Molecular architecture of language-related cortical areas revealed by integrative proteomic and connectome analyses.

Background: Protein expression asymmetry between brain hemispheres is hypothesized to influence functional connectivity, yet its role in language-related networks remains poorly understood. Additionally, how such molecular differences relate to brain reorganization in glioma requires further exploration.

Methods: We performed label-free tandem mass spectrometry on 13 left-hemispheric language-related Brodmann areas (BAs) and their right-hemispheric counterparts from 10 donor brains, identifying protein signatures across 6 language-related functional modules.

A Chromatography-Guided Co-Fractionation Mass Spectrometry Strategy for Rapid Profiling of Drug-Perturbed Protein Complexes.

Protein complexes are central to cellular function and respond rapidly to pharmacological perturbations. Co-fractionation mass spectrometry (CoFrac-MS) is widely employed to analyze protein complexes by analyzing individual chromatographic fractions, but it is labor-intensive and slow. To address these challenges, we introduce a chromatography-guided strategy enabling rapid identification of drug-perturbed protein complexes.

Ultrafast Tyrosinase-Mediated Biotinylation of Living Cell Surface Analysis Reveals Novel Cell Surface Proteins Responsible for Influenza A Virus Entry.

Cell surface proteins are integral to a myriad of biological processes, including cell-cell interactions, signal transduction, and cell adhesion. Notably, these proteins also serve as key receptors for numerous pathogens. However, a comprehensive analysis of the surfaceome remains a significant challenge, primarily due to the high hydrophobicity and low abundance of these proteins.

Large-scale glycoproteome analysis reveals inverted distribution of Neu5Gc and Neu5Ac in mouse liver tissues and cell lines.

Two common forms of sialic acid, Neu5Ac and Neu5Gc, are crucial components of mammalian glycosylation, with distinct roles in various biological processes. Despite their prevalence in mice, differences in their distribution between widely-used model systems, mouse liver tissues and cell lines, are rarely considered. In this study, we demonstrated a long-neglected phenomenon of an inversion of Neu5Gc and Neu5Ac levels between the two sample types by conducting N-glycoproteome analysis at intact glycopeptide level and independent validation assays.

Targeting KMT5C Suppresses Lung Cancer Progression and Enhances the Efficacy of Immunotherapy.

The immune evasion is one major challenge for cancer immunotherapy. Despite considerable advancements in immune checkpoint blockade (ICB) therapies for the advanced non-small cell lung cancer (NSCLC) patients, only a minority of patients receive long-term survival benefit. Here, this work demonstrates that lysine methyltransferase 5C (KMT5C) is a crucial promoter of the NSCLC progression and immune evasion.

A comprehensive view of the molecular features within the serum and serum EV of Alzheimer's disease.

Conventional Alzheimer's disease research mainly focuses on cerebrospinal fluid, which requires an invasive sampling procedure. This method carries inherent risks for patients and could potentially lower patient compliance. EVs (Extracellular Vesicles) and blood are two emerging noninvasive mediators reflecting the pathological changes of Alzheimer's disease.

Mitochondrial NAD deficiency in vascular smooth muscle impairs collagen III turnover to trigger thoracic and abdominal aortic aneurysm.

Thoracic and abdominal aortic aneurysm poses a substantial mortality risk in adults, yet many of its underlying factors remain unidentified. Here, we identify mitochondrial nicotinamide adenine dinucleotide (NAD)⁺ deficiency as a causal factor for the development of aortic aneurysm. Multiomics analysis of 150 surgical aortic specimens indicated impaired NAD salvage and mitochondrial transport in human thoracic aortic aneurysm, with expression of the NAD transporter SLC25A51 inversely correlating with disease severity and postoperative progression.

Correcting mitochondrial loss mitigates NOTCH1-related aortopathy in mice.

