In Brief Glioblastoma (GBM) is the most aggressive brain tumor. Histone deacetylase inhibitors (iHDAC) have emerged as druggable epigenetic therapies for GBM. The effects of iHDAC on the GBM matrisome is currently elusive. In this study, we performed a high throughput proteomic analysis of the GBM matrisome upon pharmacological knockdown of HDAC activity in GBM cells. We characterize the GBM angiogenic matrisome signature, the AngioMatrix, and its impact on endothelial cell behavior, strengthening our comprehension of GBM biology ..read more

In Brief This study measured IgA and IgG antibody responses against 646 viral proteins from 23 viruses in nasopharyngeal carcinoma (NPC) patients and controls using nucleic acid programmable protein arrays. We found that five anti-Epstein-Barr virus (EBV) antibodies combined with the clinical biomarker EBV nuclear antigen 1 (EBNA1) IgA could be used to diagnose NPC accurately. Additionally, two anti-EBV antibodies showed potential as prognostic biomarkers of NPC. These results indicate the possibility of developing new serological tests for NPC detection and prognosis ..read more

In Brief Proteasomes, key protein complexes in eukaryotic cells, were analyzed in various yeast strains using an activity-guided proteomic approach. We discovered notable discrepancies in proteasome distributions between mass spectrometry and peptidase activity assays, indicating substantial portion of the proteasomes have reduced activity. This reduction might be linked to Fub1 inhibition. Moreover, immature β2 and β5 proteolytic subunits were identified in fully assembled proteasomes, potentially contributing to the decreased activity observed ..read more

In Brief The purpose of this study is (i) to gain insights on molecules/pathways involved in oocyst maturation; (ii) to define the timing of expression and changes in protein abundance during oocyst maturation; and (iii) to define the topological characteristics of key biological processes by analyzing an oocyst-related protein–protein interaction network ..read more

In Brief Using bioorthogonal chemical labeling and quantitative proteomic analysis, Xu report the identification of septin proteins, the fourth mammalian cytoskeletal component, as the target proteins extensively -fatty-acylated by Rho Inactivation Domain (RID) of the MARTX toxin in living cells. Further functional studies demonstrate that RID-mediated -fatty-acylation confers localization of septins to detergent-resistant membrane rafts and disrupts the filamentous assembly and organization of septins ..read more

In Brief eTOC synopsis: The desmosome proximitome reveals novel associations with potential for desmosome regulation and signaling and shows substantial changes as the junctions mature to hyper-adhesion ..read more

In Brief Antigen-antibody interactions play a key role in the immune response post-vaccination. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in an antigen recognized by polyclonal antibodies (pAb) from two vaccinated human donors (HDs). Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb in both HDs with high similarity. Furthermore, we show that the main epitopes can be identified without the need for antigen-specific enrichment of the pAb samples ..read more

In Brief This quantitative biotinylproteomics was separately performed on MKK1-ID and MKK2-ID transgenic plants, respectively, using the genetically engineered TurboID biotin ligase expression transgenics as a universal control. WIRK1 was found to be a common interactor of both MKK1 and MKK2. It was verified to participate in wind regulation of the touch-responsive TCH3 and CML38 gene expression and the phosphorylation of a touch-regulated PATL3 phosphoprotein. This study demonstrated that WIRK1 gene is involved in both wind-triggered rosette thigmomorphogenesis and gravitropism of Arabidopsis ..read more

In Brief The era of open-modification search engines in LC-MS/MS-based proteomics has expanded the detection of post-translational modifications (PTMs). However, statistical methods for PTM-level quantification and differential analysis are lacking. To address this, we introduce msqrob2PTM, offering differential usage analysis at the PTM and peptidoform level. The workflow provides an additional normalization to correct for parent protein abundance. Demonstrating efficacy on simulated datasets and PTM-rich biological data, msqrob2PTM outperforms existing methods and uniquely provides output at ..read more

presents a comprehensive and quantitative interactome of BZW2, a lesser-studied protein associated with the progression of many human cancers. This study uncovers a novel molecular function of BZW2 including promoting mitochondria-ER contact, mitochondrial calcium, and ATP production. The finding provides molecular insights into the roles of BZW in normal and cancer cells and highlights the importance of interactome studies in understanding the function of less studied proteins ..read more