Biomedical subjects

Xiang Zhang

Publications and source records attributed to Xiang Zhang.

At least 19 recordsLinked to original sources

PubMed2026

Single-cell and spatial transcriptomics define a progenitor subpopulation and fibroinflammatory niche at the leading edge of parathyroid carcinoma.

Parathyroid carcinoma (PC) is a rare but clinically aggressive endocrine malignancy with limited treatment options and a poorly defined tumor microenvironment (TME). To elucidate its cellular heterogeneity and spatial architecture, we integrated single-cell and spatial transcriptomic profiling with whole-exome sequencing and multiplex immunohistochemistry on eight parathyroid neoplasm specimens, including PC, parathyroid adenoma, and atypical parathyroid tumor. We identified a distinct progenitor-like endocrine subpopulation (Ca-1) enriched in CDC73-mutant PC, exhibiting stem-like properties, elevated cell cycle activity, and pronounced genomic instability. Spatial mapping revealed that Ca-1 cells preferentially localize at the leading edge, forming a fibroinflammatory niche characterized by the enrichment of inflammatory cancer-associated fibroblasts (iCAFs) and SPP1+ macrophages. Within this niche, the dipeptidyl peptidase 4 (DPP4) is selectively expressed in Ca-1 cells and iCAFs, implicating a potential paracrine axis driving stromal remodeling and immunosuppression. These findings suggest that a spatially organized ecosystem may promote PC progression through TME remodeling and highlight the DPP4-CXCL2 axis as a candidate pathway for future investigation in aggressive parathyroid neoplasms.

Humans↗

PubMed2026

Bilateral Conversion Risk in Unilateral Retinoblastoma Using Age and Genetic Testing.

IMPORTANCE: Metachronous bilateral conversion in initially unilateral retinoblastoma is uncommon but clinically consequential, potentially requiring intensified treatment and carrying worse prognosis. Clarifying how age at diagnosis refines genetic-risk stratification could enable safer, more efficient surveillance protocols. OBJECTIVE: To estimate the incidence and timing of metachronous bilateral conversion in unilateral retinoblastoma and assess whether age at diagnosis and RB1 testing are associated with bilateral conversion risk. DESIGN, SETTING AND PARTICIPANTS: This was a retrospective cohort study at a tertiary center in Shanghai, China, including 1108 consecutive children with initially unilateral retinoblastoma diagnosed from July 2010 to October 2024 (after exclusions for short follow-up [n = 139], missing data [n = 53], or synchronous bilateral disease [n = 10]). The median (IQR) follow-up was 43.4 (24.2-67.6) months. EXPOSURES: Age at diagnosis and RB1 genetic status/subtypes assessed by next-generation sequencing and multiplex ligation-dependent probe amplification, including penetrance class (high vs low) and mosaic vs germline categorization. MAIN OUTCOMES AND MEASURES: Time to metachronous bilateral conversion; cumulative incidence functions with death as a competing risk; spatial distribution of fellow-eye tumors. RESULTS: Among 1108 patients (median [IQR] age at diagnosis, 22.2 [12.0-31.4] months; 591 [53.3%] male), 24 (2.2%) developed metachronous bilateral disease. At 24 months, cumulative incidence was 2.2% (95% CI, 1.3-3.1) overall. By genetic status, the 24-month cumulative incidence was 24.8% (95% CI, 13.8-35.9) in RB1 variant-positive vs 1.6% (95% CI, 0.0-3.1) in RB1 variant-negative patients. Among RB1 variant-positive patients, risk clustered among those diagnosed before 9 months, whereas no conversions were observed among those diagnosed at older than 9 months. Four RB1 variant-negative patients who were initially diagnosed at notably late ages (20.9, 42.7, 79.6, and 118 months) subsequently converted; these cases likely represent undetected low-level mosaicism, somatic variants below detection thresholds, or rare genomic events not captured by standard sequencing panels. Fellow-eye tumors did not involve macula and showed a nasal-predominant distribution. CONCLUSIONS AND RELEVANCE: The findings in this study suggest that age at diagnosis may refine genetic risk stratification for metachronous bilateral conversion. RB1 variant-positive patients diagnosed at 9 months or later represent a very low-risk subgroup that may warrant surveillance deescalation, while rare late conversions in RB1 variant-negative patients necessitate continued long-term monitoring.

