Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models.


BACKGROUND:Chromosome 1p/19q codeletion is increasingly being recognized as the crucial genetic marker for glioma patients and have been included in WHO classification of glioma in 2016. Fluorescent in situ hybridization, a widely used method in detecting 1p/19q status, has some methodological limitations which might influence the clinical management for doctors. Here, we attempted to explore an RNA sequencing computational method to detect 1p/19q status. METHODS:We included 692 samples with 1p/19q status information from TCGA cohort as training set and 222 samples with 1p/19q status information from REMBRANDT cohort as validation set. We reviewed and compared five tools: TSPairs, GSVA, PAM, Caret, smoother, with respect to their accuracy, sensitivity and specificity. RESULTS:In TCGA cohort, the GSVA method showed the highest accuracy (98.4%) in predicting 1p/19q status (sensitivity=95.5%, specificity=99.6%) and smoother method showed the second-highest accuracy (accuracy=97.8%, sensitivity=96.4%, specificity=98.3%). While in REMBRANDT cohort, smoother method exhibited the highest accuracy (98.6%) (sensitivity= 96.7%, specificity=98.9%) in 1p/19q status prediction. CONCLUSIONS:Our independent assessment of five tools revealed that smoother method was selected as the most stable and accurate method in predicting 1p/19q status. This method could be regarded as a potential alternative method for clinical practice in future.


Aging (Albany NY)




Wang ZL,Zhao Z,Wang Z,Zhang CB,Jiang T




Has Abstract


2019-02-02 00:00:00














  • Validation of the 8th edition of the American Joint Committee on Cancer Pathological Prognostic Staging for young breast cancer patients.

    abstract:PURPOSE:This study aimed to validate the newly proposed American Joint Committee on Cancer (AJCC) pathological prognostic staging system for young breast cancer patients (aged ≤40 years). RESULTS:We included 12811 women in this study. Overall, 52.8% of patients in the 7th AJCC stages were restaged to the 8th AJCC path...


    pub_type: 杂志文章


    authors: Zhou J,Lei J,Wang J,Lian CL,Hua L,Yang LC,Wu SG

    更新日期:2020-04-22 00:00:00

  • Attenuation of constitutive DNA damage signaling by 1,25-dihydroxyvitamin D3.

    abstract::In addition to its traditional role in the regulation of calcium homeostasis and bone metabolism, vitamin D also exhibits immunomodulatory, anti-proliferative and cancer preventive activities. Molecular mechanisms that confer the chemo-preventive properties to vitamin D are poorly understood. We previously reported th...


    pub_type: 杂志文章


    authors: Halicka HD,Zhao H,Li J,Traganos F,Studzinski GP,Darzynkiewicz Z

    更新日期:2012-04-01 00:00:00

  • Cytological and genetic consequences for the progeny of a mitotic catastrophe provoked by Topoisomerase II deficiency.

    abstract::Topoisomerase II (Top2) removes topological linkages between replicated chromosomes. Top2 inhibition leads to mitotic catastrophe (MC) when cells unsuccessfully try to split their genetic material between the two daughter cells. Herein, we have characterized the fate of these daughter cells in the budding yeast. Clono...


    pub_type: 杂志文章


    authors: Ramos-Pérez C,Dominska M,Anaissi-Afonso L,Cazorla-Rivero S,Quevedo O,Lorenzo-Castrillejo I,Petes TD,Machín F

    更新日期:2019-12-08 00:00:00

  • G-protein coupled estrogen receptor activation protects the viability of hyperoxia-treated primary murine retinal microglia by reducing ER stress.

    abstract::In this study, we investigated the effects of G-protein coupled estrogen receptor (GPER) activation in the early phase of retinopathy of prematurity (ROP) and its association with endoplasmic reticulum (ER) stress using primary murine retinal microglia as an experimental model. Fluorescence microscopy results show tha...


    pub_type: 杂志文章


    authors: Li R,Wang Y,Chen P,Meng J,Zhang H

    更新日期:2020-09-13 00:00:00

  • FAM83A signaling induces epithelial-mesenchymal transition by the PI3K/AKT/Snail pathway in NSCLC.

    abstract::Family with sequence similarity 83, member A (FAM83A), as a potential tumor promoter, was reported to contribute to the progression of several malignant tumors. However, the significance of FAM83A in invasion and metastasis of non-small cell lung cancer (NSCLC) remains largely unknown. In this study, we found that FAM...


    pub_type: 杂志文章


    authors: Zhou F,Geng J,Xu S,Meng Q,Chen K,Liu F,Yang F,Pan B,Yu Y

    更新日期:2019-08-24 00:00:00

  • Cumulus cell-released tumor necrosis factor (TNF)-α promotes post-ovulatory aging of mouse oocytes.

    abstract::Although previous studies indicated that cumulus cells (CCs) accelerate oocyte aging by releasing soluble factors, the factors have yet to be characterized. While demonstrating that CCs promoted oocyte aging by releasing soluble Fas ligand (sFasL), our recent study suggested that CCs might secrete other factors to med...


    pub_type: 杂志文章


    authors: Kong QQ,Wang J,Xiao B,Lin FH,Zhu J,Sun GY,Luo MJ,Tan JH

    更新日期:2018-07-26 00:00:00

  • Low circulating IGF-I bioactivity is associated with human longevity: findings in centenarians' offspring.

    abstract:UNLABELLED:Centenarians' offspring represent a suitable model to study age-dependent variables (e.g. IGF-I) potentially involved in the modulation of the lifespan. The aim of the present study was to investigate the role of the IGF-I in human longevity. We evaluated circulating IGF-I bioactivity measured by an innovati...


    pub_type: 杂志文章


    authors: Vitale G,Brugts MP,Ogliari G,Castaldi D,Fatti LM,Varewijck AJ,Lamberts SW,Monti D,Bucci L,Cevenini E,Cavagnini F,Franceschi C,Hofland LJ,Mari D,Janssen J

    更新日期:2012-09-01 00:00:00

  • TP53 and MTOR crosstalk to regulate cellular senescence.

    abstract::The full spectrum of activities of the tumor suppressor p53 (TP53) has not been completely elucidated yet. Recently, it was demonstrated that TP53 communicates with the metabolic regulator mechanistic target of rapamycin (MTOR) to determine whether stressed cells undergo cell death, reversible quiescence or irreversib...


    pub_type: 社论


    authors: Galluzzi L,Kepp O,Kroemer G

    更新日期:2010-09-01 00:00:00

  • A systematic review and network meta-analysis of single nucleotide polymorphisms associated with pancreatic cancer risk.

    abstract::In this meta-analysis, we systematically investigated the correlation between single nucleotide polymorphisms (SNPs) and pancreatic cancer (PC) risk. We searched PubMed, Network Science, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI), China Science and Technology Periodical Database (VIP), an...


    pub_type: 杂志文章


    authors: Ye ZM,Li LJ,Luo MB,Qing HY,Zheng JH,Zhang C,Lu YX,Tang YM

    更新日期:2020-11-20 00:00:00

  • miR-345-5p regulates adipogenesis via targeting VEGF-B.

    abstract::Adipocyte differentiation involves a series of highly synergistic processes, including clone amplification, proliferation arrest, and terminal differentiation. However, the mechanisms that control these different steps remain unclear. Emerging studies support that miRNAs play an important role in regulating adipogenes...


    pub_type: 杂志文章


    authors: Liu X,He Y,Feng Z,Sheng J,Dong A,Zhang M,Cao L

    更新日期:2020-09-14 00:00:00

  • Subtype-specific risk models for accurately predicting the prognosis of breast cancer using differentially expressed autophagy-related genes.

    abstract::Emerging evidence suggests that the dysregulation of autophagy-related genes (ARGs) is coupled with the carcinogenesis and progression of breast cancer (BRCA). We constructed three subtype-specific risk models using differentially expressed ARGs. In Luminal, Her-2, and Basal-like BRCA, four- (BIRC5, PARP1, ATG9B, and ...


    pub_type: 杂志文章


    authors: Han B,Zhang H,Zhu Y,Han X,Wang Z,Gao Z,Yuan Y,Tian R,Zhang F,Niu R

    更新日期:2020-07-10 00:00:00

  • Resistin enhances angiogenesis in osteosarcoma via the MAPK signaling pathway.

    abstract::Over the last two decades, there have been no significant changes in patient outcomes in relation to the treatment of osteosarcoma, an aggressive malignant neoplasm. It is known that vascular endothelial growth factor-A (VEGF-A) plays a crucial role in angiogenesis and in osteosarcoma. Moreover, VEGF-A expression corr...


    pub_type: 杂志文章


    authors: Tsai HC,Cheng SP,Han CK,Huang YL,Wang SW,Lee JJ,Lai CT,Fong YC,Tang CH

    更新日期:2019-11-13 00:00:00

  • KIAA0101 as a new diagnostic and prognostic marker, and its correlation with gene regulatory networks and immune infiltrates in lung adenocarcinoma.

    abstract::Proliferating cell nuclear antigen binding factor (encoded by KIAA0101/PCLAF) regulates DNA synthesis and cell cycle progression; however, whether the level of KIAA0101 mRNA in lung adenocarcinoma is related to prognosis and tumor immune infiltration is unknown. In patients with lung adenocarcinoma, the differential e...


    pub_type: 杂志文章


    authors: Hu S,Zeng W,Zhang W,Xu J,Yu D,Peng J,Wei Y

    更新日期:2020-11-20 00:00:00

  • LncRNA SOCS2-AS1 inhibits progression and metastasis of colorectal cancer through stabilizing SOCS2 and sponging miR-1264.

    abstract::Abnormal expression of long noncoding RNA (lncRNA) is involved in human cancers, including colorectal cancer (CRC). However, their functional mechanism is largely unknown. In this study, we explored the roles of lncRNA SOCS2-AS1 in modulating CRC progression. We showed that SOCS2-AS1 was lowly expressed in CRC tissues...


    pub_type: 杂志文章


    authors: Zheng Z,Li X,You H,Zheng X,Ruan X

    更新日期:2020-05-21 00:00:00

  • S-allyl cysteine reduces osteoarthritis pathology in the tert-butyl hydroperoxide-treated chondrocytes and the destabilization of the medial meniscus model mice via the Nrf2 signaling pathway.

    abstract::In this study, we used murine chondrocytes as an in vitro model and mice exhibiting destabilization of the medial meniscus (DMM) as an in vivo model to investigate the mechanisms through which S-allyl cysteine (SAC) alleviates osteoarthritis (OA). SAC significantly reduced apoptosis and senescence and maintained homeo...


    pub_type: 杂志文章


    authors: Shao Z,Pan Z,Lin J,Zhao Q,Wang Y,Ni L,Feng S,Tian N,Wu Y,Sun L,Gao W,Zhou Y,Zhang X,Wang X

    更新日期:2020-10-07 00:00:00

  • Mitochondria-targeted antioxidant SkQ1 inhibits age-dependent involution of the thymus in normal and senescence-prone rats.

    abstract::One of the most striking changes during mammal aging is a progressive involution of the thymus, associated with an increase in susceptibility to infections, autoimmune diseases and cancer. In order to delay age-related processes, we have developed mitochondria-targeted antioxidant plastoquinonyl decyltriphenyl phospho...


    pub_type: 杂志文章


    authors: Obukhova LA,Skulachev VP,Kolosova NG

    更新日期:2009-04-22 00:00:00

  • Rh type C-glycoprotein functions as a novel tumor suppressor gene by inhibiting tumorigenicity and metastasis in head and neck squamous cell carcinoma.

    abstract::Head and neck squamous cell carcinoma (HNSCC), a major histologic subtype of head and neck cancer, presents great mortality and morbidity worldwide. The aim of this study is to discover new potential biomarkers closely correlated with HNSCC progression. In this study, weighted gene co-expression network analysis was a...


    pub_type: 杂志文章


    authors: Xu W,Zou H,Wei Z,Song C,Tang C,Yin X,Wang Y,Han S,Cai Y,Han W

    更新日期:2019-06-06 00:00:00

  • a manually-curated database of published biomarkers of human all-cause mortality.

    abstract::Biomarkers of all-cause mortality are of tremendous clinical and research interest. Because of the long potential duration of prospective human lifespan studies, such biomarkers can play a key role in quantifying human aging and quickly evaluating any potential therapies. Decades of research into mortality biomarkers ...


    pub_type: 杂志文章


    authors: Peto MV,De la Guardia C,Winslow K,Ho A,Fortney K,Morgen E

    更新日期:2017-08-31 00:00:00

  • Association of VAMP5 and MCC genetic polymorphisms with increased risk of Hirschsprung disease susceptibility in Southern Chinese children.

    abstract::Hirschsprung disease (HSCR) is a genetic disorder characterized by the absence of neural crest cells in parts of the intestine. This study aims to investigate the association of vesicle-associated membrane protein 5 (VAMP5) and mutated in colorectal cancer (MCC) genetic polymorphisms and their correlated risks with HS...


    pub_type: 杂志文章


    authors: Zhao J,Xie X,Yao Y,He Q,Zhang R,Xia H,Zhang Y

    更新日期:2018-04-25 00:00:00

  • Recent discoveries in the cycling, growing and aging of the p53 field.

    abstract::The P53 gene and it product p53 protein is the most studied tumor suppressor, which was considered as oncogene for two decades until 1990. More than 60 thousand papers on the topic of p53 has been abstracted in Pubmed. What yet could be discovered about its role in cell death, growth arrest and apoptosis, as well as a...


    pub_type: 杂志文章,评审


    authors: McCubrey JA,Demidenko ZN

    更新日期:2012-12-01 00:00:00

  • Clinical burden of autosomal dominant polycystic kidney disease.

    abstract::There are no specific therapies for autosomal dominant polycystic kidney disease (ADPKD), and clinical data evaluating the effects of non-specific therapies on ADPKD patients are scarce. We therefore evaluated those effects using data from a longitudinal health insurance database collected from 2000-2010. We individua...


    pub_type: 杂志文章


    authors: Hung PH,Lin CH,Hung KY,Muo CH,Chung MC,Chang CH,Chung CJ

    更新日期:2020-02-24 00:00:00

  • Risk factors and prediction of second primary cancer in primary female non-metastatic breast cancer survivors.

    abstract::This study aimed to investigate the risk factors of second primary cancer among female breast cancer (BC) survivors, with emphasis on the prediction of the individual risk conditioned on the patient's characteristics. We identified 208,474 BC patients diagnosed between 2004 and 2010 from the Surveillance, Epidemiology...


    pub_type: 杂志文章


    authors: Qian X,Jia H,Zhang Y,Ma B,Qin G,Wu Z

    更新日期:2020-10-13 00:00:00

  • Overexpression of CBS and CSE genes affects lifespan, stress resistance and locomotor activity in Drosophila melanogaster.

    abstract::Recent experimental studies highlighted the role of hydrogen sulfide (H2S) in aging and longevity. The cystathionine ß-synthase (CBS) and cystathionine γ-lyase (CSE) are the key enzymes responsible for H2S production. Here we investigated the geroprotective effects of CSE and CBS overexpression in Drosophila. Overexpr...


    pub_type: 杂志文章


    authors: Shaposhnikov M,Proshkina E,Koval L,Zemskaya N,Zhavoronkov A,Moskalev A

    更新日期:2018-11-08 00:00:00

  • Downregulation of circFASTKD1 ameliorates myocardial infarction by promoting angiogenesis.

    abstract::Circular RNAs (circRNAs), a novel class of endogenous long non-coding RNAs, have attracted considerable attention due to their closed continuous loop structure and potential clinical value. In this study, we investigated the function of circFASTKD1 in vascular endothelial cells. CircFASTKD1 bound directly to miR-106a ...


    pub_type: 杂志文章


    authors: Gao WQ,Hu XM,Zhang Q,Yang L,Lv XZ,Chen S,Wu P,Duan DW,Lang YH,Ning M,Lai KG,Zhang ZY,Liang B,Bao JY,Wu HD,Li T

