli proteins in the cell cytosol and with chaperones. The results show that GroEL can assist in refolding the majority of proteins, while DnaK and GroEL have a similar set of proteins that they refold. Additionally, some proteins are not able to be refolded with any chaperones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Jeffrey Molendijk, Ronnie Blazev, Richard J. Mills, Yaan-Kit Ng, Kevin Watt, Daryn Chau, Paul Gregorevic, Peter J. Crouch, James B. W. Hilton, Leszek Lisowski, Peixiang Zhang, Karen Reue, Aldons J. Lusis, James E. Hudson, David E. James, Marcus M. Seldin, Benjamin L. Parker
Summary: By conducting proteomic analysis and correlation network analysis, multiple regulators of muscle function were identified, providing new insights for improving muscle function.
Article
Biochemistry & Molecular Biology
Alejandro Ceron-Noriega, Miguel V. Almeida, Michal Levin, Falk Butter
Summary: Nematodes are a diverse group of animals with over 24,000 described species, but most of them lack comprehensive gene annotations. This study used proteotranscriptomics to improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genomes. The methodology was validated by identifying two previously undescribed genes in the model organism Caenorhabditis elegans. Extensive analysis of the comprehensive proteome annotation provided new insights into the evolutionary processes of this metazoan group.
Article
Microbiology
Hengwei Qian, Lulu Wang, Xianliang Ma, Xingling Yi, Baoshan Wang, Wenxing Liang
Summary: Protein lysine 2-hydroxyisobutyrylation (K-hib) is a new type of post-translational modification that plays important roles in various biological processes in both eukaryotic and prokaryotic cells. This study identified 3782 K-hib sites in 1299 proteins in Fusarium oxysporum, showing involvement in a variety of pathways and interactions, particularly in the virulence and conidiation of the pathogenic fungus. The different levels of K-hib in conidial and mycelial stages suggest potential regulatory roles in pathogenesis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Endocrinology & Metabolism
Alice Giontella, Loukas Zagkos, Milan Geybels, Susanna C. Larsson, Ioanna Tzoulaki, Christos S. Mantzoros, Birgitte Andersen, Dipender Gill, Helene T. Cronje
Summary: This study investigates the effects of fibroblast growth factor 21 (FGF21) on kidney function using a genetic variant as an instrumental variable. The results suggest that genetically predicted FGF21 has renoprotective effects and is associated with lower risk of chronic kidney disease (CKD) and improved cardiometabolic profiles. This highlights the potential repurposing opportunity of FGF21 for the treatment and prevention of kidney disease.
METABOLISM-CLINICAL AND EXPERIMENTAL
(2023)
Article
Microbiology
Kaspar Valgepea, Gert Talbo, Nobuaki Takemori, Ayako Takemori, Christina Ludwig, Vishnuvardhan Mahamkali, Alexander P. Mueller, Ryan Tappel, Michael Kopke, Sean Dennis Simpson, Lars Keld Nielsen, Esteban Marcellin
Summary: Microbes that can recycle C-1 greenhouse gases into fuels and chemicals are crucial for the sustainability of future industries. In this study, the absolute proteomics technique was used to quantify protein concentrations in the acetogen Clostridium autoethanogenum, revealing the importance of proteome allocation for C-1 fixation.
Article
Biochemical Research Methods
Taylur P. P. Ma, Anita Izrael-Tomasevic, Rana Mroue, Hanna Budayeva, Sushant Malhotra, Ryan Raisner, Marie Evangelista, Christopher M. M. Rose, Donald S. S. Kirkpatrick, Kebing Yu
Summary: Recent advancements in targeted covalent inhibitors have garnered considerable interest for their potential applications in drug development for challenging therapeutic targets. In this study, a novel isobaric 11plex-AzidoTMT reagent and a new workflow called AT-MAPP were introduced, greatly enhancing the multiplexing ability compared to the traditional isoTOP-ABPP method. These techniques were successfully applied to identify cysteine on- and off-targets using a covalent inhibitor, demonstrating their potential in activity-based protein profiling and covalent drug development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Wanderson Marques da Silva, Nubia Seyffert, Artur Silva, Vasco Azevedo
Summary: This article highlights the importance of using proteomics and bioinformatics tools in genomic functional studies of Corynebacterium pseudotuberculosis, revealing different patterns of protein modulation and identifying potential drug and vaccine targets. The combination of these studies expands our knowledge of the pathophysiology of this pathogen.
Review
Biochemical Research Methods
Rui Vitorino, Manisha Choudhury, Sofia Guedes, Rita Ferreira, Visith Thongboonkerd, Lakshya Sharma, Francisco Amado, Sanjeeva Srivastava
Summary: With the availability of genomic data and advancements in high-throughput sequencing technologies, peptidomics and proteogenomics have become important tools for studying peptides and proteins associated with gene mutations or genome remodeling. This article provides an overview of techniques for analyzing peptidomics and proteogenomics, as well as bioinformatics workflows for understanding differentially expressed peptides/proteins in disease pathogenesis. Additionally, it highlights the role of these technologies in deciphering disease pathways, cancer research, and biomarker discovery using biofluids, while discussing the challenges and future requirements for their clinical use.
EXPERT REVIEW OF PROTEOMICS
(2021)
Review
Biochemical Research Methods
Luis Perpetuo, Julie Klein, Rita Ferreira, Sofia Guedes, Francisco Amado, Adelino Leite-Moreira, Artur M. S. Silva, Visith Thongboonkerd, Rui Vitorino
Summary: Peptidomics is an emerging field that utilizes advanced techniques for analyzing peptides in biological samples. Computational methods, particularly artificial intelligence, are used to predict therapeutic peptides efficiently, which have become essential tools in protein science for discovering novel therapeutic peptides.
