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
Oceane Girard, Regis Lavigne, Simon Chevolleau, Constance Onfray, Emmanuelle Com, Pierre-Olivier Schmit, Manuel Chapelle, Thomas Freour, Lydie Lane, Laurent David, Charles Pineau
Summary: The Chromosome-centric Human Proteome Project aims to identify and characterize the proteins encoded by the human genome. They have confirmed the existence of proteins for 93.2% of genes and focus on studying reproductive processes and embryonic development. Through their research, they have discovered 4 new missing proteins and deposited the data on ProteomeXchange.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemical Research Methods
Gilbert S. Omenn
Summary: The HUPO Human Proteome Project celebrates its 10th anniversary by achieving the milestone of confident detection of proteins from 90% of predicted protein-coding genes. This global project has influenced data-sharing, quality assurance, and issued stringent guidelines for detecting missing proteins. The project's impact is highlighted in special issues of Nature Communications and Journal of Proteome Research.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Multidisciplinary Sciences
Christine Olander, Jesper Edvardsson Rasmussen, Per Olof Eriksson, Goran Laurell, Helge Rask-Andersen, Jonas Bergquist
Summary: This study analyzed the proteomics of the endolymphatic sac using a refined sampling technique, identifying a total of 1656 non-redundant proteins, with 110 proteins unique to the endolymphatic sac. The results validate a strategy for in vivo and in situ human sampling during surgery and may form a platform for further investigations into the function of this intriguing part of the inner ear.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Deeptarup Biswas, Sanjyot Vinayak Shenoy, Chetanya Chetanya, Mercedes Lachen-Montes, Abhilash Barpanda, Arunachalam Paramasivan Athithyan, Susmita Ghosh, Karina Ausin, Maria Victoria Zelaya, Joaquin Fernandez-Irigoyen, Akash Manna, Sudesh Roy, Arunasu Talukdar, Graham Roy Ball, Enrique Santamaria, Sanjeeva Srivastava
Summary: This study presents the first draft of the human brain interhemispheric proteome, providing comprehensive coverage of 3300 experimentally measured proteins across multiple brain regions. Specific markers were identified in different brain regions, contributing to the understanding of brain disorders and synapse biology. An online portal, IBPM, was developed to facilitate research in neuroproteomics.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Martin D. Garlovsky, Jessica A. Sandler, Timothy L. Karr
Summary: This study provides an updated version of the Drosophila melanogaster sperm proteome (DmSP3) using improved methods and annotation, revealing reduced gene content and protein abundance on the X chromosome and supporting the meiotic sex-chromosome inactivation model.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Chemistry, Multidisciplinary
Jiaying Li, Jiahua Zhou, Kailu Tian, He Zhu, Yao Chen, Yangyu Huang, Guosheng Wang, Zhou Gong, Hongqiang Qin, Mingliang Ye, Hao Xu
Summary: The quantitative profiling of residue reactivity in proteins can help identify covalent druggable targets for precise therapy. In this study, a chemical proteomics platform was developed to analyze the reactivity of histidine (His) residues. Through this platform, the reactivity of His residues in the human proteome was characterized, and a large number of His residues with high reactivity were identified. The findings suggest that these highly reactive residues are less likely to be phosphorylation sites, which requires further research to understand the underlying mechanism. This comprehensive map of His residue reactivity provides potential bindable sites for disrupting protein activities and offers new opportunities for developing covalent inhibitors using acrolein derivatives as reactive warheads.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Kirill E. Medvedev, Jimin Pei, Nick Grishin
Summary: This study developed a database of human proteome IDRs that are significantly enriched in particular amino acids, providing information on function terms, disorder prediction, enriched IDR composition, and ranks of human proteins with similar enriched IDRs. The distribution analysis revealed significant overrepresentation of R- and Y-enriched IDRs in metabolic and enzymatic activities, and F-enriched IDRs in transport. Approximately 75% of functional categories contain IDPs with IDRs significantly enriched in hydrophobic residues important for protein-protein interactions.