    更新日期:2020-12-19 00:00:00

  • DR region specific antibody ameliorated but ouabain worsened renal injury in nephrectomized rats through regulating Na,K-ATPase mediated signaling pathways.

    abstract::Reduced Na+-K+-ATPase function is reported in various renal diseases. This implies that increase of Na+-K+-ATPase function may be a new target in treatment of renal injury. We previously reported that Na+-K+-ATPase was stabilized by DRm217, a specific antibody against DR region of Na+-K+-ATPase. In this study, we comp...


    pub_type: 杂志文章


    authors: Wang J,Ullah SH,Li M,Zhang M,Zhang F,Zheng J,Yan X

    更新日期:2019-02-26 00:00:00

  • A single-nucleotide polymorphism (rs1805087) in the methionine synthase (METH) gene increases the risk of prostate cancer.

    abstract::Methionine synthase (METH, i.e., MTR) is a key enzyme in the folate pathway, which plays a critical role in the synthesis, repair, and methylation of DNA. The association between METH gene polymorphisms and prostate cancer susceptibility remains ambiguous. Thus, we performed an updated meta-analysis of METH single-nuc...


    pub_type: 杂志文章,meta分析,评审


    authors: Zhang X,Tang J,Shen N,Ren K

    更新日期:2018-10-18 00:00:00

  • E3-ubiquitin ligase TRIM6 aggravates myocardial ischemia/reperfusion injury via promoting STAT1-dependent cardiomyocyte apoptosis.

    abstract::Cardiomyocyte apoptosis is a major cause of myocardial ischemia/reperfusion (MI/R) injury, in which the activation of the signal transducer and activator of transcription 1 (STAT1) plays an important role. The E3-ubiquitin ligase TRIM6 has been implicated in regulating STAT1 activity, however, whether it is associated...


    pub_type: 杂志文章


    authors: Zeng G,Lian C,Yang P,Zheng M,Ren H,Wang H

    更新日期:2019-06-06 00:00:00

  • Elevated homocysteine as an independent risk for intracranial atherosclerotic stenosis.

    abstract::To investigate the association of homocysteine concentration with intracranial atherosclerotic stenosis (ICAS), we assessed 933 acute ischemic stroke patients (346 with ICAS, 587 without ICAS) and 798 non-stroke controls (175 with ICAS, 623 without ICAS) with magnetic resonance angiography (MRA). Homocysteine concentr...


    pub_type: 杂志文章


    authors: Liu Y,Song JH,Hou XH,Ma YH,Shen XN,Xu W,Sun FR,Dong Q,Yu JT,Tan L,Chi S

    更新日期:2019-06-12 00:00:00

  • Neuroprotective effects and mechanisms of action of nicotinamide mononucleotide (NMN) in a photoreceptor degenerative model of retinal detachment.

    abstract::Currently, no pharmacotherapy has been proven effective in treating photoreceptor degeneration in patients. Discovering readily available and safe neuroprotectants is therefore highly sought after. Here, we investigated nicotinamide mononucleotide (NMN), a precursor of nicotinamide adenine dinucleotide (NAD+), in a re...


    pub_type: 杂志文章


    authors: Chen X,Amorim JA,Moustafa GA,Lee JJ,Yu Z,Ishihara K,Iesato Y,Barbisan P,Ueta T,Togka KA,Lu L,Sinclair DA,Vavvas DG

    更新日期:2020-12-29 00:00:00

  • Bedaquiline, an FDA-approved antibiotic, inhibits mitochondrial function and potently blocks the proliferative expansion of stem-like cancer cells (CSCs).

    abstract::Bedaquiline (a.k.a., Sirturo) is an anti-microbial agent, which is approved by the FDA for the treatment of multi-drug resistant pulmonary tuberculosis (TB). Bedaquiline is a first-in-class diaryl-quinoline compound, that mechanistically inhibits the bacterial ATP-synthase, and shows potent activity against both drug-...


    pub_type: 杂志文章


    authors: Fiorillo M,Lamb R,Tanowitz HB,Cappello AR,Martinez-Outschoorn UE,Sotgia F,Lisanti MP

    更新日期:2016-08-01 00:00:00