Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer

ABSTRACT: Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed basal-like was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes. Tumors from 62 resectable PDAC patients were subjected to metagenomic sequencing and RNA-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE172356 | GEO | 2021/08/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer.

Project description:Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed 'basal-like' was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes with resectable tumors using metagenomic sequencing. We found distinctive microbial communities in basal-like tumors and identified an increasing abundance of Acinetobacter, Pseudomonas and Sphingopyxis to be highly associated with carcinogenesis. Functional characterization of microbial genes suggested the potential to induce pathogen-related inflammation. Host-microbiota interplay analysis provided new insights into the tumorigenic role of specific microbiome compositions and demonstrated the influence of host genetics in shaping the tumor microbiome. Taken together, these findings indicated that the tumor microbiome is closely related to PDAC oncogenesis and the induction of inflammation. Additionally, our data revealed the microbial basis of PDAC heterogeneity and proved the predictive value of the microbiome, which will contribute to the intervention and treatment of disease.

| S-EPMC8408135 | biostudies-literature

SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer I

Project description:Pancreatic cancer is a heterogenous disease and consists of distinct subtypes. Here, we searched for candidate driver genes of the basal-like/squamous subtype, a more aggressive molecular subtype of pancreatic ductal adenocarcinoma (PDAC). Through an integrated transcriptome analysis, we identified the serine/cysteine protease inhibitor, SERPINB3 (squamous cell carcinoma antigen 1, SCCA1), as being upregulated in the basal-like/squamous PDAC using a discovery and validation approach. SERPINB3 upregulation associated with decreased patient survival and a transcriptome profile indicative of the basal-like/squamous subtype. The goal of this study was aimed to identify SERPINB3 induced molecular signatures in PDAC.

2023-10-12 | GSE223536 | GEO

SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer III

2023-10-12 | GSE224564 | GEO

SERPINB3 induces the aggressive basal-like/squamous subtype and promotes invasion and metastasis in pancreatic cancer II

2023-10-12 | GSE223908 | GEO

Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [HiChIP]

Project description:A major hurdle to the application of precision oncology in pancreatic cancer is the lack of molecular stratification approaches and targeted therapy for defined molecular subtypes. In this work, we sought to gain further insight and identify molecular and epigenetic signatures of the basal-like A pancreatic ductal adenocarcinoma (PDAC) subgroup that can be applied to clinical samples for both patient stratification and for choice of therapy. We generated and integrated global gene expression and epigenome mapping data from patient-derived xenograft (PDX) models to identify subtype-specific enhancer regions that were validated in patient-derived samples. In addition, complementary nascent transcription and chromatin topology (HiChIP) analysis revealed a basal-like A subtype-specific transcribed enhancer program (B-STEP) in PDAC characterized by enhancer RNA (eRNA) production that is associated with higher chromatin interactions and subtype-specific gene activation. Importantly, we successfully confirmed the validity of eRNA detection as a possible histological approach for PDAC patient stratification by performing RNA in situ hybridization analyses for subtype-specific eRNAs on pathological tissue samples. Thus, the finding in this study provides proof-of-concept that subtype-specific epigenetic changes relevant for PDAC progression can be detected at a single cell level in complex, heterogeneous, primary tumor material.

2023-09-19 | GSE213385 | GEO

Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [leChRO-seq]

2023-09-19 | GSE213396 | GEO

Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [RNA-seq]

2023-09-19 | GSE213387 | GEO

Identification of a ΔNp63-dependent Basal-like A Subtype-specific Transcribed Enhancer Program (B-STEP) in Aggressive Pancreatic Ductal Adenocarcinoma [ChIP-seq]

2023-09-19 | GSE213378 | GEO

The RNA binding protein QKI guides a pro-mesenchymal splicing program driving a subtype switch and limiting outcome in pancreatic cancer [PANC-1 and HPAF-II]

Project description:Transcriptomic analyses have identified two molecular PDAC subtypes, one of which, namely basal-like subtype, is associated with chemoresistance and worse clinical outcomes. Splicing dysregulation is known to contribute to PDAC malignancy. Functional studies in PDAC cells lines identified the splicing factor QKI as a key determinant of a basal-like splicing signature associated with increased tumor aggressiveness. Our studies demonstrate that QKI represses splicing events associated with the classical subtype and improved clinical outcome, while promoting basal-like events associated with shorter survival.

2024-02-05 | GSE234737 | GEO

ADRA2A is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer

Project description:Pancreatic cancer is a heterogeneous disease and consists of distinct subtypes. Here, we investigated candidate suppressor genes of the basal-like/squamous subtype, a more aggressive molecular subtype of pancreatic ductal adenocarcinoma (PDAC). Through an integrated transcriptome analysis, we identified the ADRA2A, as being downregulated in the basal-like/squamous PDAC using a discovery and validation approach. ADRA2A downregulation is associated with decreased patient survival. The goal of this study was to identify ADRA2A-induced molecular signatures in PDAC.

2024-06-28 | GSE259390 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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