Article
Biochemistry & Molecular Biology
Chih-Yi Gabriela Lin, Anna Christina Naeger, Thomas Lunardi, Aleksandra Vancevska, Gerald Lossaint, Joachim Lingner
Summary: Telomere shortening can lead to diseases and aging, often due to the lack of telomerase in cells. By developing a new isolation protocol, specific proteins associated with telomere replication can be purified, revealing their importance for maintaining telomere stability. This study provides a valuable resource for understanding the dynamic changes of the telomeric proteome during replication.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Dentistry, Oral Surgery & Medicine
W. W. Lau, M. Hardt, Y. H. Zhang, M. Freire, S. Ruhl
Summary: Saliva is now being used for on-site, remote, and real-time monitoring of oral and systemic health. The Human Salivary Proteome (HSP) Wiki is a public platform that integrates data from various sources to help researchers explore the protein composition of saliva.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Cardiac & Cardiovascular Systems
Michael J. Previs, Thomas S. O'Leary, Michael P. Morley, Bradley M. Palmer, Martin LeWinter, Jaime M. Yob, Francis D. Pagani, Christopher Petucci, Min-Soo Kim, Kenneth B. Margulies, Zoltan Arany, Daniel P. Kelly, Sharlene M. Day
Summary: This study identified metabolic reprogramming in human HCM hearts, characterized by deficits in nucleotide availability, reduced capacity for fatty acid oxidation, and increases in ketone bodies and branched chain amino acids. These findings have important therapeutic implications for the future design of metabolic modulators to treat HCM.
CIRCULATION-HEART FAILURE
(2022)
Article
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Alicia L. Richards, Robert J. Weatheritt, Dain R. Brademan, Harald Marx, Evgenia Shishkova, Jesse G. Meyer, Alexander S. Hebert, Michael S. Westphall, Benjamin J. Blencowe, Juergen Cox, Joshua J. Coon
Summary: Deep proteome sequencing provides an 80% coverage of the human proteome. Shotgun proteomics experiments detect about 10,000 human proteins from a single sample, but fail to distinguish protein variants and isoforms. Our study using various methods identifies a million unique peptides and provides evidence for the translation of nonsynonymous variants.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Pieter M. Dekker, Sjef Boeren, Johannes B. van Goudoever, Jacques J. M. Vervoort, Kasper A. Hettinga
Summary: The study found significant interindividual variation in proteins and peptides in human milk, and identified distinct characteristics in different protein and peptide clusters through weighted correlation network analysis. Several associations between different data sets and specific sample characteristics were also discovered.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Computer Science, Artificial Intelligence
Qingyu He, Ruigen Pan
Summary: This study analyzed the application value of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) based on computer semi-automatic segmentation (CSS) algorithm in the histological grading of breast cancer patients. Results showed that CSS had lower false positive rate (FPR) and higher true positive rate (TPR) compared to fuzzy-c-means (FCM) and wavelet transform (WT) algorithms. The CSS algorithm was found to be superior to FCM and WT in evaluating breast tumor histological grading. Furthermore, the obtained tumor diameter, fractional anisotropy (FA) value, apparent diffusion coefficient (ADC) value, and number of lymph node metastasis based on DCE-MRI were significantly different among patients with grade I, II, and III, and could be used to predict the histological grading of breast cancer patients.