Humans↗

PubMed2026

CaMYB121-CaABF2 negative feedback loop modulates CaNHX2 expression to confer salt tolerance in pepper.

Salt stress is a major abiotic factor that severely restricts pepper (Capsicum annuum) production. Although abscisic acid (ABA) is vital for salt tolerance, the transcriptional regulatory networks governing ABA-mediated salt defense remain largely unknown. Here, we uncovered a negative feedback loop between CaMYB121 and CaABF2.1/2 that modulates the expression of CaNHX2.1/2/3, thereby enhancing salt tolerance in pepper plants. RNA-seq analysis revealed that CaMYB121 displayed an expression pattern consistent with that of CaNHX2 after salt treatment. Silencing CaMYB121 markedly reduced salt tolerance and inhibited root growth. Mechanistically, CaMYB121 directly binds to the CaNHX2 promoter to activate transcription, thereby promoting salt resilience. Salt stress also robustly triggered ABA signaling genes, with CaABF2.1/2 displaying expression patterns closely mirroring those of CaMYB121. Transient silencing of CaABF2.1/2 results in phenotypes similar to those observed with CaMYB121 suppression. Notably, CaMYB121 activates CaABF2.1/2 transcription by binding to its promoters, whereas CaABF2.1/2 represses CaMYB121 expression by directly targeting its promoter, forming a self-regulating feedback loop that prevents excessive defense activation. Collectively, our findings reveal a CaMYB121-CaABF2 feedback circuit that dynamically balances growth and defense to optimize salt tolerance in pepper plants.

Salt Tolerance↗

PubMed2025

Rat somatic genome editing enables ER+ breast cancer modeling.

Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we report efficient somatic genome editing in rats, enabling both Indel and substitution mutations. We then apply this approach to model estrogen receptor (ER)-positive breast cancer, which accounts for ~70% of human cases but remains poorly represented in mice. The resulting rat tumors reproduce hallmarks of human ER+ breast cancer, including ductal histology, hormone responsiveness, and immune-microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring critical species differences in tumorigenesis. Together, this work establishes a versatile platform for rapid generation of clinically relevant rat tumor models, opening new avenues to dissect tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

Journal Article↗

PubMed2025

Streptomyces huangiella sp. nov., an endophytic actinomycete isolated from Pheretima aspergillum, a promising candidate for biological pathogen control.

UNLABELLED: Pheretima aspergillum (E. Perrier) is an annelid of the genus Pheretima in the family Megascolecidae, a species of earthworm, whose dried body (Guang Dilong) is a traditional Chinese animal medicine. A new actinobacterium strain, named HD1123-B1T, was isolated from the gut contents of Pheretima aspergillum caught in the wild in Guangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was primarily identified as a member of the genus Streptomyces, sharing more than 98% sequence identity to Streptomyces endocoffeicus CA3R110T (98.80%), Streptomyces coffeae CA1R205T (98.47%), and Streptomyces iranensis HM35T (97.93%). The whole genome size of strain HD1123-B1T was approximately 8.9 Mbp, with 7,464 predicted genes and 71.42 mol% DNA C+G content. Comparative genomic analyses based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values revealed that strain HD1123-B1T represents a novel species within the genus Streptomyces. Additionally, 38 biosynthetic gene clusters for secondary metabolites were also predicted in the genome of strain HD1123-B1T. Based on LC-MS/MS analysis, the nigericin biosynthesis gene cluster has been completely characterized. The ethyl acetate crude extract of strain HD1123-B1T exhibited remarkable antibacterial activity against gram-positive bacteria (methicillin-resistant Staphylococcus aureus ATCC 25213, etc) and gram-negative bacteria Ralstonia solanacearum GIM 1.70. Based on these results, HD1123-B1T could be confirmed as an isolate that represents a novel species of the genus Streptomyces, for which the name Streptomyces huangiella sp. nov. is proposed. IMPORTANCE: As the largest genus of the phylum Actinomycetes, Streptomyces is a kind of microbial resources with great practical and economic value. Due to their unique physiological properties and metabolic capacity, Streptomyces have become an important source of bioactive compounds in the world and play an indispensable role in medical and industrial fields. With the advancement of molecular biology and genomics, researchers can more deeply explore the metabolic potential of Actinomycetes, discovering and developing new biologically active compounds. These new compounds may possess various biological activities, such as antibacterial, antiviral, antifungal, and antiparasitic properties, further promoting the development of medicine and related industries. Based on genomic analysis and antibacterial activity, the strain HD1123-B1T was indicated to be a promising candidate for biological pathogen control.

