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Biomedical subjects

Yan Zhao

Publications and source records attributed to Yan Zhao.

At least 19 recordsLinked to original sources

The N6-methyladenosine reader IGF2BP2 in T-cell lymphoma.

Peripheral T-cell lymphoma (PTCL) represents a highly heterogeneous and aggressive lymphoid neoplasm that lacks pathogenic biomarkers of RNA modification with therapeutic potential. IGF2BP2 is recognized as an N6-methyladenosine reader critically involved in oncogenesis. In this study, we observed consistently high expression of IGF2BP2 across common nodal PTCL subtypes in 3 independent external cohorts, which was further confirmed in our RNA-sequencing (RNA-seq) data set of 196 patients with newly diagnosed PTCL. Both in vitro and in vivo, IGF2BP2 promoted tumor cell growth and inhibited CD8+ T-cell infiltration within the tumor microenvironment. Mechanistically, IGF2BP2 bound to endosome-related genes (RAB4, VPS35, RAB9, and STAM) to maintain their stability, which resulted in enhanced endocytic activity and increased internalization of membrane proteins, and ultimately induced tumor cell proliferation and inhibition of CD8+ T-cell-mediated tumor cytotoxicity. The relationship between IGF2BP2 and endocytosis-associated genes was confirmed using RNA-seq data from patients with PTCL. IGF2BP2 as an upstream regulator of both tumor growth and immune suppression was further demonstrated in patient-derived xenograft models and a coculture system established using tumor samples from patients with PTCL and peripheral blood mononuclear cells. Notably, therapeutic targeting of IGF2BP2 with CWI1-2 suppressed endocytosis and impeded tumor growth in both cell lines and patient-derived xenograft models. Collectively, our findings highlight IGF2BP2 as a clinically relevant oncogenic driver in PTCL that integrates tumor-intrinsic growth signals with immune evasion through endocytosis-centered regulation, providing a novel therapeutic rationale for RNA modification-based strategies that concurrently target tumor cells and the tumor microenvironment.

Humans↗

Tumor-Infiltrating Clonal Hematopoiesis Is Associated with Adverse Clinical Outcomes in Diffuse Large B-cell Lymphoma.

UNLABELLED: Tumor-infiltrating clonal hematopoiesis (TI-CH) contributes to the progression of nonhematologic cancers. CH is prevalent in the peripheral blood of patients with diffuse large B-cell lymphoma (DLBCL), but TI-CH prevalence and clinical relevance remain largely unexplored. In this study, through genome- and exome-wide sequencing of DLBCL biopsies and blood samples from 304 treatment-naïve patients, we identified TI-CH in 13.5% of cases, which emerged as an independent risk indicator for disease progression and death. TI-CH cases had an enrichment of inflammatory myeloid signatures revealed by gene expression profiling of tumor biopsies. In addition, we developed a TI-CH-associated prognostic signature (CAPS) based on 24 differentially expressed genes. A high CAPS score correlated with poor survival across four patient cohorts and remained significant in three cohorts after adjustment for patient age, sex, International Prognostic Index score, and cell-of-origin classification. Collectively, these findings establish a link between TI-CH and clinical outcomes and implicate the inflammatory signature as the potential underlying basis. SIGNIFICANCE: TI-CH correlates with disease progression and death in patients and with the inflammatory modeling of the DLBCL tumor microenvironment. Our results underscore the clinical and biological relevance of TI-CH and suggest its potential as a biomarker for risk stratification and as a target for therapeutic intervention in DLBCL.

Humans↗

Potato purple top phytoplasma infection induces autophagy-associated lipid dynamics that support pathogen proliferation.

Phytoplasmas are unculturable, phloem-restricted bacterial pathogens responsible for devastating diseases in crops and ornamentals worldwide. Their mechanism for nutrient acquisition from host plants remains largely unknown. This study demonstrated that infection with potato purple top phytoplasma induced extensive remodeling of lipid metabolism in tomato plants, closely linked to autophagy activation. Western blot and confocal analyses revealed increased ATG8 lipidation and autophagosome formation at endoplasmic reticulum stress sites, alongside the redistribution of lipid droplets toward phytoplasma cells. Lipidomic profiling showed a decline in chloroplast galactolipids and phospholipids with a concomitant rise in triacylglycerol, indicating accelerated membrane turnover and neutral lipid sequestration. Transmission electron microscopy further revealed frequent spatial proximity between lipid droplets and phytoplasmas. Inhibition of autophagy with 3-methyladenine blocked lipid droplet breakdown, disrupted endoplasmic reticulum organization, and reduced phytoplasma titers, suggesting that host autophagy contributes to phytoplasma proliferation. In addition, genome analysis identified a conserved phytoplasma-encoded alpha/beta hydrolase (potato purple top-lipase), predicted to be related to monoacylglycerol lipases. In vivo assays in yeast and Nicotiana benthamiana confirmed that potato purple top-lipase reduced neutral lipids, mainly triacylglycerol, and that catalytic triad mutations abolished activity. Because potato purple top-lipase lacks a predicted secretory signal peptide, it likely functions intracellularly within phytoplasma cells and may participate in the metabolism of lipid intermediates. These findings support a model in which phytoplasma infection is associated with host autophagy-associated lipid droplet mobilization and a phytoplasma lipase that may contribute to host-derived lipid resources, providing insight into potential nutrient acquisition strategies of phloem-restricted pathogens.

Autophagy↗

Normoalbuminuric and albuminuric diabetic kidney disease exhibit divergent renal proteomic characteristics: implications for management.

BACKGROUND: The pathogenesis of diabetic kidney disease (DKD) is complex. Normoalbuminuric diabetic kidney disease (NADKD) is a special subtype of DKD that often progresses insidiously without detectable albuminuria, posing diagnostic and therapeutic challenges. Its pathogenesis remains unclear. Proteomic analysis of renal tissues may offer insights into its pathogenesis and identify biomarkers. METHODS: Clinicopathological data from 295 biopsy-proven DKD patients were collected and classified into normoalbuminuric (UACR&#xa0;<&#xa0;30&#xa0;mg/g, n&#xa0;=&#xa0;25), microalbuminuric (UACR 30-300&#xa0;mg/g, n&#xa0;=&#xa0;26), and macroalbuminuric (UACR&#xa0;>&#xa0;300&#xa0;mg/g, n&#xa0;=&#xa0;244) groups. Laser microdissection combined with mass spectrometry (LMD/MS) was used to analyze glomerular and proximal tubule proteomics in 5 patients per DKD subgroup and 5 control subjects. Associations with clinical features were examined. RESULTS: Glomerular proteomic analysis revealed that oxidative stress and metabolic pathways (UQCRC1) were upregulated in NADKD group, whereas the complement and coagulation cascades (C3, C5, C6, C9, CFH, CFHR1) were significantly upregulated in the microalbuminuric and macroalbuminuric DKD groups. The proximal tubule proteomics analysis showed that oxidative phosphorylation-related proteins (SDHA, CYCS, UQCRQ) were upregulated in NADKD, and collagen I related proteins (COL1A1, COL1A2) were significantly upregulated. CONCLUSION: Oxidative stress and mitochondrial dysfunction are involved in the progression of NADKD, lesions predominantly located in the tubulointerstitium. The complement pathway participates in the pathogenesis and progression of albuminuric DKD (ADKD). These divergent molecular profiles suggest that NADKD and ADKD may reflect different pathophysiological mechanisms and have important implications for therapeutic strategies in diabetes management.

Humans↗

The circadian clock proteins PRR modulate root hair development via the RHD6/RSL module in Arabidopsis.

Root hairs, derived from trichoblasts, are critical for plant growth and environmental adaptation. Although environmental cues are known to influence root hair development, how endogenous timing systems such as the circadian clock integrate into the core transcriptional network governing root hair formation remains unclear. Here, we show that the circadian clock-associated protein PSEUDO-RESPONSE REGULATOR5 (PRR5) physically interacts with ROOT HAIR DEFECTIVE6 (RHD6) and RHD6 LIKE1 (RSL1), two basic helix-loop-helix transcription factors essential for root hair initiation. Genetic analyses suggest that PRR proteins contribute to root hair development under long-day conditions in Arabidopsis thaliana. Simultaneous disruption of PRR5, PRR7, and PRR9 results in defective root hairs, whereas PRR5 overexpression markedly increases root hair density and length. Transcriptomic and RT-qPCR analyses reveal that PRRs enhance the expression of RHD6, RSL1, and multiple downstream root hair-responsive genes, while modulating their temporal expression patterns. Furthermore, PRR5-mediated root hair promotion requires RHD6/RSL1, and PRR proteins enhance RHD6-dependent activation of the RSL4 promoter. PRRs also contribute to root hair development under phosphate-deficient and salt-stress conditions. Together, these findings establish a molecular framework in which PRR proteins regulate the RHD6/RSL network to coordinate root hair development and environmental responses.

Arabidopsis↗

Potential mitochondria-associated pathogenic genes in sepsis: a multi-omics Mendelian randomization study.

BACKGROUND: Mitochondrial dysfunction has been implicated in the pathophysiology of sepsis. However, human genetic evidence linking mitochondria-related genes to sepsis susceptibility remains limited. This study aimed to identify mitochondria-related genes associated with sepsis risk using a multi-omics Mendelian randomization framework. METHODS: Summary-data-based Mendelian randomization (SMR) was applied using sepsis genome-wide association study (GWAS) summary statistics from the UK Biobank and FinnGen databases. Expression, methylation, single-cell, and protein quantitative trait loci (QTLs) were used as genetic instruments. Colocalization analyses were conducted to evaluate whether SMR associations were driven by shared genetic variants. Expression of prioritized candidate genes was further examined in clinical septic samples, and correlations with disease severity (SOFA scores) were assessed. RESULTS: SMR analysis prioritized 13 mitochondria-related genes associated with sepsis risk. Immune cell-specific eQTL analysis suggested that genetically predicted SURF1 expression in memory B cells and na&#xef;ve T cells was associated with sepsis risk. Differential expression of 12 candidate genes was confirmed in septic patients by qPCR, and PPOX expression showed a negative correlation with SOFA scores. Integration of mQTL and eQTL data supported a regulatory relationship between methylation at cg06661924 and AK4 expression. Increased genetically predicted AK4 expression was associated with higher sepsis risk (OR&#xa0;=&#xa0;1.21, 95% CI 1.02-1.42). Protein-level analysis identified DUT as a potential sepsis-associated candidate, with consistent evidence across streptococcal and pneumococcal septicemia subtypes. Subtype analyses also suggested heterogeneous genetic signals across different sepsis subtypes. CONCLUSION: This study prioritized several mitochondria-related genes associated with sepsis susceptibility based on human genetic evidence. These findings provide candidate targets for further mechanistic and translational investigation.

Humans↗

Adjuvant oxaliplatin with S-1 (SOX) versus S-1 for stage II-III gastric cancer (CAPITAL): A randomized, open-label, phase 3 trial.

BACKGROUND: Adjuvant chemotherapy following D2 gastrectomy constitutes the standard-of-care for resectable gastric or gastroesophageal junction (GEJ) carcinoma. The CAPITAL trial is a multicenter, randomized, phase 3 study, aiming to assess the efficacy and safety of adjuvant oxaliplatin plus S-1 (SOX) versus S-1 alone. METHODS: Patients with histologically confirmed pathological stage II-III gastric or GEJ adenocarcinoma after gastrectomy with D2 lymphadenectomy were randomly assigned (1:1) to receive either the SOX regimen (n = 362) or the S-1 regimen (n = 362). The primary endpoint was overall survival. This study is registered with ClinicalTrials.gov (NCT01795027). FINDINGS: The median follow-up was 74.0 months (interquartile range [IQR], 35.5-89.3). The 5-year overall survival rates were 70.9% (95% confidence interval [CI], 66.0-76.1) in the SOX group and 62.9% (95% CI, 57.8-68.5) in the S-1 group (hazard ratio [HR], 0.74; 95% CI, 0.58-0.95; p = 0.018). The 3- and 5-year disease-free survival rates were 71.2% (95% CI, 66.5-76.3) and 66.2% (95% CI, 61.2-71.6) in the SOX group, as compared with 65.1% (95% CI, 60.2-70.5) and 55.6% (95% CI, 50.4-61.3) in the S-1 group (HR, 0.76; 95% CI, 0.61-0.96). Treatment-related adverse events of grade 3-4 occurred in 87 (25%) of 349 patients in the SOX group and 45 (13%) of 347 patients in the S-1 group. The most common grade 3-4 adverse event was neutropenia, occurring in 44 (13%) of 349 patients in the SOX group and 23 (7%) of 347 patients in the S-1 group. CONCLUSIONS: The addition of adjuvant oxaliplatin to S-1 chemotherapy significantly improved overall survival and disease-free survival in patients with gastric cancer. FUNDING: This research was supported by the National Natural Science Foundation of China (82573092 and 82573387).

Humans↗

Chromatin Remodeling Subunit ARID1A Negatively Regulates the Malignant Progression of Gastrointestinal Stromal Tumors by Targeting the MEMO1 Promoter.

Gastrointestinal stromal tumors (GISTs) are the most common sarcomas of the alimentary tract and are primarily characterized by malignant progression, a major cause of mortality. AT-rich interaction domain 1A (ARID1A), a core component of the chromatin-remodeling SWI/SNF complex, has been found to correlate with GIST tumor grade, although the underlying mechanism remains unclear. Its frequent inactivation across diverse cancer types reveals pleiotropic roles that intersect multiple hallmarks of cancer. In this study, we aimed to investigate the potential relationship between ARID1A and malignant progression in GISTs, as well as the underlying mechanism. Western blotting, real-time polymerase chain reaction, and immunohistochemistry were used to assess ARID1A expression in GIST tissues. Cell Counting Kit-8 (CCK-8) assays were performed to evaluate cell proliferation. Wound-healing and Transwell assays were conducted to assess cell migration and invasion. Flow cytometry was used to analyze apoptosis and cell cycle distribution. Label-free quantitative proteomics and chromatin immunoprecipitation sequencing (ChIP-seq) were employed to identify top candidate downstream targets of ARID1A. ARID1A expression was decreased in high-risk GIST tissues. Furthermore, ARID1A knockdown in GIST cells promoted proliferation and metastasis both in vitro and in vivo, and led to reduced apoptosis and impaired cell cycle arrest. We further demonstrated that ARID1A suppresses GIST proliferation and metastasis by inhibiting MEMO1 expression and inactivating the ERK1/2 signaling pathway. Notably, this regulatory axis was observed in KIT-null GIST cells, indicating that the ARID1A-MEMO1 pathway may function independently of canonical KIT signaling. Thus, ARID1A inhibits malignant progression in GISTs, providing new insights into its role in the prevention and treatment of human GISTs and suggesting its potential as a biomarker of malignant progression in GISTs.

Humans↗

Effects of faba bean-based crisping culture on phenotypic characteristics, muscle quality, and serum metabolome in Nile tilapia: Screening biomarkers to assess the degree of crisping.

Feeding Nile tilapia (Oreochromis niloticus) a faba bean-based crisping diet enhances muscle hardness (crispness) and overall flesh quality. However, the underlying mechanisms and reliable biomarkers remain insufficiently defined. This study integrated phenotypic traits, muscle texture, collagen content, serum antioxidant enzyme activities (SOD, CAT, and GSH-Px), MDA levels, and serum metabolomics to understand the determinants of muscle crisping. Fish were assigned to a crisping diet or a control group for 90&#xa0;days. Individuals in the crisping group were implanted with passive integrated transponder (PIT) tags to enable correlation analyses among phenotypic traits (body weight/length/frame changes), serum indicators (NAM, FAD, and GSH-Px) and muscle hardness. Compared with controls, the crisping diet significantly increased muscle hardness, gumminess, and chewiness, accompanied by elevated collagen content. Antioxidant profiles were altered, with higher activities of serum SOD and CAT, together with elevated MDA levels and reduced GSH-Px activity (P&#xa0;<&#xa0;0.05). Metabolomic analysis identified 830 differential metabolites (682 upregulated and 148 downregulated), predominantly comprising carboxylic acids and derivatives, glycerophospholipids, and benzene derivatives. Enrichment analysis indicated significant involvement in general metabolic pathways, ATP-binding cassette (ABC) transporters, amino acid biosynthesis, and glycine, serine, and threonine metabolism (P&#xa0;<&#xa0;0.05). Notably, acetylpyruvate was upregulated in glutathione metabolism, nicotinate and nicotinamide metabolism, and galactose metabolism; pantothenic acid was upregulated in glycine, serine, and threonine metabolism; whereas &#x3b4;-tocotrienol was downregulated. Correlation analysis revealed weak negative associations between muscle hardness and phenotypic traits (body weight/length/frame changes D5-7, D5-10, D7-8) (P&#xa0;<&#xa0;0.05). In contrast, serum NAM and FAD were weakly positively correlated with muscle hardness, whereas GSH-Px showed a weak negative correlation (P&#xa0;<&#xa0;0.05). Collectively, these findings suggest that body weight, body length, frame measurements (D5-7, D5-10, and D7-8), and serum NAM, FAD, and GSH-Px are associated with the degree of muscle crispness in Nile tilapia fed a faba bean-based crisping diet and may serve as candidate biomarkers under these culture conditions.

Animals↗

CSNK1E sustains stemlike drug persistence in diffuse large B-cell lymphoma.

Relapsed or refractory (R/R) disease occurs in up to 40% of patients with diffuse large B-cell lymphoma (DLBCL) following first-line immunochemotherapy. However, the molecular mechanisms underlying drug persistence remain incompletely defined. In this study, we performed single-cell RNA and B-cell receptor sequencing on paired diagnostic and R/R samples from 8 patients who were either treatment-refractory or relapsed after remission, and validated our findings in 3 independent patient cohorts. We found that drug-persistent cells exhibited a transcriptional profile indicative of a less-differentiated state and adopted a memory B-cell-like program with enhanced stemlike properties, which correlated with unfavorable clinical outcomes across multiple DLBCL cohorts. Functionally, drug-persistent cells showed significantly increased in vitro clonogenicity and in vivo tumor-initiating capacity. Mechanistically, the WNT signaling regulator casein kinase 1&#x25b; (CSNK1E) was upregulated in these stemlike drug-persistent cells, in part through the activation of the A proliferation-inducing ligand (APRIL)-TNFRSF13B axis. Notably, CSNK1E inhibition impaired the growth and tumor-initiating capacity of drug-persistent cells and potentiated the efficacy of R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone)-based treatment, both in vitro and in vivo. Together, our study reveals the stemlike transcriptional and functional properties of drug-persistent cells, and identifies CSNK1E as a critical mediator and therapeutic vulnerability that may improve the efficacy of standard immunochemotherapy in DLBCL.

Lymphoma, Large B-Cell, Diffuse↗

HnRNPR promotes non-small cell lung cancer progression by protecting XB130 mRNA from XRN1- and DIS3L2-mediated degradation.

The adaptor protein XB130 is critically implicated in tumorigenesis. However, the mechanisms regulating its expression in tumors are not well understood. Our previous studies have identified hnRNPR as a potential binding protein of XB130 3'UTR in non-small cell lung cancer (NSCLC). This study aimed to clarify hnRNPR's role in NSCLC progression and its specific mechanisms regulating XB130 expression. The expression of hnRNPR in NSCLC and normal tissues was assessed using NSCLC tissue microarray and the TCGA database. Subsequently, in vitro and in vivo experiments were conducted to investigate the impact of hnRNPR on NSCLC cell proliferation and epithelial-mesenchymal transition (EMT) by modulating XB130 expression. The underlying molecular mechanisms of hnRNPR regulating XB130 expression were explored utilizing a range of molecular biology techniques including Western blotting, Real-time quantitative PCR, Immunohistochemistry, Dual-luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation. We identified the overexpression of hnRNPR in NSCLC, with heightened hnRNPR levels significantly associated with poor prognosis in patients with lung adenocarcinoma. Functionally, hnRNPR overexpression promoted NSCLC cell proliferation and EMT and activated the Akt signaling pathway. Mechanistically, hnRNPR protected XB130 mRNA from XRN1- and DIS3L2-mediated degradation by binding to specific regions within XB130 3'UTR, consequently elevating XB130 expression. Lastly, XB130 overexpression counteracted the effects of hnRNPR silencing on NSCLC cells. Overall, our study unveils the potential of targeting the hnRNPR/XB130 axis as a promising therapeutic strategy for NSCLC.

Humans↗

The diagnosis and treatment of HIV-infected children in China: challenges and opportunities.

BACKGROUND: HIV-infected children in China have not been well studied. This national survey describes the demographic characteristics and the associated diagnostic and antiretroviral treatment (ART) efforts directed toward surviving HIV-infected children. METHODS: A cross-sectional study was conducted in the 6 provinces with the highest HIV prevalence: 4 former plasma donation (FPD) provinces and 2 intravenous drug use (IDU) provinces. A survey on demographics and treatment-related issues was distributed to the parents or guardians of all living HIV-infected children identified through the national case reporting system. Descriptive and bivariate analyses were performed on completed surveys. RESULTS: Six hundred ninety-two (62.4%) of the total 1108 surveys were returned, and 650 were eligible for analysis. The average age in FPD provinces (mean +/- SD: 8.1 +/- 3.2 years) was significantly older than in IDU provinces (mean +/- SD: 5.4 +/- 2.2 years; P < 0.001). The average lag time from the probable date of transmission to a diagnosis for patients with mother-to-child transmission (MTCT) was 6.7 +/- 3.1 years in the FPD provinces and 4.7 +/- 1.9 years in the IDU provinces (P < 0.001). On the basis of the CD4 cell count or World Health Organization staging, 29.8% (144 of 484) of children from all 6 provinces who were not on ART needed it. CONCLUSIONS: This first national pediatric survey indicates that the age and time required for diagnosis were greater in HIV-infected children from FPD provinces compared with those from IDU provinces. In addition, this survey highlights the prolonged delay in the diagnosis and initiation of ART for children in China. Aggressive efforts to identify HIV-positive pregnant women, scale up prevention of MTCT activities, and expand early diagnosis and treatment are urgently needed.

Analysis of Variance↗

Vitamin E analogs, a novel group of "mitocans," as anticancer agents: the importance of being redox-silent.

The search for a selective and efficient anticancer agent for treating all neoplastic disease has yet to deliver a universally suitable compound(s). The majority of established anticancer drugs either are nonselective or lose their efficacy because of the constant mutational changes of malignant cells. Until recently, a largely neglected target for potential anticancer agents was the mitochondrion, showing a considerable promise for future clinical applications. Vitamin E (VE) analogs, epitomized by alpha-tocopheryl succinate, belong to the group of "mitocans" (mitochondrially targeted anticancer drugs). They are selective for malignant cells, cause destabilization of their mitochondria, and suppress cancer in preclinical models. This review focuses on our current understanding of VE analogs in the context of their proapoptotic/anticancer efficacy and suggests that their effect on mitochondria may be amplified by modulation of alternative pathways operating in parallel. We show here that the analogs of VE that cause apoptosis (which translates into their anticancer efficacy) generally do not possess antioxidant (redox) activity and are prototypical of the mitocan group of anticancer compounds. Therefore, by analogy to Oscar Wilde's play The Importance of Being Earnest, we use the motto in the title "the importance of being redox-silent" to emphasize an essentially novel paradigm for cancer therapy, in which redox-silence is a prerequisite property for most of the anticancer activities described in this communication.

Animals↗

Preferential solvation within hydrophilic nanocavities and its effect on the folding of cholate foldamers.

The conformations of three cholate foldamers and one molecular basket were studied by fluorescence and NMR spectroscopy. In nonpolar solvents (e.g., hexane/ethyl acetate or ethyl acetate) mixed with a small amount of a polar solvent (e.g., alcohol or DMSO), the cholate oligomer folded into a helix with the hydrophilic faces of the cholates turned inward. Folding created a hydrophilic nanocavity preferentially solvated by the entrapped polar solvent concentrated from the bulk. This microphase separation of the polar solvent was critical to the folding process. Folding was favored by larger-sized polar solvent molecules, as fewer such molecules could occupy and solvate the nanocavity, thus requiring a smaller extent of phase separation during folding. Folding was also favored by smaller/acyclic nonpolar solvent molecules, probably because they could avoid contact with the OH/NH groups within the nanocavity better than larger/cyclic nonpolar solvent molecules.

Cholates↗

How well can new-generation density functionals describe protonated epoxides where older functionals fail?

In a recent article, Carlier et al. (J. Org. Chem. 2006, 71, 1592) examined the prediction of several DFT functionals and showed that the most popular density functional, B3LYP, and 15 others fail badly for the prediction of the structure of protonated 2-methyl-1,2-epoxypropane. In this note, we compare the performance of several recently developed density functionals for the calculation of structures and energetics of protonated cyclic ethers, including epoxides. We found that several of the newly developed DFT methods perform better than B3LYP or any of the other 17 functionals examined by Carlier. We conclude that a recently published functional, M05-2X, has greatly improved performance for an unsymmetrical protonated epoxide, and we recommend this functional for studies that involve protonated epoxides and protonated ethers.

Comment↗

[Correlation of p38 mitogen-activated protein kinase signal transduction pathway to uPA expression in breast cancer].

BACKGROUND & OBJECTIVE: p38 mitogen-activated protein kinase (p38MAPK) signal transduction pathway regulates the expression of various metastasis-related genes. Urokinase-type plasminogen activator (uPA) plays an important role in cancer invasion and metastasis. This study was to explore the correlation of p38MAPK signal transduction pathway to uPA expression in breast cancer. METHODS: SP immunohistochemistry was used to test the expression of p-p38, p-Akt, p-Erk, and uPA in 60 specimens of breast cancer. Western blot was used to detect the protein levels of p-p38 and uPA in breast cancer MDA-MB-231 and MCF-7 cells and the protein level of uPA in MDA-MB-231 cells after blocking p38MAPK signal transduction pathway by SB203580, a specific inhibitor of p38MAPK. The correlations of p-p38, p-Akt, p-Erk, and uPA expression to the clinicopathologic characteristics of breast cancer, and the correlations of p-p38, p-Akt, and p-Erk expression to uPA expression were analyzed. The mechanism of p38MAPK signal transduction pathway regulating the protein expression of uPA in breast cancer cells was investigated. The correlation of p-p38 and uPA expression to prognosis of breast cancer was analyzed. RESULTS: The positive rates of p-p38, p-Akt, p-Erk, and uPA proteins in breast cancer tissues were 56.7%, 95.0%, 93.3%, and 60.0%, respectively. The expression of p-p38 was positively correlated to the expression of uPA (r=0.316, P<0.05), while the expression of p-Akt and p-Erk was not related to uPA expression. The expression of p-p38 and uPA was correlated to lymph node metastasis and TNM stage (P<0.05), but not to patients' age and tumor size (P>0.05). The expression of p-Akt and p-Erk were correlated to lymph node metastasis (P<0.05), but not to TNM stage, patients' age, and tumor size (P>0.05). The protein levels of p-p38 and uPA in MDA-MB-231 cells were higher than that in MCF-7 cells. SB203580 concentration-dependently inhibited p38MAPK pathway and induced uPA protein expression. The expression of p-p38 and uPA was negatively correlated to prognosis of breast cancer (log-rank=4.98, 5.40, P=0.026, 0.020). CONCLUSIONS: p38MAPK signal transduction pathway might improve breast cancer progression by up-regulating uPA expression, and might be an important route in invasion and metastasis of breast cancer. p-p38 and uPA might help to evaluate prognosis of breast cancer.

Adult↗

Chromatin-modifying agents permit human hematopoietic stem cells to undergo multiple cell divisions while retaining their repopulating potential.

Human hematopoietic stem cells (HSCs) exposed to cytokines in vitro rapidly divide and lose their characteristic functional properties presumably due to the alteration of a genetic program that determines the properties of an HSC. We have attempted to reverse the silencing of this HSC genetic program by the sequential treatment of human cord blood CD34(+) cells with the chromatin-modifying agents, 5-aza-2'-deoxycytidine (5azaD) and trichostatin A (TSA). We determined that all CD34(+)CD90(+) cells treated with 5azaD/TSA and cytokines after 9 days of incubation divide, but to a lesser degree than cells exposed to only cytokines. When CD34(+)CD90(+) cells that have undergone extensive number of cell divisions (5-10) in the presence of cytokines alone were transplanted into immunodeficient mice, donor cell chimerism was not detectable. By contrast, 5azaD/TSA-treated cells that have undergone similar numbers of cell divisions retained their marrow repopulating potential. The expression of several genes and their products previously implicated in HSC self-renewal were up-regulated in the cells treated with 5azaD/TSA as compared to cells exposed to cytokines alone. These data indicate that HSC treated with chromatin-modifying agents are capable of undergoing repeated cell divisions in vitro while retaining their marrow-repopulating potential.

Animals↗

Density functional for spectroscopy: no long-range self-interaction error, good performance for Rydberg and charge-transfer states, and better performance on average than B3LYP for ground states.

We present a new density functional called M06-HF. The new functional has full Hartree-Fock exchange, and therefore it eliminates self-exchange interactions at long range. This leads to good performance in TDDFT calculations of both Rydberg and charge-transfer states. In addition, the functional satisfies the uniform electron gas limit, and it is better than the popular B3LYP functional, on average, for ground-electronic-state energetics.

Journal Article↗