Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of ADAMTS9-AS2 and MBNL1-AS1 as subtype-specific dysregulated lncRNAs in basal and luminal muscle-invasive bladder cancer via RNA sequencing

ABSTRACT: Muscle-invasive bladder cancer (MIBC) is an aggressive disease with high morbidity and mortality that can be divided into basal and luminal subtypes based on genomic characteristics. Due to the complex heterogeneity of MIBC, specific markers are needed to distinguish MIBC subtypes to guide future clinical treatment. In this study, we explore abnormal lncrnas that are specific to the basic and intracavitary subtypes of MIBC, which will provide potential biomarkers for precision therapy of MIBC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE229410 | GEO | 2023/04/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Integrative Transcriptomic, Lipidomic, and Metabolomic Analysis Reveals Potential Biomarkers of Basal and Luminal Muscle Invasive Bladder Cancer Subtypes

Project description:Muscle invasive bladder cancer (MIBC) is a heterogeneous disease with a high recurrence rate and poor clinical outcomes. Molecular subtype provides a new framework for the study of MIBC heterogeneity. Clinically, MIBC can be classified as basal and luminal subtypes, they display different clinical and pathological characteristics, but the molecular mechanism is still unclear. Lipidomic and metabolomic molecules have recently been considered to play an important role in the genesis and development of tumors, especially as potential biomarkers. Their different expression profiles in basal and luminal subtypes provide clues for the molecular mechanism of basal and luminal subtypes and the discovery of new biomarkers. Herein, we stratified MIBC patients into basal and luminal subtype using a MIBC classifier based on transcriptome expression profiles. We qualitatively and quantitatively analyzed the lipids and metabolites of basal and luminal MIBC subtypes, and identified differential lipid and metabolite profiles of them. Our results suggest that free fatty acids (FFA) and sulfatides (SL), which are closely associated with immune and stromal cell types, can contribute to the diagnosis of basal and luminal subtypes of MIBC. Moreover, we showe that glycerophosphocholine (GCP)/imidazoles and nucleosides/imidazoles ratios can accurately distinguish the basal and luminal tumors. Overall, by integrating transcriptomic, lipidomic, and metabolomic data, our study reveals specific biomarkers to differentially diagnose basal and luminal MIBC subtypes and may provide a basis for precision therapy of MIBC.

2021-07-08 | GSE179440 | GEO

Analysis of genes regulated by AS1 and AS2

Project description:AS1 and AS2 encode MYB related protein and AS2-domain containing protein, respectively and may regulate transcription. These genes are involved in the determination of axes of leaves of Arabidopsis thaliana. To know the gene regulation in the leaf development, expression profile among wild-type, as1 and as2 mutants and AS2 overexpression plants were compaired. shoot apices from as1-1, as2-1, AS2 overexpressing, and wild type embryos

2013-03-01 | E-GEOD-44028 | biostudies-arrayexpress

Impact of molecular subtypes in muscle-invasive bladder cancer on predicting response and survival outcome to neoadjuvant chemotherapy: results from a multi-institutional validation study

Project description:Four different molecular classifications of muscle-invasive bladder cancer (MIBC) based on gene expression have been proposed. With the ultimate goal of utilizing these molecular subtypes for personalized treatment, we investigated their significance in the context of neoadjuvant cisplatin-based chemotherapy (NAC).

2017-05-25 | GSE87304 | GEO

Differential Expression Profiles of tRNA-derived Small RNAs in Muscle-Invasive Bladder Cancer in Chinese Population

Project description:The goals of this study are to screen differential expression profiles of tRNA-Derived small RNAs (tsRNAs) in muscle-invasive bladder cancer (MIBC) in Chinese population using next-generation sequencing and qRT-PCR.As a result, in MIBC tissues, 406 tsRNAs were differentially expressed between in MIBC tissues. Of them, 91 tsRNAs were significantly differentially expressed (fold change>1.5; P<0.05): 65 tsRNAs were significantly up-regulated whereas 26 were significantly down-regulated in MIBC.Taken together,this study explored, for the first time, the significant alteration of tsRNA expression profiles in MIBC in Chinese population and offered deep insights into many possible treatment targets of MIBC by regulating tsRNAs.

2022-04-27 | GSE192651 | GEO

In silico analyses identify lncRNAs: WDFY3-AS2, BDNF-AS and AFAP1-AS1 as potential prognostic factors for patients with triple-negative breast tumors.

Project description: Not available

| S-EPMC7219740 | biostudies-literature

Expression profiles and functional prediction of long non-coding RNAs LINC01133, ZEB1-AS1 and ABHD11-AS1 in the luminal subtype of breast cancer.

Project description: Not available

| S-EPMC8390237 | biostudies-literature

Kinome expression profiling of muscle invasive bladder cancer (MIBC) patients

Project description:Muscle invasive bladder cancer (MIBC) is one of the aggressive cancer with limited treatment options. Targeted gene expression profiling in normal and tumor samples from MIBC patients could aid in identification of potential therapeutic targets. Thus we used kinase specific panel to study their expression pattern and to identify targetable genes.

2020-04-20 | GSE130598 | GEO

Luminal B breast cancer subtype displays a dichotomic epigenetic pattern

Project description:Purpose In breast cancer, specific aberrant methylation patterns have been associated with different BC histologic and molecular subtypes and data suggest that DNA methylation profiles may play an important role in the development and progression of distinct breast subtypes. However, the epigenome of the newly defined luminal B and luminal B-HER2 positive breast cancers has not yet been characterized. Therefore the main goal of the current study is to deciphered the aberrant DNA methylation profiles associated with these breast cancer subtypes. Experimental Design 29 luminal subtype breast cancer samples along with 8 control tissue were epigenetically interrogated using the HumanMethylation27 DNA Analysis BeadChip. Results Luminal B-HER2 + subtype displays the most aggressive phenotype and shows the highest number of aberrantly methylated CpG markers. On the other hand, the luminal B subtype harbours an heterogeneous DNA methylation profile that seems to be half way between the luminal A and luminalB-HER2+ subtypes. Conclusions The heterogeneous epigenetic and genetic profile of the luminal B subtype, might indicate that a further stratification has to be done for this specific breast cancer subtype.

2016-12-18 | GSE73808 | GEO

Analysis of direct target genes regulated by AS1 and AS2

Project description:Analysis of tiling array data identified 358 genomic regions commonly enriched by the AS1 and T7 antibody datasets. AS1 antibody data set (AS1 antibody versus mock) and the T7 antibody data set (T7 antibody versus mock)

2013-03-06 | E-GEOD-44872 | biostudies-arrayexpress

Different gene expression profiles between de novo and progressive muscle invasive bladder cancer: prognostic implications

Project description:INTRODUCTION: Progressive muscle-invasive bladder cancer (MIBC) has more aggressive behavior than de novo MIBC. This study aimed to ascertain the differences in gene expression profiles between both MIBC groups and to identify prognostic biomarkers to improve the treatment in these patients. MATERIAL AND METHODS: Retrospective multicentre study in which 212 MIBC patients (104 progressive and 108 de novo) who underwent radical cystectomy in the Hospital Clinic (Barcelona) and Radboud UMC (Nijmegen) were included. Total RNA from formalin-fixed paraffin-embedded tissue samples was obtained. Gene expression profiles of 27,965 coding transcripts were determined in 26 patients using Illumina microarrays. Expression levels of 94 genes selected from microarray data and literature were studied by quantitative PCR in an independent series of 186 de novo and progressive MIBC patients. Survival analysis was performed with the Kaplan-Meier method. R-software and SPSSv23 were used for all calculations. RESULTS: A total of 480 genes were found differently expressed (FDR<0.01) between progressive and de novo MIBC samples. Differential expression of 23 out of the 94 genes selected was validated in an independent set of samples. Survival analysis showed that expression of eight genes were prognostic factors of BCR. CONCLUSION: De novo and progressive MIBC patients show different gene expression profiles. In addition, we have identified eight genes with prognostic value which may contribute to improve BC risk stratification and, consequently, to tailor treatment and surveillance strategies in these patients.

2021-03-23 | GSE149582 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data