Streptomyces↗

PubMed2025

Abnormal levels of miRNA in pancreatic cancer are linked to tumor progression by regulating the translation of tumor-associated mRNA.

BACKGROUND: Pancreatic cancer remains one of the most malignant tumors, characterized by limited treatment efficacy. MAIN FINDINGS: microRNAs (miRNAs) play a crucial role in regulating the proliferation, invasion, migration, drug resistance, apoptosis, and cell cycle progression of pancreatic cancer cells by inhibiting tumor-associated proteins. Metscape analysis revealed that miRNA-targeted proteins associated with pancreatic cancer are enriched in processes such as cell proliferation, mitosis, and cell migration, and participate in multiple signaling pathways. These proteins primarily localize to classical pathways, including JAK/STAT, PI3K/AKT, and Wnt/β-catenin. Furthermore, gene mutations or abnormal alternative poly(A)denylation (APA) within miRNA-targeted regions can disrupt base pairing to the 3'-Untranslated Region (3'-UTR), thereby enhancing the translation of oncogenic mRNA translation. FUTURE DIRECTIONS: Collectively, these findings indicate that multiple miRNAs act cooperatively to influence pancreatic cancer progression. Consequently, therapeutic strategies aimed at restoring the balance of the miRNA system are essential to disrupt the 'mRNA-oncogene' vicious cycle.

Humans↗

PubMed2024

Integrative Omics Reveals the Metabolic Patterns During Oocyte Growth.

Well-controlled metabolism is associated with high-quality oocytes and optimal development of a healthy embryo. However, the metabolic framework that controls mammalian oocyte growth remains unknown. In the present study, we comprehensively depict the temporal metabolic dynamics of mouse oocytes during in vivo growth through the integrated analysis of metabolomics and proteomics. Many novel metabolic features are discovered during this process. Of note, glycolysis is enhanced, and oxidative phosphorylation capacity is reduced in the growing oocytes, presenting a Warburg-like metabolic program. For nucleotide biosynthesis, the salvage pathway is markedly activated during oocyte growth, whereas the de novo pathway is evidently suppressed. Fatty acid synthesis and channeling into phosphoinositides are specifically elevated in oocytes accompanying primordial follicle activation; nevertheless, fatty acid oxidation is reduced in these oocytes simultaneously. Our data establish the metabolic landscape during in vivo oocyte growth and serve as a broad resource for probing mammalian oocyte metabolism.

Animals↗

PubMed2024

A statistical simulation model to guide the choices of analytical methods in arrayed CRISPR screen experiments.

An arrayed CRISPR screen is a high-throughput functional genomic screening method, which typically uses 384 well plates and has different gene knockouts in different wells. Despite various computational workflows, there is currently no systematic way to find what is a good workflow for arrayed CRISPR screening data analysis. To guide this choice, we developed a statistical simulation model that mimics the data generating process of arrayed CRISPR screening experiments. Our model is flexible and can simulate effects on phenotypic readouts of various experimental factors, such as the effect size of gene editing, as well as biological and technical variations. With two examples, we showed that the simulation model can assist making principled choice of normalization and hit calling method for the arrayed CRISPR data analysis. This simulation model is implemented in an R package and can be downloaded from Github.

CRISPR-Cas Systems↗

PubMed2007

Study of methylation of nitrogen-containing compounds in the gas phase.

