Biomedical subjects

Shuang Feng

Publications and source records attributed to Shuang Feng.

5 recordsLinked to original sources

PubMed2026

Methylation-Associated Differentiation Features Define Biological and Prognostic Heterogeneity in CMS4 Colorectal Cancer.

Consensus molecular subtype 4 (CMS4) colorectal cancer (CRC) is associated with an aggressive clinical course and poor survival, yet the biological basis of heterogeneity within this subtype remains incompletely understood. DNA methylation is an epigenetic mechanism involved in transcriptional regulation, cellular differentiation, and colorectal tumorigenesis. Here, we integrated single-cell RNA sequencing (scRNA-seq), bulk data, and promoter DNA methylation data to characterize CMS4-associated cancer cell states and methylation-related features. Using the scAB algorithm, we integrated scRNA-seq with bulk CMS4 data and identified CMS4-related cells distributed across multiple patients. Single-cell analyses of cell-cell communication and transcriptional regulation revealed a CMS4-related cancer cell population characterized by macrophage migration inhibitory factor (MIF)-centered intercellular communication, enhanced caudal type homeobox 1 (CDX1) and Kruppel-like factor 5 (KLF5) regulon activity, and gene modules enriched in differentiation-related pathways. CytoTRACE analysis further stratified CMS4 cancer cells into poorly and well-differentiated states, yielding 802 differentially expressed genes (DEGs). Linking these differentiation-associated DEGs with bulk expression and promoter methylation data identified 218 methylation-associated DEGs showing significant inverse methylation expression correlations, suggesting a link between differentiation-related heterogeneity and promoter methylation. Univariable Cox regression followed by LASSO regression further prioritized eight genes for construction of the methylation and differentiation-related prognostic model (MeDiff-PM). MeDiff-PM consistently stratified overall survival in the TCGA CMS4 cohort and two independent validation cohorts, with cutoff-independent continuous Cox analyses further supporting its prognostic association across cohorts. And MeDiff-PM remained prognostically significant after adjustment for available clinical variables. High MeDiff-PM risk scores were associated with activation of P53, WNT, and ubiquitin-mediated proteolysis pathways and with consistent predicted drug response differences for compounds across three CMS4 cohorts. While individual in silico knockout analysis suggested links between MeDiff-PM genes and metallothionein-related and immune-associated transcriptional responses. Collectively, these findings indicate that methylation-associated differentiation features represent a molecular dimension of intra-CMS4 heterogeneity and provide a biologically informed framework for prognostic stratification within CMS4 CRC.

Humans↗

PubMed2026

Vortex-assisted liquid-liquid microextraction based on natural deep eutectic solvents for the determination of pyrethroid pesticides in urine.

A novel, facile, and environmentally friendly analytical method was developed based on vortex-assisted liquid-liquid microextraction and high-performance liquid chromatography with diode-array detection for detecting pyrethroid pesticides (PPs) in urine. Natural deep eutectic solvents (NADESs) were prepared using plant essential oil-derived monoterpenoids (thymol, carvacrol, and menthol) combined with aromatic primary alcohols (benzyl alcohol, phenethyl alcohol, and phenylpropyl alcohol) as hydrogen bond donors and acceptors. These solvents served as environmentally benign extraction media, thereby avoiding the use of conventional volatile, toxic organic solvents. NADESs are naturally derived, easy to prepare, biodegradable, and environmentally friendly solvents. Hydrophobic and π-π interactions between the NADESs and PPs may contribute to enhancing the affinity of PPs toward the NADESs phase. Vortex technology, accelerating mass transfer between the sample and extractant phases, enables fast extraction of PPs. Under optimized conditions, the method achieved a low detection limit (0.002 mg L-1), satisfactory precision with relative standard deviations (0.3%-2.4%), and acceptable recovery (80.7%-86.2%). The method demonstrated excellent performance in urine analysis and was feasible as a facile and green strategy for monitoring the content of PPs in biological matrices and assessing exposure risk.

Liquid Phase Microextraction↗

PubMed2005

[Expression of a human myofibrillogenesis regulator 1 gene in E. coli and its immunogenicity].

OBJECTIVE: To study the expression of human myofibrillogenesis regulator 1 (MR-1) gene in E. coli and obtain the MR-1 protein and its antibody for further investigation of its biological function. METHODS: Expression vectors pGEX-5X-1, pET30a (+), and pET24a (+), as well as host strain E. coli BL21 (DE3) and BL21-CodonPlus (DE3) -RIL were used for expression of MR-1. MR-1 N-terminal with GST or T7-tag or C-terminal with His-tag, separately, or N terminal with T7-tag and C terminal with His-tag, simultaneously, were fused in plasmids pGEX-5X-1, pET30a (+) , and pET24a (+). The expressed MR-1-T protein, separated and purified by preparative SDS-PAGE, was applied to immunize the rabbits. The titer of the antibody was assayed by ELISA and its immunogenicity was tested by Western blot with pcDNA3/MR-1 transfected human breast cancer cell MCF7. RESULTS: The MR-1 protein was successfully expressed as inclusion body by fusing its N-terminal with T7-tag in E. coli BL21-CodonPlus (DE3) -RIL. MR-1 protein was purified by electro-elution from SDS-PAGE gel. Using this purified protein, polyclonal antibody in rabbit against MR-1 was essentially generated. ELISA and Western blot showed the titer of this antibody was about 1:10(5) with high immunogenicity. CONCLUSIONS: The N-terminal fusion tag is the most important mechanism for MR-1 expression. The polyclonal antibody of the generated MR-1 protein in E. coli may be applied for its further biological function studies.

Animals↗

PubMed2005

[Interaction between ATM and radiation-activated phosphorylation of P53 and P21].

BACKGROUND & OBJECTIVE: ATM gene is a member of PI-3K kinase family. ATM protein is capable of controlling DNA repair process and cell cycle checkpoint. In AT cells from ataxia-telangiectasia (AT) patients, ATM gene mutation leads to the deficiency of ionizing radiation-activated phosphorylation of P53 and P21. It shows ATM gene could mediate the phosphorylation of P53 and P21. This study was to explore the interaction between ATM and P53, and to observe whether ATM directly medicates the phosphorylation of P21 in a P53-independent way. METHODS: pEBS7-YZ5 vector containing ATM cDNA was transfected into AT cells by electroperforation. The cells expressing ATM protein stably were screened with hygromycin, and identified by reverse transcription-polymerase chain reaction (RT-PCR). The interaction between ATM and P53 in pEBS7-YZ5-AT cells was assessed by co-immunoprecipitation and Western blot. K562 cells served as a P53 mutation cell model to study whether ATM could interact with the phosphorylation of P21. RESULTS: pEBS7-YZ5 was transfected into AT cells successfully. RT-PCR detected fragment of ATM cDNA. After exposed to ionizing radiation, P53 of pEBS7-YZ5-AT cells was phosphorylated, and immunoprecipitation showed interaction between ATM and P53; P21 of K562 cells was phosphorylated, P21 protein was detected in the immunoprecipitation of ATM antibody-complex. CONCLUSION: Ionizing radiation-activated ATM kinase could interact with the phosphorylation of P53 and P21 in both P53 wild type and mutant type cells.

Ataxia Telangiectasia↗

PubMed2004

Characterization of MR-1, a novel myofibrillogenesis regulator in human muscle.

The actin-myosin contractile apparatus consists of several thick filament and thin filament proteins. Specific regulatory mechanisms are involved in this highly ordered process. In this paper, we reported the identification and characterization of a novel myofibrillogenesis regulator, MR-1. The MR-1 gene was cloned from human skeletal muscle cDNA library by using a strategy that involves EST data base searching, PCR and RACE. The MR-1 gene is located on human chromosome 2q35 and encodes a 142 aa protein. Northern blot revealed that the mRNA level of MR-1 was highest in the skeletal muscle and certain level of MR-1 expression was also observed in heart, liver and kidney. Immunohistochemical assay confirmed that the MR-1 protein existed in human myocardial myofibrils. It was found by yeast two-hybrid screening and confirmed by in vitro binding assay that MR-1 could interact with sarcomeric proteins, such as myosin regulatory light chain, myomesin 1 and beta-enolase. These studies suggested that MR-1 might play a regulatory role in the muscle cell and it was worth investigating further.

Amino Acid Sequence↗