CD14 facilitates perinatal human cytomegalovirus infection in biliary epithelial cells via CD55.

Background & Aims: A high human cytomegalovirus (HCMV) infection rate accompanied by an increased level of bile duct damage is observed in the perinatal period. The possible mechanism was investigated.

Methods: A total of 1,120 HCMV-positive and 9,297 HCMV-negative children were recruited, and depending on age, their liver biochemistry profile was compared.

CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation.

Chromatin is spatially organized into three-dimensional structures at different levels including A/B compartments, topologically associating domains and loops. The canonical CTCF-mediated loop extrusion model can explain the formation of loops. However, the organization mechanisms underlying long-range chromatin interactions such as interactions between A-A compartments are still poorly understood.

Integrated Analysis of Glutathione Metabolic Pathway in Pancreatic Cancer.

Metabolic enzyme-genes (MEs) play critical roles in various types of cancers. However, MEs have not been systematically and thoroughly studied in pancreatic cancer (PC). Global analysis of MEs in PC will help us to understand PC progressing and provide new insights into PC therapy.

Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions.

Topological-associated domains (TADs) are thought to be relatively stable across cell types, although some TAD reorganization has been observed during cellular differentiation. However, little is known about the mechanisms through which TAD reorganization affects cell fate or how master transcription factors affect TAD structures during cell fate transitions. Here, we show extensive TAD reorganization during somatic cell reprogramming, which is correlated with gene transcription and changes in cellular identity.

PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions.

Polycomb group (PcG) ring finger protein 6 (PCGF6), though known as a member of the transcription-repressing complexes, PcG, also has activation function in regulating pluripotency gene expression. However, the mechanism underlying the activation function of PCGF6 is poorly understood. Here, we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as OCT4.

Sialylation is involved in cell fate decision during development, reprogramming and cancer progression.

Sialylation, or the covalent addition of sialic acid to the terminal end of glycoproteins, is a biologically important modification that is involved in embryonic development, neurodevelopment, reprogramming, oncogenesis and immune responses. In this review, we have given a comprehensive overview of the current literature on the involvement of sialylation in cell fate decision during development, reprogramming and cancer progression. Sialylation is essential for early embryonic development and the deletion of UDP-GlcNAc 2-epimerase, a rate-limiting enzyme in sialic acid biosynthesis, is embryonically lethal.

Elevated serum levels of circulating immunoinflammation-related protein complexes are associated with cancer.

Disease-specific immune response-related protein complexes in the bloodstream are associated with disease status. We used proteomic technologies to screen novel circulating immunoinflammation-related protein complexes (IIRPCs) and to evaluate their diagnostic accuracy. The discovery study included 96 gastric cancer patients and 83 healthy controls and was designed to isolate and identify the IIRPCs.

Dephosphorylation of intact glycoprotein to greatly improve digestion efficiency coupled with matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometric analysis.

Sialylation is essential for a variety of cellular functions. Herein, we used bovine fetuin with three potential N-linked glycosylation sites containing complex-type glycan structures, four potential O-linked glycosylation sites and six potential phosphorylation sites as a model compound to develop a highly-efficient digestion strategy for sialylated glycoproteins and efficient enrichment strategy for sialylated glycopeptides using titanium dioxide. The former according to the process of alkaline phosphatase digestion followed by tryptic digestion and then proteinase K digestion could greatly improve the enzymatic efficiency on fetuin, and the latter could obviously enhance the enrichment efficiency for multisialylated glycopeptides using phosphoric acid solution as elution buffer.

Change in IgG1 Fc N-linked glycosylation in human lung cancer: age- and sex-related diagnostic potential.

The interactions of IgG Fc region with Fc receptors are optimized by the tailoring of a single-conserved N-linked glycosylation site at Asn-297. Our previous study has demonstrated that the age-related Fc-glycosylation change is featured by sex specificity and that the Fc-glycosylation has the potential for disease discrimination. Here, we conducted a Fourier transform ion cyclotron resonance MS-based profiling study involving 410 control individuals and 259 lung cancer (LC) patients.

Lipid profiling for early diagnosis and progression of colorectal cancer using direct-infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Rationale: Colorectal cancer (CRC) has attracted increasing attention due to its common occurrence and worldwide distribution.

Methods: Direct-infusion positive and negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (DI-ESI(±)-FTICR MS) was applied to analyze the serum metabolites from 52 CRC patients and 52 healthy controls. Metabolites whose inter-group intensities were determined to be statistically significant by univariate and multivariate statistical analyses were further identified by a combination of the Human Metabolome Database, accurate mass measurement, isotopic abundance distribution simulation, and tandem mass spectrometry.

Probing gender-specific lipid metabolites and diagnostic biomarkers for lung cancer using Fourier transform ion cyclotron resonance mass spectrometry.

Background: There are no effective clinical biomarkers for early and specific detection of lung cancer (LC). The changes in the levels of some serum metabolites of LC patients are associated with patient gender and LC stages.

Methods: Serum metabolites of the LC patients (n=58) and healthy controls (n=495) were performed using direct-infusion positive ion electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry in combination with univariate and partial least squares discriminant analyses (PLS-DA).

Broad-spectrum four-dimensional orthogonal electrophoresis: a novel comprehensively feasible system for protein complexomics investigation.

The major challenge of "protein complexomics" is to separate intact protein complexes or interactional proteins without dissociation or denaturation from complex biological samples and to characterize structural subunits of protein complexes. To address these issues, we developed a novel approach termed "broad-spectrum four-dimensional orthogonal electrophoresis (BS4-DE) system," which is composed of a nondenaturing part I and denaturing part II. Here we developed a mild acidic-native-PAGE to constitute part I, together with native-thin-layer-IEF and basic-native-PAGE, widening the range of BS4-DE system application for extremely basic proteins with the range of pI from about 8 to 11 (there are obviously 1000 kinds of proteins in this interval), and also speculated on the mechanism of separating.

Human IgG Fc-glycosylation profiling reveals associations with age, sex, female sex hormones and thyroid cancer.

IgG functions rely on interactions of the Fc region with other proteins, which are optimized by tailoring of a conserved N-linked glycosylation at Asn-297. We conducted a study involving 735 control individuals and 138 thyroid cancer patients. Here we demonstrated that previously described age-related change in Fc-glycosylation was further characterized by definite sex specificity.