Loss-of-function mutations in NOTCH1 were previously linked to thoracic aortopathy, a condition for which non-surgical treatment options are limited. Based on clinical proteome analysis, we hypothesized that mitochondrial fusion and biogenesis in aortic smooth muscle cells (SMCs) are crucial for regulating the progression of NOTCH1-related aortopathy. Here we demonstrate that SMC-specific Notch1 knockout mice develop aortic pathology, including stiffening, dilation and focal dissection.

Multidimensional Proteomic Landscape Reveals Distinct Activated Pathways Between Human Brain Tumors.

Brain metastases (BrMs) and gliomas are two typical human brain tumors with high incidence of mortalities and distinct clinical challenges, yet the understanding of these two types of tumors remains incomplete. Here, a multidimensional proteomic landscape of BrMs and gliomas to infer tumor-specific molecular pathophysiology at both tissue and plasma levels is presented. Tissue sample analysis reveals both shared and distinct characteristics of brain tumors, highlighting significant disparities between BrMs and gliomas with differentially activated upstream pathways of the PI3K-Akt signaling pathway that have been scarcely discussed previously.

Unraveling of Phosphotyrosine Signaling Complexes Associated with T Cell Exhaustion Using Multiplex Co-Fractionation/Mass Spectrometry.

T cell exhaustion, characterized by the upregulation of inhibitory receptors and loss of effector functions, plays a crucial role in tumor immune evasion. This study utilizes a high-throughput, reproducible, and robust integrated ion-exchange chromatography-tandem mass tag (IEC-TMT) platform, coupled with a complex-centric quantification algorithm, to thoroughly profile phosphotyrosine (pTyr) protein complex changes during T cell exhaustion. The platform's high reproducibility is evidenced by >0.

Efficient Cancer Biomarker Screening and Multicancer Detection Enabled by a Multidimensional Serum Proteomic Strategy.

Biomarker discovery and application are paramount for the early diagnosis, treatment, and prognosis assessment of diseases. Novel proteomic strategies have been developed for high-efficiency biomarker screening. However, evaluating various strategies and applying them for the in-depth mining of biomarkers from blood need to be elucidated.

Glyco-signatures in patients with advanced lung cancer during anti-PD-1/PD-L1 immunotherapy.

Immune checkpoint inhibitors (ICIs) targeting programmed cell death 1/programmed cell death ligand-1 (PD-1/PD-L1) have significantly prolonged the survival of advanced/metastatic patients with lung cancer. However, only a small proportion of patients can benefit from ICIs, and clinical management of the treatment process remains challenging. Glycosylation has added a new dimension to advance our understanding of tumor immunity and immunotherapy.

Integrated Platform for Large-Scale Quantitative Profiling of Phosphotyrosine Signaling Complexes Based on Cofractionation/Mass Spectrometry and Complex-Centric Algorithm.

The scarcity and dynamic nature of phosphotyrosine (pTyr)-modified proteins pose a challenge for researching protein complexes with pTyr modification, which are assembled through multiple protein-protein interactions. We developed an integrated complex-centric platform for large-scale quantitative profiling of pTyr signaling complexes based on cofractionation/mass spectrometry (CoFrac-MS) and a complex-centric algorithm. We initially constructed a trifunctional probe based on pTyr superbinder (SH2-S) for specifically binding and isolation of intact pTyr protein complexes.

Picoliter Single-Cell Reactor for Proteome Profiling by In Situ Cell Lysis, Protein Immobilization, Digestion, and Droplet Transfer.

Global profiling of single-cell proteomes can reveal cellular heterogeneity, thus benefiting precision medicine. However, current mass spectrometry (MS)-based single-cell proteomic sample processing still faces technical challenges associated with processing efficiency and protein recovery. Herein, we present an innovative sample processing platform based on a picoliter single-cell reactor (picoSCR) for single-cell proteome profiling, which involves in situ protein immobilization and sample transfer.

Global analysis of N-myristoylation and its heterogeneity by combining N-terminomics and nanographite fluoride-based solid-phase extraction.

