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Rong Chen

Publications and source records attributed to Rong Chen.

At least 19 recordsLinked to original sources
PubMed2026

Comparative metabolomic and transcriptomic profiling of flavonoid diversity and antioxidant capacity in three Isatis species.

Flavonoids are key bioactive compounds in plants with significant health benefits. This study employs an integrated multi-omics approach to investigate flavonoid diversity and antioxidant capacity across three Isatis species: I. oblongata, I. tinctoria, and I. indigotica. Metabolomic profiling identified 200 flavonoids, with glycosides being the most abundant class. I. tinctoria exhibited the highest total flavonoid content and antioxidant activity, strongly correlated with the accumulation of 53 core differential flavonoid metabolites, most of which were glycosylated derivatives. Transcriptomic analysis revealed coordinated upregulation of phenylpropanoid pathway genes and specific UDP-glycosyltransferases (UGTs) in I. tinctoria, providing a genetic basis for its enhanced glycoside production. The study establishes a clear genotype-metabolite-phenotype linkage, highlighting glycosylation as a key mechanism underlying flavonoid-driven antioxidant superiority in Isatis. Although the current evidence is primarily correlative, the consistent and strong associations across independent transcriptomic, metabolomic, and antioxidant datasets provide a robust foundation for this conclusion. These findings offer new insights into the metabolic evolution and regulatory networks of flavonoids, with implications for breeding and metabolic engineering of high-value medicinal plants.

Flavonoids↗
PubMed2026

Overexpression of TCF7L2 promotes the viability and migration of MHCC-97H human hepatocellular carcinoma cells by upregulating MT-ND4L.

BACKGROUND: Hepatocellular carcinoma (HCC) is a highly aggressive cancer with high metabolic adaptability. TCF7L2, a transcription factor implicated in type 2 diabetes and cancer, is overexpressed in HCC. However, its specific role in HCC metabolic reprogramming is not well defined. We aimed to elucidate the previously unrecognized molecular mechanisms through which TCF7L2 impacts HCC progression. METHODS: To investigate the function of TCF7L2, a stable MHCC-97H cell line with TCF7L2 overexpression was established via lentiviral transduction. Cell viability and migration were assessed by Cell Counting Kit-8 (CCK-8) and Transwell assays. Transcriptomic profiling [RNA sequencing (RNA-seq)] was performed to identify differentially expressed genes (DEGs). Functional enrichment analysis [Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA)] and bioinformatics promoter analysis (the JASPAR CORE database) were conducted. Clinical correlations, survival analysis, and tumor microenvironment (TME) interrogation were performed using The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) cohort and single-cell datasets [Human Protein Atlas (HPA), CellChat]. Drug sensitivity was predicted via the Genomics of Drug Sensitivity in Cancer (GDSC) database. RESULTS: TCF7L2 overexpression significantly promoted HCC cell proliferation and migration. Transcriptomic analysis revealed that TCF7L2 drives a profound metabolic shift, with key enrichments in lipid homeostasis, fatty acid β-oxidation, and the PI3K/Akt pathway. Mechanistically, TCF7L2 directly binds to the promoter of CPT1A, the rate-limiting enzyme of fatty acid oxidation, and indirectly upregulates the mitochondrial gene MT-ND4Lvia a strong positive correlation with the mitochondrial transcription factor TFAM. In clinical cohorts, TCF7L2 was overexpressed in HCC and its expression correlated positively with MT-ND4L, MKI67, and SNAI1, and served as a predictor of poor overall survival (OS). Furthermore, TCF7L2-high tumors were enriched in hepatic progenitor cell (HPC)-like niches, mediated by enhanced ANGPTL4 signaling. High TCF7L2 expression predicted increased sensitivity to PI3K/mTOR pathway inhibitors. CONCLUSIONS: TCF7L2 acts as a master metabolic regulator in HCC, coordinating lipid catabolism and mitochondrial biogenesis to drive aggressive tumor behavior. It further remodels the TME towards an HPC-like state and predicts sensitivity to metabolic-targeted therapies. These findings identify TCF7L2 as a key prognostic biomarker and a promising therapeutic target.

MHCC-97H hepatocellular carcinoma cells (MHCC-97H ↗
PubMed2026

Chromosome-level genome assembly of the hemiparasitic Taxillus sutchuenensis (Loranthaceae).

Taxillus sutchuenensis, an ecologically and medicinally important hemiparasitic plant that parasitizes diverse woody hosts, was sequenced to generate a high-quality chromosome-level genome assembly. PacBio HiFi long reads, RNA-seq transcriptome data, and Hi-C data were used to assemble a 406.32 Mb genome anchored onto nine pseudo-chromosomes, with a scaffold N50 of 45.59 Mb. The assembly showed high completeness and accuracy, supported by BUSCO (93.6%) and Merqury QV (70.6) assessments. The LTR Assembly Index (LAI) of 13.98 indicated excellent continuity. A total of 21,795 protein-coding genes were predicted, with 94.46% functionally annotated. Repetitive sequences accounted for 50.05% of the genome, primarily LTR retrotransposons. This genome provides a valuable resource for investigating the evolution, functional genomics, and parasitic mechanisms of hemiparasitic plants.

Genome, Plant↗
PubMed2024

A comprehensive analysis of ribonucleotide reductase subunit M2 for carcinogenesis in pan-cancer.

BACKGROUND: Although there is evidence that ribonucleotide reductase subunit M2 (RRM2) is associated with numerous cancers, pan-cancer analysis has seldom been conducted. This study aimed to explore the potential carcinogenesis of RRM2 in pan-cancer using datasets from The Cancer Genome Atlas (TCGA). METHODS: Data from the UCSC Xena database were analyzed to investigate the differential expression of RRM2 across multiple cancer types. Clinical data such as age, race, sex, tumor stage, and status were acquired to analyze the influence of RRM2 on the clinical characteristics of the patients. The role of RRM2 in the onset and progression of multiple cancers has been examined in terms of genetic changes at the molecular level, including tumor mutational burden (TMB), microsatellite instability (MSI), biological pathway changes, and the immune microenvironment. RESULTS: RRM2 was highly expressed in most cancers, and there was an obvious correlation between RRM2 expression and patient prognosis. RRM2 expression is associated with the infiltration of diverse immune and endothelial cells, immune checkpoints, tumor mutational burden (TMB), and microsatellite instability (MSI). Moreover, the cell cycle is involved in the functional mechanisms of RRM2. CONCLUSIONS: Our pan-cancer study provides a comprehensive understanding of the carcinogenesis of RRM2 in various tumors.

Humans↗
PubMed2007

Monte Carlo sampling of near-native structures of proteins with applications.

Since a protein's dynamic fluctuation inside cells affects the protein's biological properties, we present a novel method to study the ensemble of near-native structures (NNS) of proteins, namely, the conformations that are very similar to the experimentally determined native structure. We show that this method enables us to (i) quantify the difficulty of predicting a protein's structure, (ii) choose appropriate simplified representations of protein structures, and (iii) assess the effectiveness of knowledge-based potential functions. We found that well-designed simple representations of protein structures are likely as accurate as those more complex ones for certain potential functions. We also found that the widely used contact potential functions stabilize NNS poorly, whereas potential functions incorporating local structure information significantly increase the stability of NNS.

Computer Simulation↗
PubMed2006

Monte Carlo simulation of cutaneous reflectance and fluorescence measurements--the effect of melanin contents and localization.

Melanin content and distribution in skin were studied by examining a patient with white, brown and blue skin tones expressed on skin affected by vitiligo. Both diffuse reflectance and autofluorescence spectra of the three distinction skin sites were measured and compared. Monte Carlo simulations were then performed to help explain the measured spectral differences. The modeling is based on a six-layer skin optical model established from published skin optical parameters and by adding melanin content into different locations in the model skin. Both the reflectance and fluorescence spectra calculated by Monte Carlo (MC) simulation were approximately in agreement with experimental results. The study suggests that: (1) trichrome vitiligo skin may be an ideal in vivo model for studying the effect of skin melanin content and distribution on skin spectroscopy properties. (2) Based on the skin optical model and MC simulation, the content and distribution of melanin in skin, or other component of skin could be simulated and predicted. (3) Both reflectance and fluorescence spectra provided information about superficial skin structures but fluorescence spectra are capable of providing information from deeper cutaneous structures. (4) The research method, including the spectral ratio method, the method of adding and modifying the melanin content in skin optical models, and MC simulation could be applied in other non-invasive optical studies of the skin.

Computer Simulation↗
PubMed2006

Adventitial fibroblasts are activated in the early stages of atherosclerosis in the apolipoprotein E knockout mouse.

The role of the adventitia in vascular function and vascular lesion formation has been largely ignored. This study observed the activation of the adventitia and specifically the fibroblasts in the development of atherosclerosis in the apoE(-/-) mouse. The results showed a gradual increase in expression of collagen types I and III after 2, 4, and 8 weeks of hyperlipidic diet. The earliest expression of monocyte chemoattractant protein-1 (MCP-1) protein and mRNA was detected in the adventitial fibroblast before the formation of intimal lesions. Proliferation, too, was first found in the adventitial fibroblasts. We hypothesize that the adventitial fibroblast is activated in the early stage of atherosclerosis. Adventitial inflammation may be an early event in the development of atherosclerotic lesions.

Animals↗
PubMed2006

Direct evidence that two cysteines in the dopamine transporter form a disulfide bond.

We have generated a fully functional dopamine transporter (DAT) mutant (dmDATx7) with all cysteines removed except the two cysteines in extracellular loop 2 (EL2). Random mutagenesis at either or both EL2 cysteines did not produce any functional transporter mutants, suggesting that the two cysteines cannot be replaced by any other amino acids. The cysteine-specific reagent MTSEA-biotin labeled dmDATx7 only after a DTT treatment which reduces disulfide bond. Since there are no other cysteines in dmDATx7, the MTSEA-biotin labeling must be on the EL2 cysteines made available by the DTT treatment. This result provides the first direct evidence that the EL2 cysteines form a disulfide bond. Interestingly, the DTT treatment had little effect on transport activity suggesting that the disulfide bond is not necessary for the uptake function of DAT. Our results and previous results are consistent with the notion that the disulfide bond between EL2 cysteines is required for DAT biosynthesis and/or its delivery to the cell surface.

Amino Acid Sequence↗
PubMed2006

A sequential blockade strategy for the design of combination therapies to overcome oncogene addiction in chronic myelogenous leukemia.

Some tumors are dependent on the continued activity of a single oncogene for maintenance of their malignant phenotype. The best-studied example is the Bcr-Abl fusion protein in chronic myelogenous leukemia (CML). Although the clinical success of the Abl kinase inhibitor imatinib against chronic-phase CML emphasizes the importance of developing therapeutic strategies aimed at this target, resistance to imatinib poses a major problem for the ultimate success of CML therapy by this agent. We hypothesized a sequential blockade strategy that is designed to decrease the expression of the Bcr-Abl protein, with the goal of complementing the action of imatinib on kinase activity. In this study, flavopiridol, an inhibitor of transcription, homoharringtonine (HHT), a protein synthesis inhibitor, and imatinib were used singly and in combination against the Bcr-Abl-positive human CML cell line K562. Flavopiridol alone inhibited phosphorylation of the RNA polymerase II COOH-terminal domain, specifically reduced RNA polymerase II-directed mRNA synthesis, and decreased the Bcr-Abl transcript levels. HHT inhibited protein synthesis and reduced the Bcr-Abl protein level. Imatinib directly inhibited the kinase activity of Bcr-Abl. The combinations of flavopiridol and HHT and flavopiridol and imatinib synergistically decreased clonogenicity as evaluated by the median-effect method. Greater synergy was observed when HHT and imatinib were given sequentially compared with simultaneous administration. Imatinib-resistant Ba/F3 cells that were transfected to express the E255K and T315I mutations of Bcr-Abl were not cross-resistant to flavopiridol and HHT. These results provided a rationale for the combination of inhibitors of transcription and/or translation with specific kinase inhibitors.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2006

Bulbourethral composite suspension for treatment of male-acquired urinary incontinence.

