Integrated strategy for high-confident global profiling of the histidine phosphoproteome.

Background: Histidine phosphorylation (pHis) plays a key role in signal transduction in prokaryotes and regulates tumour initiation and progression in mammals. However, the pHis substrates and their functions are rarely known due to the lack of effective analytical strategies.

Results: Herein, we provide a strategy for unbiased enrichment and assignment of the pHis peptides.

Asymmetrical Contrastive Learning Network via Knowledge Distillation for No-Service Rail Surface Defect Detection.

Owing to extensive research on deep learning, significant progress has recently been made in trackless surface defect detection (SDD). Nevertheless, existing algorithms face two main challenges. First, while depth features contain rich spatial structure features, most models only accept red-green-blue (RGB) features as input, which severely constrains performance.

Novel potent molecular glue degraders against broad range of hematological cancer cell lines via multiple neosubstrates degradation.

Background: Targeted protein degradation of neosubstrates plays a crucial role in hematological cancer treatment involving immunomodulatory imide drugs (IMiDs) therapy. Nevertheless, the persistence of inevitable drug resistance and hematological toxicities represents a significant obstacle to their clinical effectiveness.

Methods: Phenotypic profiling of a small molecule compounds library in multiple hematological cancer cell lines was conducted to screen for hit degraders.

The CDK4/6 Inhibitor Palbociclib Induces Cell Senescence of High-grade Serous Ovarian Cancer Through Acetylation of p53.

Cell senescence is an anti-cancer strategy following DNA repair and apoptosis, which is associated with the initiation, progression, and treatment of ovarian cancer. The CDK4/6 inhibitor alters cell cycle and induces cell senescence dependent on retinoblastoma (RB) family proteins. Objective Herein, we aimed to explore the effects of Palbociclib (a CDK4/6 inhibitor) on cellular senescence of high-grade serous ovarian cancer (HGSOC).

Incidence and risk factors of stress urinary incontinence after laparoscopic hysterectomy.

Objective: To observe the long-term effects of total hysterectomy on urinary function, evaluate the effects of preoperative nutritional status, urinary occult infection, and surgical factors on the induction of postoperative stress urinary incontinence (SUI), and explore the incidence and risk factors of SUI.

Study Design: From January 2017 to December 2017, 164 patients with benign non-prolapsing diseases who underwent a laparoscopic total hysterectomy in the First People's Hospital of Taicang were selected as the analysis objects. The International Incontinence Standard Questionnaire for Female Lower Urinary Tract Symptoms (ICIQ-FLUTS) and Pelvic Floor Impact Questionnaire-short version 20 (PFDI-20) were used for telephone follow-up to subjectively assess the urinary function of patients, collect their medical records, and statistically analyze the number of postoperative SUI cases.

Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction.

The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.

Noninvasive urinary protein signatures combined clinical information associated with microvascular invasion risk in HCC patients.

Background: Microvascular invasion (MVI) is the main factor affecting the prognosis of patients with hepatocellular carcinoma (HCC). The aim of this study was to identify accurate diagnostic biomarkers from urinary protein signatures for preoperative prediction.

Methods: We conducted label-free quantitative proteomic studies on urine samples of 91 HCC patients and 22 healthy controls.

Discovery of highly potent and selective KRAS degraders by VHL-recruiting PROTACs for the treatment of tumors with KRAS-Mutation.

Although several covalent KRAS inhibitors have made great progress in the treatment of KRAS-mutant cancer, their clinical applications are limited by adaptive resistance, motivating novel therapeutic strategies. Through drug design and structure optimization, a series of highly potent and selective KRAS Proteolysis Targeting Chimeras (PROTACs) were developed by incorporating AMG510 and VHL ligand VH032. Among them, degrader YN14 significantly inhibited KRAS-dependent cancer cells growth with nanomolar IC and DC values, and ＞ 95 % maximum degradation (D).

Integrative proteomics and n-glycoproteomics reveal the synergistic anti-tumor effects of aspirin- and gemcitabine-based chemotherapy on pancreatic cancer cells.

Objective And Design: Pancreatic cancer is a highly malignant tumor that is well known for its poor prognosis. Based on glycosylation, we performed integrated quantitative N-glycoproteomics to investigate the synergistic anti-tumor effects of aspirin and gemcitabine on pancreatic cancer cells and explore the potential molecular mechanisms of chemotherapy in pancreatic cancer.

Methods And Results: Two pancreatic cancer cell lines (PANC-1 and BxPC-3) were treated with gemcitabine, aspirin, and a combination (gemcitabine + aspirin).

Differential analysis of core-fucosylated glycoproteomics enabled by single-step truncation of N-glycans.

Alpha-1,6 fucosylation of N-glycans (core fucosylation, CF) represents a unique form of N-glycans and is widely involved in disease progression. In order to accurately identify CF glycoproteins, several approaches have been developed based on sequential cleavage with different glycosidases to truncate the N-glycans. Since multi-step sample treatments may introduce quantitation bias and affect the practicality of these approaches in large-scale applications.

Absolute Quantification of Dynamic Cellular Uptake of Small Extracellular Vesicles via Lanthanide Element Labeling and ICP-MS.

Small extracellular vesicles (sEVs) are increasingly reported to play important roles in numerous physiological and pathological processes. Cellular uptake of sEVs is of great significance for functional regulation in recipient cells. Although various sEV quantification, labeling, and tracking methods have been reported, it is still highly challenging to quantify the absolute amount of cellular uptake of sEVs and correlate this information with phenotypic variations in the recipient cell.

Proteomic overview of hepatocellular carcinoma cell lines and generation of the spectral library.

Cell lines are extensively used tools, therefore a comprehensive proteomic overview of hepatocellular carcinoma (HCC) cell lines and an extensive spectral library for data independent acquisition (DIA) quantification are necessary. Here, we present the proteome of nine commonly used HCC cell lines covering 9,208 protein groups, and the HCC spectral library containing 253,921 precursors, 168,811 peptides and 10,098 protein groups. The proteomic overview reveals the heterogeneity between different cell lines, and the similarity in proliferation and metastasis characteristics and drug targets-expression with tumour tissues.

A Cytological Atlas of the Human Liver Proteome from PROTEOME-LIVER 2.0, a Publicly Available Database.

The liver plays a unique role as a metabolic center of the body, and also performs other important functions such as detoxification and immune response. Here, we establish a cell type-resolved healthy human liver proteome including hepatocytes (HCs), hepatic stellate cells (HSCs), Kupffer cells (KCs), and liver sinusoidal endothelial cells (LSECs) by high-resolution mass spectrometry. Overall, we quantify total 8354 proteins for four cell types and over 6000 proteins for each cell type.

Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells.

Peripheral blood mononuclear cells (PBMCs) play vital roles in physiological and pathological processes and represent a rich source for disease monitoring. Typical molecular profiling on PBMCs involves the sorting of cell subsets and thus requires a large volume of peripheral blood (PB), which impedes the clinical practicability of omics tools in PBMC measurements. It would be clinically invaluable to develop a convenient approach for preparing PBMCs from small volumes of PB and for deep proteome profiling of PBMCs.

Pancreatic cancer cells spectral library by DIA-MS and the phenotype analysis of gemcitabine sensitivity.

Data-independent acquisition (DIA)-mass spectrometry (MS)-based proteome strategies are increasingly used for detecting and validating protein biomarkers and therapeutic targets. Here, based on an in-depth proteome analysis of seven pancreatic cancer cell lines, we built a pancreas-specific mass spectrum library containing 10633 protein groups and 184551 peptides. The proteome difference among the seven pancreatic cancer cells was significant, especially for the divergent expression of proteins related to epithelial-mesenchymal transition (EMT).

Global characterization of modifications to the charge isomers of IgG antibody.

Posttranslational modifications of antibody products affect their stability, charge distribution, and drug activity and are thus a critical quality attribute. The comprehensive mapping of antibody modifications and different charge isomers (CIs) is of utmost importance, but is challenging. We intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge heterogeneity.

YTHDF2 Inhibits the Migration and Invasion of Lung Adenocarcinoma by Negatively Regulating the FAM83D-TGFβ1-SMAD2/3 Pathway.

Objective: YTH domain family 2 (YTHDF2) is an important N6-methyladenosine (m6A) reader, but its role in lung adenocarcinoma remains elusive. This study assessed its function in lung adenocarcinoma.

Methods: YTHDF2 expression in lung adenocarcinoma was explored using public databases, such as The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumour Analysis Consortium (CPTAC).

Integrated Strategy for Unbiased Profiling of the Histidine Phosphoproteome.

Histidine phosphorylation (pHis), which plays a key role in signal transduction in bacteria and lower eukaryotes, has been shown to be involved in tumorigenesis. Due to its chemical instability, substoichiometric properties, and lack of specific enrichment reagents, there is a lack of approaches for specific and unbiased enrichment of pHis-proteins/peptides. In this study, an integrated strategy was established and evaluated as an unbiased tool for exploring the histidine phosphoproteome.

An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells.

Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules.

[Large-scale enrichment and identification of human urinary -glycoproteins/-glycopeptides].

-Glycosylation of proteins, an important post-translational modification in eukaryotic cells, plays an essential role in the regulation of cell adhesion, migration, signal transduction, and apoptosis. Abnormal changes in protein glycosylation are closely related to the occurrence of many critical diseases, including diabetes, tumors, and neurological, kidney, and inflammatory diseases. A non-invasive type of liquid biopsy, urine sampling has the advantage of reducing the complexity of proteomic analysis.

An Ultrafast Glycoproteome Analysis Method Using Thermoresponsive Magnetic Fluid-Immobilized Enzymes.

Glycosylation is one of the most common and important post-translational modification methods, and it plays a vital role in controlling many biological processes. Increasing discovery of abnormal alterations in linked glycans associated with many diseases leads to greater demands for rapid and efficient glycosylation profiling in large-scale clinical samples. In the workflow of global glycosylation analysis, enzymatic digestion is the main rate-limiting step, and it includes both protease digestion and peptide-4-(-acetyl-beta-glucosaminyl) asparagine amidase (PNGase) F deglycosylation.

An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition.

RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment.