Deciphering the MHC immunopeptidome of human cancers with Ligand.MHC atlas.

A fundamental principle of immunotherapy is that T cells are capable of detecting tumor epitopes presented on cancer cell surfaces. Immunopeptidomic strategies empowered by liquid chromatography-tandem mass spectrometry have transformed tumor epitopes identification and provided novel insights into tumor immunology. It enables in-depth profiling of major histocompatibility complex (MHC) presented ligands, thereby offering valuable perspectives on the molecular dialog among tumor and T cells.

Dr. Kinase: predicting the drug-resistance hotspots of protein kinases.

Protein kinases (PKs) regulate various cellular functions, and are targeted by small-molecule kinase inhibitors (KIs) in cancers and other diseases. However, drug resistance (DR) of KIs occurs through critical mutations in four types of representative hotspots, including gatekeeper, G-loop, αC-helix, and A-loop. KI DR has become a common clinical complication affecting multiple cancers, targeted kinases, and drugs.

Nanoparticles-based electrochemical sensing platform for high-through immunoassay with redox-activity CaCO nanotags on a magnetic microfluidic device.

A new nanoparticles-based sensing platform was designed for high-through electrochemical immunoassay of ferritin (FET) biomarker on a magneto-controlled microfluidic device by using anti-FET capture antibody-conjugated magnetic sensing probes. Thionine-doped calcium carbonate (CaCO) nanoparticles labeled with anti-FET detection antibodies were utilized as the recognition elements. Introduction of target FET caused the sandwich-type immunoreaction between two antibodies.

MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons.

Protein degradation through the ubiquitin proteasome system at the spatial and temporal regulation is essential for many cellular processes. E3 ligases and degradation signals (degrons), the sequences they recognize in the target proteins, are key parts of the ubiquitin-mediated proteolysis, and their interactions determine the degradation specificity and maintain cellular homeostasis. To date, only a limited number of targeted degron instances have been identified, and their properties are not yet fully characterized.

m7GRegpred: substrate prediction of N7-methylguanosine (m7G) writers and readers based on sequencing features.

N7-Methylguanosine (m7G) is important RNA modification at internal and the cap structure of five terminal end of message RNA. It is essential for RNA stability of RNA, the efficiency of translation, and various intracellular RNA processing pathways. Given the significance of the m7G modification, numerous studies have been conducted to predict m7G sites.

Combination of neutrophil-to-lymphocyte ratio and albumin concentration to predict the prognosis of esophageal squamous cell cancer patients undergoing esophagectomy.

Background: Esophageal squamous cell cancer (ESCC) is an aggressive cancer with high incidence and mortality. It is crucial to predict prognosis of these patients individually. Neutrophil-to-lymphocyte ratio (NLR) has been reported as a prognostic indicator in several tumors, including esophageal cancer.

PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest.

Protein kinase-mediated phosphorylation plays a critical role in many biological processes. However, the identification of key regulatory kinases is still a great challenge. Here, we develop a trans-omics-based method, central kinase inference, to predict potentially key kinases by integrating quantitative transcriptomic and phosphoproteomic data.

iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death.

Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational modifications play critical roles in PCD process and the rapid advances in proteomics have facilitated the discovery of new PCD proteins.

Characterization of Tumor Mutation Burden-Based Gene Signature and Molecular Subtypes to Assist Precision Treatment in Gastric Cancer.

Objective: Tumor mutation burden (TMB) represents a useful biomarker for predicting survival outcomes and immunotherapy response. Here, we aimed to conduct TMB-based gene signature and molecular subtypes in gastric cancer.

Methods: Based on differentially expressed genes (DEGs) between high- and low-TMB groups in TCGA, a LASSO model was developed for predicting overall survival (OS) and disease-free survival (DFS).

Multi-Region Genomic Landscape Analysis for the Preoperative Prediction of Lymph Node Metastasis in Esophageal Carcinoma.

Esophageal cancer is an aggressive malignant tumor, with 90 percent of the patients prone to recurrence and metastasis. Although recent studies have identified some potential biomarkers, these biomarkers' clinical or pathological significance is still unclear. Therefore, it is urgent to further identify and study novel molecular changes occurring in esophageal cancer.

GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites.

As an important post-translational modification, lysine ubiquitination participates in numerous biological processes and is involved in human diseases, whereas the site specificity of ubiquitination is mainly decided by ubiquitin-protein ligases (E3s). Although numerous ubiquitination predictors have been developed, computational prediction of E3-specific ubiquitination sites is still a great challenge. Here, we carefully reviewed the existing tools for the prediction of general ubiquitination sites.

Combination of albumin concentration and neutrophil-to-lymphocyte ratio for predicting overall survival of patients with non-small cell lung cancer.

Background: Lung cancer contributes significantly to the total of cancer-linked deaths globally, accounting for 1.3 million deaths each year. Preoperative albumin (Alb) concentration and neutrophil-to-lymphocyte ratio (NLR) may reflect chronic inflammation and be used to predict lung cancer outcomes.