EXPERT REVIEW OF PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Thiago Seraphim, Nardin Nano, Yiu Wing Sunny Cheung, Siripat Aluksanasuwan, Carolina Colleti, Yu-Qian Mao, Vaibhav Bhandari, Gavin Young, Larissa Holl, Sadhna Phanse, Yuliya Gordiyenko, Daniel R. Southworth, Carol Robinson, Visith Thongboonkerd, Lisandra M. Gava, Julio C. Borges, Mohan Babu, Leandro R. S. Barbosa, Carlos H. Ramos, Philipp Kukura, Walid A. Houry
Summary: The R2TP complex, formed by RUVBL1 and RUVBL2 ATPases, associates with PIH1D1 and RPAP3 proteins and plays a role in promoting the formation of macromolecular complexes. RPAP3 is identified as the central subunit of R2TP, linking PIH1D1 and RUVBL1/2. The study provides insights into the structure and function of the R2TP complex.
Article
Oncology
Paleerath Peerapen, Kanyarat Sueksakit, Wanida Boonmark, Sunisa Yoodee, Visith Thongboonkerd
Summary: Loss of ARID1A is associated with higher grade of colorectal cancer. In this study, knockdown of ARID1A resulted in decreased cell death and senescence, enhanced cell proliferation, chemoresistance and invasion. Additionally, ARID1A knockdown led to the formation of polyploid giant cancer cells, increased cell aggregation and secretion of vascular endothelial growth factor (VEGF).
Article
Medicine, Research & Experimental
Paleerath Peerapen, Wanida Boonmark, Visith Thongboonkerd
Summary: This study investigated the protective effects and mechanisms of trigonelline against kidney stone formation. The results showed that trigonelline can reduce stone formation by inhibiting crystallization, crystal growth, and crystal-cell adhesion. Additionally, trigonelline downregulated crystal receptors on the apical membranes of renal tubular cells.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Chadanat Noonin, Paleerath Peerapen, Sunisa Yoodee, Chompunoot Kapincharanon, Rattiyaporn Kanlaya, Visith Thongboonkerd
Summary: This study clarifies the inhibitory roles of native human urinary THP in calcium oxalate monohydrate (COM) kidney stone formation. THP reduces COM crystal size, inhibits crystal growth and aggregation, and prevents crystal-cell adhesion. These inhibitory effects are predominantly mediated via the high affinity of THP with calcium ions.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Rattiyaporn Kanlaya, Chompunoot Kapincharanon, Kedsarin Fong-ngern, Visith Thongboonkerd
Summary: This study investigated the potential of epigallocatechin-3-gallate (EGCG) to reverse epithelial-mesenchymal transition (EMT) and restore normal cell morphology. The results demonstrated that EGCG effectively reversed EMT and inhibited tumor and fibrosis.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2022)
Article
Toxicology
Chanettee Chanthick, Visith Thongboonkerd
Summary: This study found that hyaluronic acid promotes the formation of calcium oxalate kidney stones by enhancing crystal growth, adhesion to cells, and invasion through the extracellular matrix. These findings provide an explanation for the higher levels of hyaluronic acid in the urine of stone patients.
TOXICOLOGY IN VITRO
(2022)
Article
Genetics & Heredity
Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert S. Omenn, Peter L. Freddolino, Dong-Jun Yu, Yang Zhang
Summary: This study proposes a new method called TripletGO, which deduces GO terms of genes through the integration of four complementary pipelines. Experimental results show that TripletGO achieves significantly better function annotation accuracy compared to the current state-of-the-art approaches.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Rattiyaporn Kanlaya, Visith Thongboonkerd
Summary: This study demonstrates that persistent infection by E. coli may contribute to COM metabolic stone formation by translocation of ezrin to apical membranes, thereby promoting COM crystal-cell adhesion.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sunisa Yoodee, Paleerath Peerapen, Sirikanya Plumworasawat, Visith Thongboonkerd
Summary: This study found that heat-shock protein 90 (HSP90) and its four functional domains play important roles in the formation of kidney stones, promoting the crystallization, growth, aggregation, adhesion onto renal cells, and invasion through the extracellular matrix (ECM) of calcium oxalate monohydrate (COM) crystals.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Visith Thongboonkerd, Rattiyaporn Kanlaya
Summary: Exosomes are nanoscale vesicles derived from late endosomes and released from cells. They selectively encapsulate biomolecules and play roles in cell-cell communication. In kidney diseases, exosomes have divergent roles in pathogenesis, diagnostics, prognostics, and therapeutics.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sakdithep Chaiyarit, Visith Thongboonkerd
Summary: The research reveals that oxidative modification can reverse the modulatory activity of the urinary protein uromodulin (UMOD), promoting calcium oxalate stone formation. Oxidized forms of UMOD facilitate CaOx crystallization and crystal growth, while having no effect on crystal aggregation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Medicine, Research & Experimental
Sudarat Hadpech, Visith Thongboonkerd
Summary: CyPA is an immunophilin widely expressed in various cell types and tissues, with higher expression in proximal tubular epithelial cells in the kidney. Changes in CyPA expression and secretion play important roles in kidney diseases. Urinary CyPA shows promise as a diagnostic/prognostic marker in several kidney diseases. Understanding the theranostic roles of CyPA in kidney diseases may offer insights for designing new therapeutic interventions and prevention strategies.