The methyl migration between the protonated N,N-dimethylisopropylamine and other neutral aliphatic amines in the gas phase has been investigated by a hybrid external chemical ionization source ion trap mass spectrometer. Similar reactions have been found in the aqueous solution by Callahan and Wolfenden (J. Am. Chem. Soc. 2003; 125: 310). At the same time, density functional theory (DFT) calculations show that in contrast with the neutral N,N-dimethylisopropylamine, protonated N,N-dimethylisopropylamine is a better methyl donor. These results indicate that protonation promotes the methyl migration between aliphatic amines both in the gas phase and in the aqueous solution. In addition, methyl transfer also exists between the protonated N,N-dimethylisopropylamine and some other nitrogen-containing compounds.

Gases↗

PubMed2006

Altered host:pathogen interactions conferred by the Blau syndrome mutation of NOD2.

Blau syndrome (BS) is a rare familial granulomatous disease manifested by uveitis, arthritis and skin rash. BS has recently been found to be associated with a distinctive mutation in NOD2, which encodes an intracellular toll-like receptor. We have compared host cell interaction with bacterial challenge in U937 cells expressing wild type human NOD2 (NOD2(wt)), mutant NOD2 (NOD2(Blau)), or a vector control (VC). The cells were incubated with Salmonella typhimurium. Intracellular uptake was assessed by harvesting the cells at different time points following invasion and quantitating the CFU, recovered after gentamicin treatment to kill extracellular organisms. Expression of TNF-alpha, TLR2 and TLR4 was determined by semi-quantitative RT-PCR under resting conditions and after stimulation by bacteria. Invasion of target cells with S. typhimurium was diminished in the presence of NOD2(Blau). Expression of TNF-alpha mRNA was enhanced following bacterial invasion in all cell lines but NOD2(Blau) was associated with a more rapid decline in TNF-alpha expression. Kinetics of intracellular clearance of bacteria indicated a relative defect in NOD2(Blau) compared to controls. This clearance defect may be related to the lack of sustained TNF-alpha seen in the early stages. These events were not related to differential TLR2 or TLR4 expression since there were no significant differences seen between the cell lines after bacterial stimulation. Our findings indicate that the NOD2 mutation associated with this syndrome alters host:microbial interaction, and this may have relevance to triggering factors in the ocular and joint inflammation seen in BS.

Arthritis↗

PubMed2006

Neural network prediction of peptide separation in strong anion exchange chromatography.

MOTIVATION: The still emerging combination of technologies that enable description and characterization of all expressed proteins in a biological system is known as proteomics. Although many separation and analysis technologies have been employed in proteomics, it remains a challenge to predict peptide behavior during separation processes. New informatics tools are needed to model the experimental analysis method that will allow scientists to predict peptide separation and assist with required data mining steps, such as protein identification. RESULTS: We developed a software package to predict the separation of peptides in strong anion exchange (SAX) chromatography using artificial neural network based pattern classification techniques. A multi-layer perceptron is used as a pattern classifier and it is designed with feature vectors extracted from the peptides so that the classification error is minimized. A genetic algorithm is employed to train the neural network. The developed system was tested using 14 protein digests, and the sensitivity analysis was carried out to investigate the significance of each feature. AVAILABILITY: The software and testing results can be downloaded from ftp://ftp.bbc.purdue.edu.

Algorithms↗

PubMed2006

Resveratrol inhibits cell growth and induces apoptosis of rat C6 glioma cells.

Resveratrol (Res) has been reported to inhibit tumor initiation, promotion, and progression in a variety of cell culture systems depending on the specific cell type and cellular environment. In the present study, we determined the effect of Res on the cell growth and apoptosis of rat glioma C6 cell line as well as mouse fibroblast 3T3 cell line, in vitro. Concurrently, we investigated whether caspase-3 is involved in the Res-induced apoptosis of rat glioma cells. Exposure to Res exhibits a significant anti-proliferative effect and induces an increase in the population of apoptotic cells on C6 cells in a concentration- and time-dependent manner, but not for normal 3T3 fibroblast cells, as measured by methyl thiazolyl tetrazolium assay and flow cytometer. Distinguished increase of C6 cells in S phase is observed after the treatment of Res as compared to insignificant change in cell cycle distribution of 3T3 cells. TdT-mediated dUTP nick end labeling fluorescence staining, HE staining, and scanning electron microscope revealed abnormal morphology and ultrastructure in C6 cells treated with Res. Our data showed that Res can increase the expression and induced the activation of caspase-3 in rat glioma C6 cells. These results suggest that Res has significant apoptosis-inducing effect on C6 glioma cells other than normal fibroblast 3T3 cells in vitro and caspase-3 may act as a potential mediator in the process.