CPLM 4.0: an updated database with rich annotations for protein lysine modifications.

Here, we reported the compendium of protein lysine modifications (CPLM 4.0, http://cplm.biocuckoo.

Comparison of a modified one-piece mechanical and double-layer hand-sewn anastomosis in McKeown esophagogastrectomy: A single-institute retrospective study.

The present study aimed to introduce a novel method of cervical esophagogastric anastomosis, so-called 'modified one-piece mechanical anastomosis' (MOMA) in McKeown esophagogastrectomy and to compare its feasibility, efficacy and safety with those of 'conventionally double-layer hand-sewn anastomosis' (CDHA). Between March 2016 and March 2018, 80 consecutive patients with thoracic esophageal squamous cell carcinoma undergoing McKeown esophagogastrectomy with a curative intent were included in the present study. Among them, 40 received MOMA and the other 40 received CDHA.

Development and validation of a novel mRNA signature for predicting early relapse in non-small cell lung cancer.

Background: Recurrence after initial primary resection is still a major and ultimate cause of death for non-small cell lung cancer patients. We attempted to build an early recurrence associated gene signature to improve prognostic prediction of non-small cell lung cancer.

Methods: Propensity score matching was conducted between patients in early relapse group and long-term survival group from The Cancer Genome Atlas training series (N = 579) and patients were matched 1:1.

Hypoxia-inducible factor-1α cooperates with histone Lys methylation to predict prognosis in esophageal squamous cell carcinoma.

To investigate hypoxia-inducible factor-1α (HIF-1α) and histone methylation markers as potential indicators of prognosis in esophageal squamous cell carcinoma (ESCC). The prognostic value of HIF-1α and histone methylation markers levels was analyzed using Kaplan-Meier survival analysis. HIF-1α protein expression was higher in ESCC tumors than in paracancerous tissues.

Atg9-centered multi-omics integration reveals new autophagy regulators in .

In , Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by in transcriptional and translational levels, respectively.

Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation.

O-linked β-N-acetyl glucosamine (O-GlcNAc) is attached to proteins under glucose-replete conditions; this posttranslational modification results in molecular and physiological changes that affect cell fate. Here we show that posttranslational modification of serine/arginine-rich protein kinase 2 (SRPK2) by O-GlcNAc regulates de novo lipogenesis by regulating pre-mRNA splicing. We found that O-GlcNAc transferase O-GlcNAcylated SRPK2 at a nuclear localization signal (NLS), which triggers binding of SRPK2 to importin α.

PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification.

High-throughput sequencing technologies have identified millions of genetic mutations in multiple human diseases. However, the interpretation of the pathogenesis of these mutations and the discovery of driver genes that dominate disease progression is still a major challenge. Combining functional features such as protein post-translational modification (PTM) with genetic mutations is an effective way to predict such alterations.

Impact of treatment modality on long-term survival of stage IA small-cell lung cancer patients: a cohort study of the U.S. SEER database.

Background: The optimal treatment modality for patients with stage IA (T1N0M0) small-cell lung cancer (SCLC) is still unclear.

Methods: Patients who received surgical resection or chemo-radiotherapy (CRT) between January 2004 and December 2014 were identified from The Surveillance, Epidemiology and End Results (SEER) database. Surgical resection included lobectomy, wedge resection, segmentectomy with lymphadenectomy [examined lymph node (ELN) ≥1].

LINC00673 Represses CDKN2C and Promotes the Proliferation of Esophageal Squamous Cell Carcinoma Cells by EZH2-Mediated H3K27 Trimethylation.

Long non-coding RNAs (lncRNAs), some of the most abundant epigenetic regulators, play an important role in esophageal squamous cell carcinoma (ESCC). In the current study, the functions and mechanisms of the lncRNA LINC00673 were investigated. The expression levels of LINC00673 and its potential target genes were assessed by quantitative real-time polymerase chain reaction (qPCR) in ESCC surgical specimens and ESCC cell lines.

Evaluating the Potential of T Cell Receptor Repertoires in Predicting the Prognosis of Resectable Non-Small Cell Lung Cancers.

For resectable cancer patients, a method that could precisely predict the risk of postoperative recurrence would be crucial for guiding adjuvant treatment. Since T cell receptor (TCR) repertoires had been shown to be closely related to the dynamics of cancers, here we enrolled a cohort of patients to evaluate the potential of TCR repertoires in predicting the prognosis of resectable non-small cell lung cancers. Specifically, TCRβ repertoires were analyzed in surgical tumor tissues and matched adjacent non-tumor tissues from 39 patients enrolled with resectable non-small cell lung cancer, through target enrichment and high-throughput sequencing.

Integrated omics in Drosophila uncover a circadian kinome.

Most organisms on the earth exhibit circadian rhythms in behavior and physiology, which are driven by endogenous clocks. Phosphorylation plays a central role in timing the clock, but how this contributes to overt rhythms is unclear. Here we conduct phosphoproteomics in conjunction with transcriptomic and proteomic profiling using fly heads.

dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes.

In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea.