Identification of GBN5 as a molecular biomarker of pan-cancer species by integrated multi-omics analysis by Qian Guo, Xinxin Zhong, Zihan Dang, Baiquan Zhang, Zixin Yang

“…Materials and methods We employed a multi-omics approach, including transcriptomic, genomic, proteomic, single-cell cytomic, spatial transcriptomic, and genomic data, to explore the prognostic value and potential oncogenic mechanisms of GBN5 across pan-cancers from multiple perspectives. …”
Get full text

Methods of yeast genome editing by A. S. Rozanov, V. N. Shlyahtun, L. A. Tekutieva, O. M. Son, S. V. Sizova, S. E. Peltek

“…Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. …”
Get full text

Electrophysiology-based screening identifies neuronal HtrA serine peptidase 2 (HTRA2) as a synaptic plasticity regulator participating in tauopathy by Naizhen Zheng, Kun Li, Jing Cao, Zijie Wang, Liang Zhang, Zihao Zhao, Jiawei He, Yong Wang, Xiang Zhu, Yiqing Chen, Jian Meng, Dongdong Zhao, Mengxi Niu, Hong Luo, Xian Zhang, Hao Sun, Yun-wu Zhang

“…Herein, we induced LTP and LTD in the hippocampal CA3-CA1 Schaffer collateral pathway, respectively, and then performed proteomic analysis of the CA1 region. We identified 20 differentially expressed proteins (DEPs) shared by the LTP and the LTD processes. …”
Get full text

Palmitic Acid Accelerates Endothelial Cell Injury and Cardiovascular Dysfunction via Palmitoylation of PKM2 by Yu He, Senlin Li, Lujing Jiang, Kejue Wu, Shanshan Chen, Linjie Su, Cui Liu, Peiqing Liu, Wenwei Luo, Shilong Zhong, Zhuoming Li

“…In endothelial cells, inhibition of palmitoylation bypalmitoyl‐transferase inhibitor 2‐BP eliminates PA‐induced endothelial injury, whereas promotion of palmitoylation by depalmitoylase inhibitor ML349 exacerbates the harmful effect of PA. Palmitoyl‐proteomics analysis identifies pyruvate kinase isozyme type M2 (PKM2) as the palmitoylated protein responsible for PA‐induced endothelial injury, and Cys31 as the predominant palmitoylated site. …”
Get full text

Arabidopsis apoplast TET8 positively correlates to leaf senescence, and tet3tet8 double mutants are delayed in leaf senescence by Jayde A. Zimmerman, Benjamin Verboonen, Andrew P. Harrison Hanson, Luis R. Arballo, Judy A. Brusslan

“…Both PEN1 and PEN3 are abundant in EV proteomes suggesting that EVs might regulate leaf senescence in soil‐grown plants. …”
Get full text

Natural population cohort study on long-lived adults: West China longevity and ageing procedure (WCLAP) by Li Wang, Yan Zhang, Qiukui Hao, Xiaoyan Chen, Birong Dong, Yan He, Meijuan Chen, Jirong Yue, Xiaochu Wu, Tianyao Zhang, Yan She, Yanling Gao, Yiping Deng

“…Analysis of biological samples facilitates biological characterisation at the microscopic level through proteomics, metabolomics, genomics and other techniques. …”
Get full text

NTHi killing activity is reduced in COPD patients and is associated with a differential microbiome by Vancheswaran Gopalakrishnan, Ben Sparklin, Jung Hwan Kim, Jerome Bouquet, Margaret Kehl, Tara Kenny, Christopher Morehouse, Carolina Caceres, Paul Warrener, Ventzislava A. Hristova, Susan Wilson, Harini Shandilya, Arnita Barnes, Alexey Ruzin, Junmin Wang, Lisa Oberg, Bastian Angermann, Christopher McCrae, Adam Platt, Daniel Muthas, Sonja Hess, Christine Tkaczyk, Bret R. Sellman, Kristoffer Ostridge, Maria G. Belvisi, Tom M. A. Wilkinson, Karl J. Staples, Antonio DiGiandomenico, on behalf of the MICA II Study Group

“…Microbial composition, proteomics and NTHi killing activity was analyzed using bronchoalveolar lavage fluid (BALF). …”
Get full text

Hepatocyte-derived liver progenitor-like cells attenuate liver cirrhosis via induction of apoptosis in hepatic stellate cells by Xu Zhou, Wen-Ming Liu, Han-Yong Sun, Yuan Peng, Ren-Jie Huang, Cai-Yang Chen, Hong-Dan Zhang, Shen-Ao Zhou, Hong-Ping Wu, Dan Tang, Wei-Jian Huang, Han Wu, Qi-Gen Li, Bo Zhai, Qiang Xia, Wei-Feng Yu, He-Xin Yan

“…In vitro experiments used HSCs to explore the antifibrotic properties of HepLPC-secretomes and their underlying molecular mechanisms. Additionally, proteomic analysis was conducted to characterize the protein composition of HepLPC-secretomes. …”
Get full text

Pan-caspase inhibitors induce secretion of HIV-1 latency reversal agent lymphotoxin-alpha from cytokine-primed NK cells by Zamaneh Hajikhezri, Ioannis Zygouras, Anders Sönnerborg, Robert van Domselaar

“…Here, we aimed to identify this LRA using a targeted proteomic approach. We identified lymphotoxin-α (LTα) as the key LRA secreted by NK cells following pan-caspase inhibitor treatment. …”
Get full text

Identification of Host–Protein Interaction Network of Canine Parvovirus Capsid Protein VP2 in F81 Cells by Hongzhuan Zhou, Huanhuan Zhang, Xia Su, Fuzhou Xu, Bing Xiao, Jin Zhang, Qi Qi, Lulu Lin, Kaidi Cui, Qinqin Li, Songping Li, Bing Yang

“…According to the results of proteomics analysis, we randomly selected seven proteins for co-immunoprecipitation verification, and the experimental results were consistent with the LC-MS/MS data. …”
Get full text

TMEM97 governs partial epithelial-mesenchymal transition of retinal pigment epithelial cells via the CTNND2-ADAM10 axis by Jing Li, Yosuke Nagasaka, Hongtao Shen, Xinyu Zhou, Jianjie Ma, Dilza Trevisan-Silva, Nicholas E. Sherman, Jayakrishna Ambati, Bradley D. Gelfand, Lian-Wang Guo

“…Interestingly, TMEM97 knockout in ARPE19 cells in vitro led to upregulation of cadherin/adhesion-binding pathways, even without oxidant exposure. Integrated proteomic, transcriptomic, segmentation, and immunoblot analyses revealed that TMEM97 ablation induces pEMT, marked by the concurrent expression of epithelial E-cadherin and mesenchymal N-cadherin, a process reversed upon TMEM97 re-expression. …”
Get full text

The role of VANGL2 in glioma oncogenesis and progression: insights into expression profiles and prognostic relevance by Mingyu Zhao, Mingyu Zhao, Mingyu Zhao, Mingyu Zhao, Shanshuang Chen, Shanshuang Chen, Shanshuang Chen, Shanshuang Chen

“…Our study focused on VANGL2, a core PCP gene, to elucidate its potential mechanistic involvement in cancer development.MethodsA systematic analysis was conducted to assess VANGL2 expression patterns at both transcriptional and proteomic levels. Functional enrichment analysis was performed to investigate the biological pathways associated with VANGL2 in glioma. …”
Get full text

Leveraging Single-Cell Multi-Omics to Decode Tumor Microenvironment Diversity and Therapeutic Resistance by Hussein Sabit, Borros Arneth, Timothy M. Pawlik, Shaimaa Abdel-Ghany, Aysha Ghazy, Rawan M. Abdelazeem, Amany Alqosaibi, Ibtesam S. Al-Dhuayan, Jawaher Almulhim, Noof A. Alrabiah, Ahmed Hashash

“…These technologies are able to integrate data from molecular genomic, transcriptomic, proteomics, and metabolomics studies of cells at a single-cell resolution scale that give rise to the full cellular and molecular complexity in the TME. …”
Get full text