Animals↗

PubMed2006

[Inhibition of growth and angiogenesis of U251 cell xenograft in vivo by short hairpin RNA targeting survivin gene].

OBJECTIVE: To observe the impact of specific short hairpin RNA (shRNA) targeting survivin gene on tumorigenesis and angiogenesis of human brain glioblastoma U251 cells in vivo of nude mice. METHODS: U251 cells, U251-SR cells transfected stably with shRNA eukaryotic expression vector pWH1-SR targeting survivin gene, and U251-P cells transfected stably with blank pWH1 vector, were inoculated respectively into subcutaneous tissue in flank of 15 nude mice (each group 5 mice), and the tumor growth status was observed and measured. Protein expressions of survivin, proliferating cell nuclear antigen (PCNA) and factor VIII related antigen (F VIII RAg) were investigated by immunohistochemistry SABC method, apoptotic cells were screened by TUNEL method, furthermore proliferative index (PI), apoptotic index (AI) and microvessel density (MVD) were measured respectively in each group of tumor specimens. RESULTS: Comparing with those in U251 and U251-P groups, in U251-SR group, the tumorigenesis time delayed, tumor grew slowly, both tumor volume and tumor weight decreased significantly (P < 0.01 for both); Survivin protein expression was down-regulated markedly; PI and MVD decreased significantly, whereas AI increased remarkably (P < 0.01 for all). CONCLUSIONS: The specific shRNA targeting survivin gene can inhibit significantly tumorigenesis and angiogenesis of U251 cells in vivo.

Animals↗

PubMed2006

A method for the identification of glycoproteins from human serum by a combination of lectin affinity chromatography along with anion exchange and Cu-IMAC selection of tryptic peptides.

This paper reports a method for identifying glycoproteins from human serum. Glycoproteins were selected with a concanavalin A (Con A) lectin column and then tryptically digested prior to sequential chromatographic selection of acidic and histidine containing peptides. Acidic peptides were selected with a strong anion exchange (SAX) column. Peptides captured by the SAX columns were then released and histidine-containing peptides in the mixture selected with a copper loaded immobilized metal affinity chromatography (Cu-IMAC) column. This serial chromatographic selection process reduced the complexity of proteolytic digests by more than an order of magnitude. Peptides selected by this serial process were then fractionated by reversed-phase chromatography (RPC) and identified by tandem mass spectrometry. The method was initially validated using human transferrin before application to human serum. The results show that all the peptides identified except one contained histidine and acidic amino acids.

Amino Acid Sequence↗

PubMed2006

Optimizing immunotherapy in multiple myeloma: Restoring the function of patients' monocyte-derived dendritic cells by inhibiting p38 or activating MEK/ERK MAPK and neutralizing interleukin-6 in progenitor cells.

Previous studies demonstrated that circulating dendritic cells (DCs) in myeloma patients were functionally abnormal. However, the phenotype and function of patients' monocyte-derived DCs (MoDCs), which are commonly used for immunotherapy, were poorly defined. This study was undertaken to examine the quality of MoDCs from myeloma patients compared with cells from healthy donors. We found that patient-derived MoDCs are phenotypically and functionally defective. Compared with their normal counterparts, patient-derived, mature MoDCs expressed significantly lower levels of CD1a, CD40, CD80, and HLA-DR and were poor at activating alloreactive T cells, presenting recall antigen, and activating autologous antigen- and myeloma-specific T cells. These abnormalities may be attributed to elevated production of autocrine cytokines such as IL-6, activated p38 and STAT3, and inhibited MEK/ERK signaling pathways in the progenitor cells. Treatment with neutralizing IL-6-specific antibody and, more importantly, p38 inhibitor, or both, could correct these abnormalities. Treating patient-derived cells with these agents not only significantly increased cell yield but also produced MoDCs that were as functional as their normal counterparts. Thus, this study has delineated the mechanistic defects of MoDCs from myeloma patients and identified ways for restoring the function of the cells to improve the efficacy of DC-based immunotherapy in this disease.

Antibodies↗

PubMed2006

Tubeimoside V (1), a new cyclic bisdesmoside from tubers of Bolbostemma paniculatum, functions by inducing apoptosis in human glioblastoma U87MG cells.

Malignant glioblastoma is one of the most common malignant tumors in the neurological system. Tubeimoside V (1), a new cyclic bisdesmoside from tubers of Bolbostemma paniculatum, appears to exhibit various biological activities, including antitumor effect, but the function and mechanism of this new agent on glioblastoma cells has not previously been determined. In the present study, we investigated the proliferation change of human glioblastoma U87MG cells exposured to different concentrations (0.9-14.8 microM) of Tubeimoside V (1) for a certain time. The results showed that Tubeimoside V (1) significantly suppressed U87MG cell proliferation in a time- and dose-dependent manner (IC(50) = 3.6 microM). Flow cytometric analysis of DNA in U87MG cells showed that Tubeimoside V (1) induces the prominent appearance of a sub-G1 peak in the cell cycle suggestive of apoptosis. Furthermore, U87MG cells' treatment with Tubeimoside V (1) resulted in nuclear condensation with apoptotic bodies observed by both fluorescence and electron microscopy. The result of annexin V/PI assay showed that phosphatidylserine externalization began after treatment, and then increased in the following 24h. Molecular changes explored through Western-blot staining showed Tubeimoside V (1) decreased the expression levels of Bcl-2 protein and increased the expression levels of Bax protein. The novel findings suggest that the cytotoxic actions of Tubeimoside V (1) toward U87MG cells result from the induction of cell apoptosis. Overall, our data demonstrate that Tubeimoside V (1) is an efficient apoptotic killing agent of glioblastoma cells and suggest that this mechanism may play a critical role in anti-tumor chemotherapy.

Antineoplastic Agents↗

PubMed2006

Ultrasonic metamaterials with negative modulus.

The emergence of artificially designed subwavelength electromagnetic materials, denoted metamaterials, has significantly broadened the range of material responses found in nature. However, the acoustic analogue to electromagnetic metamaterials has, so far, not been investigated. We report a new class of ultrasonic metamaterials consisting of an array of subwavelength Helmholtz resonators with designed acoustic inductance and capacitance. These materials have an effective dynamic modulus with negative values near the resonance frequency. As a result, these ultrasonic metamaterials can convey acoustic waves with a group velocity antiparallel to phase velocity, as observed experimentally. On the basis of homogenized-media theory, we calculated the dispersion and transmission, which agrees well with experiments near 30 kHz. As the negative dynamic modulus leads to a richness of surface states with very large wavevectors, this new class of acoustic metamaterials may offer interesting applications, such as acoustic negative refraction and superlensing below the diffraction limit.

Journal Article↗

PubMed2006

Resveratrol reduces the elevated level of MMP-9 induced by cerebral ischemia-reperfusion in mice.

Stroke is one of the leading causes of mortality; however, its treatment remains obscure and largely empirical. Since matrix metalloproteinase 9 (MMP-9) has been postulated to be the major contributor of neuronal injury during reperfusion, inhibition of MMP-9 could be a potential approach in maintaining the viability of neurons. Trans-resveratrol (resveratrol), a polyphenolic compound has recently been shown to have neuroprotective activity against cerebral ischemia. Therefore, the aim of the present study was to evaluate the effect of resveratrol on MMP-9 induced by cerebral ischemia-reperfusion in vivo. Male Balb/C mice were treated with resveratrol for 7 days (50 mg/kg, gavage). Thereafter, middle cerebral artery occlusion (MCAo) was performed for 2 h with the help of intraluminal thread. Drug-treated mice showed improvement in necrotic changes in cortex and basal ganglia. Detection of MMP-9 activity and gene expression was performed at various time points after MCAo. The elevated levels of MMP-9 were significantly attenuated in the resveratrol-treated mice as compared to the vehicle MCAo mice. The study suggests that resveratrol has protective effects against acute ischemic stroke, which could be attributed to its property against MMP-9. Thus, resveratrol may be a potential agent for the treatment of neuronal injury associated with stroke.

Animals↗