Causal effects of thyroid volume change on thyroid disease: a Mendelian randomization study.

Background: Observational studies have suggested an association between thyroid volume changes and thyroid disease, but the causal relationship and direction of these effects remain unclear. This study employs a two-sample Mendelian randomization (MR) approach to assess the effect of thyroid volume on clinically common benign and malignant thyroid diseases.

Methods: Summary data from genome-wide association studies (GWAS) were utilized for secondary data analysis to investigate the link between thyroid volume and disease.

Single-Cell Secretome Profiling Enabled by Selective Enrichment and NanoLC-MS/MS Analysis.

Recent advances in single-cell proteomics enable the direct profiling of thousands of proteins from a single mammalian cell. However, due to the bottlenecks in detecting low-abundance secreted proteins and extracellular vesicle (EV) proteins (collectively referred to as the secretome) against a background of high-abundance proteins in serum-containing culture medium, the comprehensive investigation of the secretome at the single-cell level using nanoLC-MS/MS still remains challenging. Herein, we report a novel single-cell secretome profiling (SCSP) method by integrating the metabolic labeling of newly synthesized proteins, click chemistry-based enrichment, and in situ digestion of the labeled secretome in an alkyne-functionalized capillary micro-reactor, followed by nanoLC-MS/MS analysis.

Electric Field Assisted Tangential Flow Filtration Device for Highly Effective Isolation of Bioactive Small Extracellular Vesicles from Cell Culture Medium.

Small extracellular vesicles (sEVs) are proven to hold great promise for diverse therapeutic and diagnostic applications. However, batch preparation of sEVs with high purity and bioactivity is a prerequisite for their clinical translations. Herein, we present an electric field assisted tangential flow filtration system (E-TFF), which integrates size-based filtration with electrophoretic migration-based separation to synergistically achieve the isolation of high-quality sEVs from cell culture medium.

Differential alterations of CXCR3, CXCR5 and CX3CR1 in patients with immune thrombocytopenia.

As a versatile element for maintaining homeostasis, the chemokine system has been reported to be implicated in the pathogenesis of immune thrombocytopenia (ITP). However, research pertaining to chemokine receptors and related ligands in adult ITP is still limited. The states of several typical chemokine receptors and cognate ligands in the circulation were comparatively assessed through various methodologies.

On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells.

Single-cell multi-omics analysis can provide comprehensive insights to study cell-to-cell heterogeneity in normal and disease physiology. However, due to the lack of amplification technique, the measurement of proteome and metabolome in the same cell is challenging. Herein, a novel on-capillary alkylation micro-reactor (OCAM) was developed to achieve proteo-metabolome profiling in the same single cells, by which proteins were first covalently bound to an iodoacetic acid functionalized open-tubular capillary micro-reactor sulfhydryl alkylation reaction, and metabolites were rapidly eluted, followed by on-column digestion of captured proteins.

Emodin Ameliorates Severe Acute Pancreatitis-Associated Acute Lung Injury in Rats by Modulating Exosome-Specific miRNA Expression Profiles.

Background: Numerous preclinical investigations have exhibited the beneficial impact of emodin (EMO) on the management of severe acute pancreatitis (SAP)-associated acute lung injury (ALI). However, the potential of EMO to mitigate organ damage through the modulation of exosome (Exo)-specific miRNA expression profiles remains unclear.

Methods: The SAP rat model was established by retrograde injection of 5% sodium taurocholate into the pancreatic bile duct.

A multi-omics dataset of human transcriptome and proteome stable reference.

The development of high-throughput omics technology has greatly promoted the development of biomedicine. However, the poor reproducibility of omics techniques limits their application. It is necessary to use standard reference materials of complex RNAs or proteins to test and calibrate the accuracy and reproducibility of omics workflows.

High-Sensitivity Detection toward SARS-CoV-2 S1 Glycoprotein by Parallel Reaction Monitoring Mass Spectrometry.

The outbreak of coronavirus disease 2019 (COVID-19) has overwhelmed the global economy and human well-being. On account of the sharp increase in test demand, there is a need for an accurate and alternative diagnosis method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, with the aim to specifically identify the trace SARS-CoV-2 S1 glycoprotein, we developed a high-sensitivity and high-selectivity diagnostic method based on the targeted parallel reaction monitoring (PRM) assay of eight selected peptides.

The efficacy and safety of epirubicin and cyclophosphamide combined with pyrotinib in neoadjuvant treatment for HER2-positive breast cancer: A real-world study.

Purpose: Long-term survival benefit of anthracyclines for human epidermal growth factor receptor 2 (HER2)-positive breast cancer is clear. In the neoadjuvant treatment, compared with the monoclonal antibody such as trastuzumab and pertuzumab, the clinical benefit of pyrotinib, a new small-molecule tyrosine kinase inhibitor (TKI), as the main anti-HER2 strategy currently requires more research to determine. Our real-world study is the first prospective observational study in China to evaluate the efficacy and safety of epirubicin (E) and cyclophosphamide (C) with pyrotinib as anti-HER2 therapy in the neoadjuvant setting of patients with stage II-III HER2-positive breast cancer.

Coexistence of tet(A) and bla in the ST11 hypervirulent tigecycline- and carbapenem-resistant Klebsiella pneumoniae isolated from a blood sample.

Carbapenem-resistant Klebsiella pneumoniae are distributed worldwide. This study aimed to characterize a hypervirulent tigecycline-resistant and carbapenem-resistant Klebsiella pneumoniae strain, XJ-K2, collected from a patient's blood. We tested antimicrobial susceptibility, virulence, and whole-genome sequencing (WGS) on strain XJ-K2.

Widespread protein N-phosphorylation in organism revealed by SiO@DpaZn beads based mild-acidic enrichment method.

Protein phosphorylation is one of the most commonly studied and ubiquitous post-translational modifications (PTMs), and defining site-specific phosphorylation is essential to understand basic and disease biology. However, the chemical properties and biological activities hamper the detection of non-canonical N-phosphorylation from biological samples, and the study of N-phosphorylation over the last half century has lagged behind canonical O-phosphorylation. Here, a mild-acidic method based-on SiO@DpaZn beads was developed for protein N-phosphorylation sites identification.

A Temporal PROTAC Cocktail-Mediated Sequential Degradation of AURKA Abrogates Acute Myeloid Leukemia Stem Cells.

AURKA is a potential kinase target in various malignancies. The kinase-independent oncogenic functions partially disclose the inadequate efficacy of the kinase inhibitor in a Phase III clinical trial. Simultaneously targeting the catalytic and noncatalytic functions of AURKA may be a feasible approach.

Surface Nanosieving Polyether Sulfone Particles with Graphene Oxide Encapsulation for the Negative Isolation toward Extracellular Vesicles.

Extracellular vesicles (EVs) contain specific biomarkers for disease diagnosis. Current EV isolation methods are hampered in important biological applications due to their low recovery and purity. Herein, we first present a novel EV negative isolation strategy based on surface nanosieving polyether sulfone particles with graphene oxide encapsulation (SNAPs) by which the coexisting proteins are irreversibly adsorbed by graphene oxide (GO) inside the particles, while EVs with large sizes are excluded from the outside due to the well-defined surface pore sizes (10-40 nm).

The expression and potential mechanism of and in breast cancer.

Background: The purpose of our research was to investigate the expression of epidermal growth factor receptor () and zeste gene enhancer homolog 2 () in breast cancer, and to explore their potential common pathways.

Methods: Western blot and quantitative real-time polymerase chain reaction (qRT-PCR) were used to detect the protein and corresponding mRNA expression of and in breast cancer tissues and benign tissues. Then, the relationship between and along with the corresponding clinicopathological parameters were also analyzed.

Diel rhythm of urotensin I mRNA expression and its involvement in the locomotor activity and appetite regulation in olive flounder Paralichthys olivaceus.

Urotensin I (UI), a member of the corticotropin-releasing hormone family of peptides, regulates a diverse array of physiological functions, including appetite regulation, defensive behavior and stress response. In this study, firstly, the tissue-specific distribution of UI mRNA in olive flounder (Paralichthys olivaceus) was characterized and we found that UI mRNA was highly expressed in caudal neurosecretory system (CNSS) tissue. Secondly, alignment analysis found that a conserved cAMP response binding (CREB) site and a TATA element were located in the proximal promoter of UI gene.

Integrated proteomic sample preparation with combination of on-line high-abundance protein depletion, denaturation, reduction, desalting and digestion to achieve high throughput plasma proteome quantification.

In this study, we developed an integrated plasma proteome sample preparation system, by which high-abundance proteins from human plasma were first depleted by immunoaffinity column, followed by on-line middle and low-abundance proteins denaturation, reduction, desalting and tryptic digestion. To evaluate the performance of such a system, 20 μL plasma was processed automatically, followed by 1-h gradient liquid chromatography-mass spectrometry analysis (LC-MS). Compared to conventional in-solution protocols, not only the sample preparation time could be shortened from 20 h to 20 min, but also the number of identified proteins were greatly increased by 1.

Fully integrated protein absolute quantification platform for analysis of multiple tumor markers in human plasma.

In this study, we developed a fully integrated protein absolute quantification platform for simultaneous analysis of multiple tumor markers in human plasma, by which multiple target proteins (alpha-fetoprotein, prostate-specific antigen, carcino-embryonic antigen and mucin-1) were firstly enriched by aptamers immobilized capillary column using graphene oxide modified polymer microsphere as the separation matrix, and then the eluted target proteins were online denatured, reduced, desalted and digested by our developed fully automated sample treatment device (FAST), finally the resulting peptides were analyzed by parallel reaction monitoring (PRM) on LTQ-orbitrap velos mass spectrometry. Compared to traditional ELISA assay, the platform exhibited significant advantages such as short analysis time, low limit of detection, and ease of automation. Furthermore, our developed platform was also applied in the absolute quantification of tumor markers from clinical human plasma samples, and the results were comparable to those obtained by clinical immunoassay.

Analysis of factors related to N2- or N3-stage breast cancer associated with 1-2 positive sentinel lymph nodes in Chinese patients.

Background: This study aims to determine the incidence of N2- or N3-stage disease in a cohort of patients with T1-T2 invasive breast cancer and one or two positive sentinel lymph nodes (SLNs), and identify the risk factors for N2/3 disease in this cohort.

Methods: The present study involved 298 patients with T1-T2 tumors who underwent SLN biopsy and were found to have one or two metastatic SLNs. The proportion of patients with N2/3 disease was calculated in the whole cohort, and in the T1 and T2 subgroups.

A multi-omics investigation of the molecular characteristics and classification of six metabolic syndrome relevant diseases.

Metabolic syndrome (MTS) is a cluster of concurrent metabolic abnormal conditions. MTS and its component metabolic diseases are heterogeneous and closely related, making their relationships complicated, thus hindering precision treatment. : We collected seven groups of samples (group a: healthy individuals; group b: obesity; group c: MTS; group d: hyperglycemia, group e: hypertension, group f: hyperlipidemia; group g: type II diabetes, n=7 for each group).

Comprehensive Analysis of Protein N-Terminome by Guanidination of Terminal Amines.

Protein N-termini and their modifications not only represent different protein isoforms but also relate to the functional annotation and proteolytic activities. Currently, negative selection methods, such as terminal amine isotopic labeling of substrates (TAILS), are the most popular strategy to analyze the protein N-terminome, in which dimethylation or acetylation modification is commonly used to block the free amines of proteome samples. However, after tryptic digestion, the generated long peptides, caused by the missing cleavage of blocked lysine, could hardly be identified by MS, which hindered the deep-coverage analysis of N-terminome.

Site-Specific Quantification of Persulfidome by Combining an Isotope-Coded Affinity Tag with Strong Cation-Exchange-Based Fractionation.

Protein persulfidation is one of the most important oxidative translational modifications and plays vital roles in various important biological processes. However, the proteome-wide identification of persulfidation sites is a great challenge because of the difficulties in accurately differentiating persulfide groups with disulfide and thiol groups in proteins as well as the extremely low abundance of persulfidated peptides. By current approaches, the persulfidated peptides were often identified by the cleavage of their persulfide groups by reductants prior to MS analysis; therefore, it would bring about a false positive identification and was unable to identify persulfidation sites accurately for a single peptide with multiple cysteine residues.

Comparison of 21-gene assay and St.Gallen International Expert Consensus in the treatment decision for patients with early invasive breast cancers.

This study aimed to evaluate the impacts of 21-gene recurrence score (RS) and St. Gallen International Expert Consensus on treatment decision and prognosis of patients with invasive breast cancer. We retrospectively analyzed the therapy protocol and outcome of 134 cases based on age, body mass index (BMI), menopause, pathological types, tumor-node-metastasis (TNM) stages, percentage of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor 2 (HER2), Ki-67, molecular subtype, and tumor biomarkers.

[A novel method for the selective enrichment of persulfidated peptides based on iodoacetic acid functionalized dendrimer].

Protein persulfidation is an important oxidative translational modification which plays vital roles in many important processes including cellular senescence, endoplasmic reticulum stress, vasorelaxation, and apoptosis. The proteome-wide analysis of persulfidation is of great importance; therefore, this study combines filter-aided sample preparation with an iodoacetic acid functionalized polyamidoamine dendrimer to enrich persulfidated peptides (denoted as filter-aided dendrimer enrichment strategy, FADE). To evaluate the performance of this strategy, the synthetic persulfidated standard peptide was spiked into bovine serum albumin (BSA) digests at a mass ratio of 1:100, and was successfully identified by FADE.

Advances in exosome isolation methods and their applications in proteomic analysis of biological samples.

Exosomes are membrane-bound vesicles secreted by cells, and contain various important biological molecules, such as lipids, proteins, messenger RNAs, microRNAs, and noncoding RNAs. Emerging evidence demonstrates that proteomic analysis of exosomes is of great significance in studying metabolic diseases, tumor metastasis, immune regulation, and so forth. However, exosome proteomic analysis has high requirements with regard to the purity of collected exosomes.