SpecPCM: A Low-Power PCM-Based In-Memory Computing Accelerator for Full-Stack Mass Spectrometry Analysis by Keming Fan, Ashkan Moradifirouzabadi, Xiangjin Wu, Zheyu Li, Flavio Ponzina, Anton Persson, Eric Pop, Tajana Rosing, Mingu Kang

“…Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. …”
Get full text

Isoforsythiaside confers neuroprotection against Alzheimer’s disease by attenuating ferroptosis and neuroinflammation in vivo and in vitro by Chunyue Wang, Hongbo Jiang, Honghan Liu, Shanshan Chen, Hangyu Guo, Shuoshuo Ma, Weiwei Han, Yu Li, Di Wang

“…In APP/PS1 mice, erastin-damaged HT22 cells, and LPS-exposed BV2 cells, the neuroprotective effects against ferroptosis and neuroinflammation were investigated using immunohistochemistry, label-free proteomics, western blot, ELISA, MTT, fluorescence, and TEM. …”
Get full text

Core-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii by Fizza Arshad, Asifa Sarfraz, Muhammad Shehroz, Umar Nishan, Asia Perveen, Riaz Ullah, Mohamed A. Ibrahim, Mohibullah Shah

“…In order to find new therapeutic targets and create multiepitope vaccines, this study integrated subtractive proteomics with reverse vaccinology. The core genome of R. rickettsii was investigated, resulting in the identification of seven essential, human non-homologous proteins as potential drug targets, as well as four antigenic, non-allergenic proteins suitable for vaccine development. …”
Get full text

Exploring the Mesenchymal Stem Cell Secretome for Corneal Endothelial Proliferation by Bert Van den Bogerd, Nadia Zakaria, Steffi Matthyssen, Carina Koppen, Sorcha Ní Dhubhghaill

“…Specific identification of the underlying proteins using proteomics could render a bioactive protein that can be used for ex vivo expansion of cells or as an in vivo drug to treat early corneal endothelial damage.…”
Get full text

Salivary metabolomics in oral cancer: A systematic review by Rita Antonelli, Giacomo Setti, Nathaniel S. Treister, Thelma A. Pertinhez, Elena Ferrari, Mariana Gallo, Ronell Bologna-Molina, Paolo Vescovi, Marco Meleti

“…., genomic, transcriptomic, proteomic), metabolomics appears promising in identifying the presence of small, specific molecules directly released from malignant cells that could potentially serve as diagnostic biomarkers.This systematic review evaluates the scientific evidence that supports the role of salivary metabolites in the early diagnosis of OSCC.Medline, Scopus and Web of Science databases were searched until February 2024. …”
Get full text

Genetic and pharmacological targeting of HINT2 promotes OXPHOS to alleviate inflammatory responses and cell necrosis in acute pancreatitis by Jiaqi Yao, Yuhong Jiang, Pengcheng Zhang, Yifan Miao, Xiajia Wu, Hang Lei, Zhijun Xie, Yong Tian, Xianlin Zhao, Juan Li, Lv Zhu, Meihua Wan, Wenfu Tang

“…The results of glutathione-S-transferase (GST) pull-down and proteomics analyses revealed the involvement of HINT2 in regulating mitochondrial oxidative phosphorylation (OXPHOS) in AP mice. …”
Get full text

The endonuclease activity of MCPIP1 controls the neoplastic transformation of epithelial cells via the c-Met/CD44 axis by Paulina Marona, Rafał Myrczek, Iga Piasecka, Judyta Gorka, Oliwia Kwapisz, Ewelina Pospiech, Janusz Rys, Jolanta Jura, Katarzyna Miekus

“…In vivo studies demonstrated that MCPIP1 inactivation in normal epithelial cells leads to significant tumor formation and increased c-Myc phosphorylation, indicating enhanced cell proliferation. Proteomic analysis of mouse plasma revealed increased secretion of cancer-related proteins (CXCL13, CXCL16, and MMP2) in the MCPIP1-mutant group. …”
Get full text