N-myristoylation is one of the most widespread and important lipidation in eukaryotes and some prokaryotes, which is formed by covalently attaching various fatty acids (predominantly myristic acid C14:0) to the N-terminal glycine of proteins. Disorder of N-myristoylation is critically implicated in numerous physiological and pathological processes. Here, we presented a method for purification and comprehensive characterization of endogenous, intact N-glycine lipid-acylated peptides, which combined the negative selection method for N-terminome and the nanographite fluoride-based solid-phase extraction method (NeS-nGF SPE).

Immunomagnetic capture and traceless release of native tumor-derived exosomes from human plasma for exploring interaction with recipient cells by aptamer-functionalized nanoflowers.

Background: Tumor-derived exosomes (TEXs) play an important role in the development process of cancer, which can transport a large number of carcinogenic molecules to normal cells, and subsequently promote tumor metastasis. However, TEXs that were utilized in most of previous researches were obtained from the cell medium of tumor cell lines, which cannot reflect the physiological state of primary cells in vivo. Isolation of native TEXs from human plasma with intact function is contributed to exploring the interaction between TEXs and recipient cells for understanding their true biological functions.

Elucidation of -/-glycosylation and site-specific mapping of sialic acid linkage isomers of SARS-CoV-2 human receptor angiotensin-converting enzyme 2.

Human angiotensin-converting enzyme 2 (hACE2) is the primary receptor for cellular entry of SARS-CoV-2 into human host cells. hACE2 is heavily glycosylated and glycans on the receptor may play a role in viral binding. Thus, comprehensive characterization of hACE2 glycosylation could aid our understanding of interactions between the receptor and SARS-CoV-2 spike (S) protein, as well as provide a basis for the development of therapeutic drugs targeting this crucial interaction.

Rapid and High-Sensitive Phosphoproteomics Elucidated the Spatial Dynamics of the Mouse Brain.

Recent developments in phosphoproteomics have enabled signaling studies where over 10,000 phosphosites can be routinely identified and quantified. Yet, current analyses are limited in sample size, reproducibility, and robustness, hampering experiments that involve low-input samples such as rare cells and fine-needle aspiration biopsies. To address these challenges, we introduced a simple and rapid phosphorylation enrichment method (miniPhos) that uses a minimal amount of the sample to get enough information to decipher biological significance.

Nascent Proteome and Glycoproteome Reveal the Inhibition Role of ALG1 in Hepatocellular Carcinoma Cell Migration.

Unlabelled: Asparagine-linked glycosylation protein 1 homolog (ALG1) participates in the initial stage of protein -glycosylation and -glycosylation has been implicated in the process of hepatocellular carcinoma (HCC) progression. However, whether ALG1 plays a role in human HCC remains unknown. In this study, the expression profile of ALG1 in tumorous and corresponding adjacent non-tumor tissues was analyzed.

Multi-comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in a System-wide Method.

Among diverse protein post-translational modifications, O-GlcNAcylation, a simple but essential monosaccharide modification, plays crucial roles in cellular processes and is closely related to various diseases. Despite its ubiquity in cells, properties of low stoichiometry and reversibility are hard nuts to crack in system-wide research of O-GlcNAc. Herein, we developed a novel method employing multi-comparative thermal proteome profiling for O-GlcNAc transferase (OGT) substrate discovery.

pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level.

Large-scale intact glycopeptide identification has been advanced by software tools. However, tools for quantitative analysis remain lagging behind, which hinders exploring the differential site-specific glycosylation. Here, we report pGlycoQuant, a generic tool for both primary and tandem mass spectrometry-based intact glycopeptide quantitation.

AMPK induces degradation of the transcriptional repressor PROX1 impairing branched amino acid metabolism and tumourigenesis.

Tumour cell metabolic plasticity is essential for tumour progression and therapeutic responses, yet the underlying mechanisms remain poorly understood. Here, we identify Prospero-related homeobox 1 (PROX1) as a crucial factor for tumour metabolic plasticity. Notably, PROX1 is reduced by glucose starvation or AMP-activated protein kinase (AMPK) activation and is elevated in liver kinase B1 (LKB1)-deficient tumours.