OBJECTIVES: We evaluated the efficacy of bulbourethral composite sling procedure in the treatment of male urinary incontinence after radical prostatectomy, transurethral resection of the prostate, or prostatic enucleation for benign prostatic hyperplasia, and posterior urethroplasty. METHODS: Between May 2000 and April 2005, a bulbourethral composite sling was performed in 26 patients with acquired urinary incontinence. Eight (30.8%) of these patients had severe urinary incontinence, and 18 (69.2%) had mild to moderate urinary incontinence. A polyester patch plus tension-free vaginal tape (TVT) device was used in the procedure. Prolene threads were attached to the two ends of polyester taper then passed from the perineal incision to a suprapubic incision with a TVT needle. The ends of the sutures and TVT were tied over the rectus fascia in the midline after repeated urethral pressure measurements reached 80-90 cm H2O. RESULTS: The follow-up period was 8-54 mo (mean: 28.3). The primary procedure failed in one patient. Of the remaining 25 patients, 1 patient died of cerebral hemorrhage 2 yr postoperatively, and 2 patients had recurrent stress incontinence in 1.5 and 2 yr postsurgery, respectively. The recurrent incontinence was severe in one patient and mild (one to two pads per day) in the other. The remaining 22 patients maintained urination and continence. The total success rate (cure and improved) was 92% (23 of 25). CONCLUSIONS: Bulbourethral composite sling procedure is a minimally invasive, safe, effective surgical option in the treatment of male patients with mild to moderate incontinence, but is not suitable for severe incontinence. Temporary perineal discomfort or pain is a common complication of the procedure.

Adolescent↗
PubMed2006

Single-based resolution for oligodeoxynucleotides and their phosphorothioate modifications by replaceable capillary gel electrophoresis.

A replaceable capillary gel electrophoretic (replaceable CGE) method was developed for the separation of two sets of model compounds of single-stranded oligodeoxynucleotide mixtures (18-20 mers), phosphodiester oligodeoxynucleotides (PO-ODNs) and their phosphorothioate modifications (PS-ODNs), with equal sequences differing in a single base. Polyethylene glycol (PEG) 35000 was chosen as the sieving matrix. It was confirmed that PEG polymer solution less influenced resolutions of the PS-ODNs compared with those of the PO-ODNs, while acetonitrile used as an additive in the system improved the separation significantly. It was also noticed that the effect of temperature on separation was much larger than that of denaturant urea.

Acetonitriles↗
PubMed2006

Abolished cocaine reward in mice with a cocaine-insensitive dopamine transporter.

There are three known high-affinity targets for cocaine: the dopamine transporter (DAT), the serotonin transporter (SERT), and the norepinephrine transporter (NET). Decades of studies support the dopamine (DA) hypothesis that the blockade of DAT and the subsequent increase in extracellular DA primarily mediate cocaine reward and reinforcement. Contrary to expectations, DAT knockout (DAT-KO) mice and SERT or NET knockout mice still self-administer cocaine and/or display conditioned place preference (CPP) to cocaine, which led to the reevaluation of the DA hypothesis and the proposal of redundant reward pathways. To study the role of DAT in cocaine reward, we have generated a knockin mouse line carrying a functional DAT that is insensitive to cocaine. In these mice, cocaine suppressed locomotor activity, did not elevate extracellular DA in the nucleus accumbens, and did not produce reward as measured by CPP. This result suggests that blockade of DAT is necessary for cocaine reward in mice with a functional DAT. This mouse model is unique in that it is specifically designed to differentiate the role of DAT from the roles of NET and SERT in cocaine-induced biochemical and behavioral effects.

Animals↗
PubMed2006

Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors.

An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only Calpha or backbone atoms are attractive because they enable efficient search of the conformational space. We show residue-specific reduced discrete-state models can represent the backbone conformations of proteins with small RMSD values. However, no potential functions exist that are designed for such simplified protein models. In this study, we develop optimal potential functions by combining contact interaction descriptors and local sequence-structure descriptors. The form of the potential function is a weighted linear sum of all descriptors, and the optimal weight coefficients are obtained through optimization using both native and decoy structures. The performance of the potential function in a test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. Our potential function requiring only backbone atoms or Calpha atoms have comparable or better performance than several residue-based potential functions that require additional coordinates of side-chain centers or coordinates of all side-chain atoms. By reducing the residue alphabets down to size 10 for contact descriptors, the performance of the potential function can be further improved. Our results also suggest that local sequence-structure correlation may play important role in reducing the entropic cost of protein folding.

Amino Acid Sequence↗
PubMed2006

X-ray structure of a native calicivirus: structural insights into antigenic diversity and host specificity.

Caliciviruses, grouped into four genera, are important human and veterinary pathogens with a potential for zoonosis. In these viruses, capsid-related functions such as assembly, antigenicity, and receptor interactions are predominantly encoded in a single protein that forms an icosahedral capsid. Understanding of the immunologic functions and pathogenesis of human caliciviruses in the Norovirus and Sapovirus genera is hampered by the lack of a cell culture system or animal models. Much of our understanding of these viruses, including the structure, has depended on recombinant capsids. Here we report the atomic structure of a native calicivirus from the Vesivirus genus that exhibits a broad host range possibly including humans and map immunological function onto a calicivirus structure. The vesivirus structure, despite a similar architectural design as seen in the recombinant norovirus capsid, exhibits novel features and indicates how the unique modular organization of the capsid protein with interdomain flexibility, similar to an antibody structure with a hinge and an elbow, integrates capsid-related functions and facilitates strain diversity in caliciviruses. The internally located N-terminal arm participates in a novel network of interactions through domain swapping to assist the assembly of the shell domain into an icosahedral scaffold, from which the protruding domain emanates. Neutralization epitopes localize to three hypervariable loops in the distal portion of the protruding domain surrounding a region that exhibits host-specific conservation. These observations suggest a mechanism for antigenic diversity and host specificity in caliciviruses and provide a structural framework for vaccine development.

Amino Acid Sequence↗
PubMed2006

[The treatment of complex urethral stricture greater than 8 cm long].

OBJECTIVE: To evaluate the selection of different procedures and the feasibility for the treatment of long segment urethral stricture. METHODS: Seventy-six patients with complex urethral stricture greater than 8 cm long underwent different procedures of urethroplasty. Of them various mucosa grafts urethral reconstruction were adopted in 42 cases (colonic mucosal graft, n = 26; buccal mucosal graft, n = 10; bladder mucosal graft, n = 6); One-stage pedicle flaps urethroplasty in 20; two-stage urethroplasty of Johanson procedure in 12; and penile urethra-prostatic urethra anastomosis, three-stage urethroplasty in 2. RESULTS: In early followed up (within 6 months postoperatively), 67 patients (88%) voided well and complications developed in 10. Among the 70 patients who lasted more than 1 year after operation, 51 cases were followed up. Forty-four patients voided well, and complications developed in 8. Of the 8 cases urethral restructure developed in 2 (18%) for pedicle flaps urethroplasty, 2 for colonic mucosal urethroplasty (9%), 1 for buccal mucosal graft (1/7), 1 for bladder mucosal graft (1/3); penile chordee in 2 (2/5), and one of them was accompanied by hair bearing neourethra for two-stage urethroplasty of Johanson procedure. CONCLUSIONS: Colonic mucosal and buccal mucosal grafts urethroplasty are feasible procedures for the treatment of long segment urethral stricture, and Colonic mucosal graft urethroplasty may be considered when more conventional procedures fail or complicated urethral strictures greater than 10 cm long.

Adolescent↗
PubMed2006

Fabrication of bismuth subcarbonate nanotube arrays from bismuth citrate.

Bismuth subcarbonate ((BiO)2CO3) nanotubes with uniform diameters of about 3-5 nm were fabricated from bismuth citrate; these nanotubes exhibit antibacterial properties against Helicobacter pylori (50% inhibition at 10 microg mL(-1)), a bacterium causing peptic ulcers and gastritis.

Anti-Bacterial Agents↗