Article
Biochemical Research Methods
Xuejuan Gao, Qionghua Lian, Baiye Guan, Qiu-Yu Liu, Meng Meng, Yang Chen, Jingjie Jin, Huihua Li, Xiaohui Liu, Zhenghua Sun, Langxia Liu, Qing-Yu He, Gong Zhang
Summary: This study investigated the function and mechanism of ZSWIM1 in lung adenocarcinoma. ZSWIM1 was found to be upregulated in lung adenocarcinoma and correlated with poor prognosis. It promoted cancer cell proliferation, migration, invasion, and epithelial-to-mesenchymal transition. The protein interactome of ZSWIM1 was identified, and its interaction with STK38 was verified. ZSWIM1 antagonized the function of STK38 and activated the MEKK2/ERK1/2 pathway. Overall, ZSWIM1 acts as an oncogene in lung adenocarcinoma and its effects are mediated through the STK38/MEKK2/ERK1/2 axis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Hui-Fang Hu, Gui-Bin Gao, Xuan He, Yu-Ying Li, Yang-Jia Li, Bin Li, Yunlong Pan, Yang Wang, Qing-Yu He
Summary: This study identifies the ARF1-IQGAP1 interaction-mediated reactivation of ERK signaling as critical for vemurafenib resistance and cancer metastasis. LY2835219 is shown to be a promising therapeutic agent for CRC, both alone and in combination with vemurafenib, with significant inhibitory effects on ARF1-mediated cancer.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Oncology
Kun Meng, Yuyu Hu, Dingkang Wang, Yuying Li, Fujin Shi, Jiangli Lu, Yang Wang, Yun Cao, Chris Zhiyi Zhang, Qing-Yu He
Summary: A seven-mitochondrial-gene signature was generated to predict prognosis of ccRCC patients, with EFHD1 being less studied but found to be correlated with unfavorable outcome. Overexpression of EFHD1 reduced mitochondrial Ca2+ and inhibited cell migration and tumor metastasis by binding to mitochondrial calcium uniporter (MCU) and deactivating the Hippo/YAP pathway. Upregulation of STARD13 induced by EFHD1 enhanced the phosphorylation of YAP at Ser-127. The EFHD1-MCU-STARD13 axis serves as a novel regulator in ccRCC progression.
Article
Biochemistry & Molecular Biology
Kun Meng, Shaohua Lu, Yu-Ying Li, Li-Ling Hu, Jing Zhang, Yun Cao, Yang Wang, Chris Zhiyi Zhang, Qing-Yu He
Summary: The study discovered a microprotein encoded by LINC00493, called SMIM26, which is localized in mitochondria and tends to be downregulated in ccRCC. SMIM26 suppresses ccRCC growth and metastasis by interacting with AGK and SLC25A11. This interaction increases the mitochondrial localization of AGK and inhibits AGK-mediated AKT phosphorylation. The study shows the importance of hidden proteins in human cancers.
Article
Infectious Diseases
Dan Lei, Linlin Cao, Tairan Zhong, Qing-Yu He, Xuesong Sun
Summary: In this study, the researchers found that the mutation of the key residue Lys219 leads to a conformational change in CpxR, resulting in loss of its regulatory ability in antibiotic resistance.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Instruments & Instrumentation
Lihui Zhou, Qingyu He, Xinglu Que, Andreas W. W. Rost, Hide Takagi
Summary: Cryogenic scanning tunneling microscopy and spectroscopy with a high vector magnetic field is used to image surface magnetic structures, study anisotropic superconductivity, and explore spin physics in quantum materials. This paper describes the design, construction, and performance of a low-temperature, ultra-high-vacuum spectroscopic imaging STM with a vector magnet capable of applying a field of up to 3 T in any direction. The STM can operate at variable temperatures and is suitable for studying layered compounds and thin films.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2023)
Article
Medicine, General & Internal
Wen Wen, Long Liao, Wei Dai, Can-Can Zheng, Xiang-Peng Tan, Yan He, Qi-Hua Zhang, Zhi-Hao Huang, Wen-You Chen, Yan-Ru Qin, Kui-Sheng Chen, Ming-Liang He, Simon Law, Maria Li Lung, Qing-Yu He, Bin Li
Summary: Through genome-wide CRISPR/Cas9 screening and gene profiling, the MEST-PURA-SRCIN1/RASAL1-ERK-snail signaling cascade was identified as an important mechanism underlying cancer metastasis in esophageal squamous cell carcinoma. Blocking the interaction between MEST and PURA could be a potential therapeutic approach for managing tumor metastasis.
Article
Biochemistry & Molecular Biology
Qianqian Yang, Lulu Wang, Yuehong Liang, Qingyu He, Qi Sun, Jing Luo, Hongdi Cao, Yi Fang, Yang Zhou, Junwei Yang, Ping Wen, Lei Jiang
Summary: Mitochondrial dysfunction, regulated by UCP2, plays a crucial role in the development of podocyte injury and proteinuria.
