A5100684039- Seismic Waves and Analysis
- Methane Hydrates and Related Phenomena
- Earthquake Detection and Analysis
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Seismology and Earthquake Studies
- Astrophysics and Cosmic Phenomena
- Solar and Space Plasma Dynamics
- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- Circular RNAs in diseases
- Metabolomics and Mass Spectrometry Studies
- Ferroptosis and cancer prognosis
- Mathematical Biology Tumor Growth
- Viral Infections and Immunology Research
- Analytical Chemistry and Chromatography
- Computational Drug Discovery Methods
- Biosensors and Analytical Detection
- Cancer-related gene regulation
- Single-cell and spatial transcriptomics
Second Affiliated Hospital of Harbin Medical University
2015-2025
Harbin Medical University
2015-2025
Environmental Molecular Sciences Laboratory
2013-2024
Pacific Northwest National Laboratory
2013-2024
Harbin Veterinary Research Institute
2024
Chinese Academy of Agricultural Sciences
2024
Xinjiang Agricultural University
2024
First Affiliated Hospital of Wenzhou Medical University
2024
First Affiliated Hospital of Bengbu Medical College
2021-2024
Henan Normal University
2024
Abstract Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands cells to provide in-depth profiling. Here, we report the development nanoPOTS (nanodroplet processing in one pot trace samples) platform small cell population proteomics analysis. NanoPOTS enhances efficiency and recovery sample by downscaling volumes <200 nL minimize surface losses....
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences perturbations to the p53 Wnt/β-catenin pathways, identified potential role for circRNAs in epithelial-mesenchymal transition, provided information about proteomic markers clinical genomic tumor subgroups, including relationships known druggable pathways. An extensive genome-wide...
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA and proteomics phosphoproteomics profiling, of 218 tumors across 7 histological types childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span boundaries, suggesting treatments used for one type may be applied...
Sensitive detection of low-abundance proteins in complex biological samples has typically been achieved by immunoassays that use antibodies specific to target proteins; however, de novo development is associated with high costs, long lead times, and failure rates. To address these challenges, we developed an antibody-free strategy involves PRISM (high-pressure, high-resolution separations coupled intelligent selection multiplexing) for sensitive selected reaction monitoring (SRM)–based...
Abstract Background Laryngeal cancer has the highest mortality rate among head and neck tumours. RNA N6-methyladenosine (m6A) is most plentiful variable in mammalian mRNA. Yet, m6A regulatory mechanism underlying carcinogenesis or progression of LSCC remains poorly understood. Methods The methylation quantification kit was used to detect tissue levels. microarray analysis, mRNA transcriptomic sequencing (mRNA-seq), proteomics were determine RBM15, TMBIM6, IGF2BP3. Immunohistochemical (IHC),...
Effective extension of mass spectrometry-based proteomics to single cells remains challenging. Herein we combined microfluidic nanodroplet technology with tandem tag (TMT) isobaric labeling significantly improve analysis throughput and proteome coverage for mammalian cells. Isobaric facilitated multiplex cell-sized protein quantities a depth ∼1 600 proteins median CV 10.9% correlation coefficient 0.98. To demonstrate in-depth high cell analysis, the platform was applied measure expression in...
Single-cell proteomics can provide unique insights into biological processes by resolving heterogeneity that is obscured bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements sample processing analysis increase information content obtained from each cell, particularly for less abundant proteins. Here we report on improved single-cell combination of previously developed nanoPOTS platform with further miniaturization liquid chromatography (LC)...
The use of artificial neural networks (ANNs) is described for predicting the reversed-phase liquid chromatography retention times peptides enzymatically digested from proteome-wide proteins. To enable accurate comparison numerous LC/MS data sets, a genetic algorithm was developed to normalize peptide into range (from 0 1), improving elution time reproducibility ∼1%. network in this study based on amino acid residue composition and consists 20 input nodes, 2 hidden 1 output node. A set ∼7000...
Proteomics analysis based-on reversed-phase liquid chromatography (RPLC) is widely practiced; however, variations providing cutting-edge RPLC performance have generally not been adopted even though their benefits are well established. Here, we describe an automated format 20 kpsi system for proteomics and metabolomics that includes on-line coupling of micro-solid phase extraction sample loading allows electrospray ionization emitters to be readily replaced. The uses 50 μm i.d. × 40−200 cm...
DNA hypermethylation is a common epigenetic alteration in human prostate cancer and considered to contribute development of this disease. Accumulating data suggest that dietary factors may alter risk by modifications processes the cell. The present study was designed investigate whether selenium (Se) would events regulate methylation-silenced genes cells. methylation, histone gene expression were studied LNCaP cells after selenite treatment using polymerase chain reaction, western blot...
Abstract Post-translational modifications (PTMs) of core histones work synergistically to fine tune chromatin structure and function, generating a so-called histone code that can be interpreted by variety interacting proteins. We report novel online two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) platform for high-throughput sensitive characterization PTMs at the intact protein level. The enables unambiguous identification 708 isoforms from single 2D LC-MS/MS...
In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding biology ovarian high-grade serous cancer (HGSC) requires analysis at functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization 83 prospectively collected HGSC appropriate normal precursor tissue samples (fallopian tube) under strict control ischemia time reveals pathways that significantly differentiate between...
We characterized a prospective endometrial carcinoma (EC) cohort containing 138 tumors and 20 enriched normal tissues using 10 different omics platforms. Targeted quantitation of two peptides can predict antigen processing presentation machinery activity, may inform patient selection for immunotherapy. Association analysis between MYC activity metformin treatment in both patients cell lines suggests potential role non-diabetic with elevated activity. PIK3R1 in-frame indels are associated AKT...
Although genomic anomalies in glioblastoma (GBM) have been well studied for over a decade, its 5-year survival rate remains lower than 5%. We seek to expand the molecular landscape of high-grade glioma, composed IDH-wildtype GBM and IDH-mutant grade 4 astrocytoma, by integrating proteomic, metabolomic, lipidomic, post-translational modifications (PTMs) with transcriptomic measurements uncover multi-scale regulatory interactions governing tumor development evolution. Applying 14 proteogenomic...
We describe a four-column, high-pressure capillary liquid chromatography (LC) system for robust, high-throughput chromatography-mass spectrometry (LC-MS(/MS)) analyses. This performs multiple LC separations in parallel, but staggers each of them such that the data-rich region separation is sampled sequentially. By allowing nearly continuous data acquisition, this design maximizes use mass spectrometer. Each analytical column connected to corresponding ESI emitter order avoid postcolumn...
We describe the preparation and performance of high-efficiency 70 cm × 20 μm i.d. silica-based monolithic capillary LC columns. The columns at a mobile-phase pressure 5000 psi provide flow rates ∼40 nL/min linear velocity ∼0.24 cm/s. separation peak capacity ∼420 in conjunction with both on-line coupling microsolid-phase extraction nanoelectrospray ionization-mass spectrometry. Performance was evaluated using Shewanella oneidensis tryptic digest, ∼15-amol detection limits for peptides were...
We recently reported an antibody-free targeted protein quantification strategy, termed high-pressure, high-resolution separations with intelligent selection and multiplexing (PRISM), for achieving significantly enhanced sensitivity using selected reaction monitoring (SRM) mass spectrometry. Integrating PRISM front-end IgY14 immunoaffinity depletion, sensitive detection of proteins at 50-100 pg/mL levels in human blood plasma/serum was demonstrated. However, depletion is often associated...