Article
Engineering, Electrical & Electronic
Xu Zhang, Honglin Ji, Ming Luo, Qingyu He, Chao Yang, Jie Li, Wu Liu, Chao Li, Qibing Wang, Zichen Liu, Chuyu Peng, Hao Guo, Huang Yu, Zhiwen Fan, Zhixue He, Xi Xiao, Shaohua Yu
Summary: We experimentally demonstrate a 3.61 Pbit/s estimated throughput of generalized mutual information (GMI) achieved through combined space division multiplexing (SDM) and wavelength division multiplexing (WDM) over a 19-core single-mode fiber. The transmission utilizes 680 wavelength channels covering a 17 THz bandwidth in the S, C, and L bands, delivering probabilistically constellation-shaped (PCS) 256 quadrature amplitude modulation (QAM) and PCS-64QAM signals at a data rate of 24.5 GBaud. The measured data rate shows significant potential for enhancing the achievable data rate in multi-core fibers.
IEEE PHOTONICS TECHNOLOGY LETTERS
(2023)
Article
Multidisciplinary Sciences
Shaohua Lu, Hong Lu, Tingkai Zheng, Huiming Yuan, Hongli Du, Youhe Gao, Yongtao Liu, Xuanzhen Pan, Wenlu Zhang, Shuying Fu, Zhenghua Sun, Jingjie Jin, Qing-Yu He, Yang Chen, Gong Zhang
Summary: The development of high-throughput omics technology has greatly promoted the development of biomedicine, but its poor reproducibility limits its application. The use of standard reference materials is necessary to test and calibrate the accuracy and reproducibility of omics workflows. In this study, we demonstrated that the human hepatocellular cell line MHCC97H has a very stable transcriptome and proteome after 9 subculturing generations, providing a steady standard sample for industrial-scale production in the long term. Furthermore, this stability was consistent across labs and platforms.
Review
Chemistry, Physical
Yisha Huang, Xuejuan Gao, Qing-Yu He, Wanting Liu
Summary: This article investigates the role of TRIM21 in intracellular immunity and proposes a model for how TRIM21 interacts with proteins. The model suggests that TRIM21 participates in inflammatory responses through ubiquitination and facilitates antibody destruction of target proteins by detecting antibody complexes. This systematic understanding of TRIM21's interactions provides insights into the pathogenesis of related diseases and potential applications.
Article
Public, Environmental & Occupational Health
Jing Wang, Patrick Kwan, Gong Zhang, Mingwang Shen, Loretta Piccenna, Terence J. O'Brien, Lei Zhang
Summary: China is faced with a growing aging population and understanding the health status of older adults is crucial for resource allocation and healthcare provision. This study aimed to comprehensively assess the disability level and identify risk factors associated with disability among older adults in China. A multidimensional ability assessment survey was used to evaluate daily living activities, mental status, sensory and communication abilities, and social participation. Demographic risk factors were analyzed using logistic regression and the correlations between the four dimensions of ability were assessed.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2023)
Article
Biochemistry & Molecular Biology
Kun Meng, Yu-Ying Li, Dan-Ya Liu, Li-Ling Hu, Yun-Long Pan, Chris Zhiyi Zhang, Qing-Yu He
Summary: By analyzing the datasets of TCGA and CPTAC, we established a five-protein prognostic signature for ccRCC. This signature was closely correlated with advanced stage, higher pathological grade, and unfavorable survivals in ccRCC patients. Further studies revealed that GBP2 plays an oncogenic role by modulating JAK-STAT signaling and tumor immune infiltration.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiaolong Lu, Yang Chen, Gong Zhang
Summary: We analyzed SARS-CoV-2 sequence data from the end of 2019 to January 2023 and found that most genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. The Ka/Ks of the S-gene increases from the original strain to different variants, but decreases within one variant over time. Additionally, only S-gene mutations show a trend of accumulating more positive charges, indicating a functional evolution that facilitates infection.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
