Pancreatic Tumor Specimens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008674 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25744549_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744549_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744550_1.fastq.gz | Fastqsanger.gz | |||
| SRR25744550_2.fastq.gz | Fastqsanger.gz | |||
| SRR25744551_1.fastq.gz | Fastqsanger.gz |
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Project description:Heterogeneity in DNA methylation status may exist between primary tumors and cfDNA. We compared the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients. MBD-sequencing (seq) was performed in paired samples of FNA and cfDNA from two patients. The majority of DNA methylation peaks overlapped in FNA and cfDNA samples (82.6% and 82.9% in patients #1 and #73, respectively). DNA methylation levels of each gene in FNA and cfDNA samples were highly correlated with each other (r=0.98 and 0.97 in samples 1 and 73, respectively)
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Project description:Pancreatic cancer is among the deadliest cancers that affects almost 54,000 patients in United States alone, with 90% of them succumbing to the disease. Lack of early detection is considered to be the foremost reason for such dismal survival rates. Our study shows that resident gut microbiota is altered at the early stages of tumorigenesis much before development of observable tumors in a spontaneous, genetically engineered mouse model for pancreatic cancer. In the current study, we analyzed the microbiome of in a genetic mouse model for PDAC (KRASG12DTP53R172HPdxCre or KPC) and age-matched controls using WGS at very early time points of tumorigenesis. During these time points, the KPC mice do not show any detectable tumors in their pancreas. Our results show that at these early time points, the histological changes in the pancreas correspond to a significant change in certain gut microbial population. Our predictive metabolomic analysis on the identified bacterial species reveal that the primary microbial metabolites involved in progression and development of PDAC tumors are involved in polyamine metabolism.
2019-07-07 | E-MTAB-6921 | biostudies-arrayexpress
Project description:loss of Men1 in mouse pancreatic islet cells alters the epigenetic landscape of a subset of target genes. H3K4me3 ChIP-seq from either mouse pancreatic islets or mouse pancreatic islet tumors harvested at different stages.
2015-04-16 | E-GEOD-63020 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE23384: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FFPE samples) GSE23385: Gene profiling using archival formalin-fixed paraffin-embedded breast cancer specimens can generate informative microarray data: A comparison with matched fresh fine needle aspiration biopsy samples (FNA samples) Refer to individual Series
2011-06-22 | E-GEOD-23386 | biostudies-arrayexpress
Project description:Pancreatic Tumor samples from biopsy collected at different stages along with normal tissue samples from various organ sites including commercial normals arrayed on 2channel Agilent 60mer Oligo arrays (human v1 & v2), median normalized for cross comparison. Some normal samples temporarily removed to public due to Intelectual property conflict. Keywords: Pancreatic tumor comparison to normals for multimetric study
2008-09-15 | GSE11838 | GEO
Project description:Background: Integration of transcriptomic testing into EUS-FNA samples is a growing need for precision oncology in pancreatic ductal adenocarcinoma (PDAC). The NanoString platform is suitable for transcriptome profiling in low yield RNA samples. Methods: Inclusion of patients that underwent EUS-FNA cytological diagnosis of pancreatic ductal adenocarcinoma using 19G and/or 22G needles and subsequent surgical resection. Formalin fixed paraffin embedded (FFPE) cytological and surgical samples underwent RNA extraction and transcriptomic analysis using a custom 52-gene NanoString panel of stromal PDAC features. Cell type abundance was quantified in FFPE specimens and correlated. Results: 18 PDAC patients were included. Mean EUS-FNA passes was 2 + 0.7. All FFPE passed the RNA quality control for genomic analysis. Hierarchical clustering on the global gene expression data showed that genes were differentially expressed between EUS and surgical samples. A more enriched cancerassociated fibroblasts and epithelial-mesenchymal transition transcriptomic profile was observed across surgical specimens whereas immunological biomarkers were more represented in EUS-FNA samples. Cytological examination confirmed a scanty representation of CAF and more immunological cell abundance in cytological samples in comparison to surgical specimens. Conclusion: Targeted transcriptomic NanoString profiling of PDAC samples obtained by EUS-FNA is a feasible approach for pre-surgical molecular analysis although stromal CAF/EMT mRNA biomarkers are underrepresented.
2023-05-04 | GSE225953 | GEO
Project description:Pancreatic Tumor samples from biopsy collected at different stages along with normal tissue samples from various organ sites including commercial normals arrayed on 2channel Agilent 60mer Oligo arrays (human v1 & v2), median normalized for cross comparison. Some normal samples temporarily removed to public due to Intelectual property conflict. Keywords: Pancreatic tumor comparison to normals for multimetric study Single channel array expression from two Agilent versions (V1:18k,V2: 22k) (i.e: GPL885,GPL887) combined based on matching probes, remove repeating control substituted with median values, final probe down to ~17k.
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Project description:The grade of pancreatic neuroendocrine tumors principally influences therapy. Grading is currently done by the histological examination of biopsy samples, which is an invasive and time-consuming method. We performed an NGS on FFPE tumor tissue samples to find microRNAs that show a significant difference in expression according to grade, thus could be suitable for grade determination.
2024-08-02 | GSE265752 | GEO
Project description:Pancreatic cancer is the 3rd most prevalent cause of cancer related deaths in United states alone, with over 55000 patients being diagnosed in 2019 alone and nearly as many succumbing to it. Late detection, lack of effective therapy and poor understanding of pancreatic cancer systemically contributes to its poor survival statistics. Obesity and high caloric intake linked co-morbidities like type 2 diabetes (T2D) have been attributed as being risk factors for a number of cancers including pancreatic cancer. Studies on gut microbiome has shown that lifestyle factors as well as diet has a huge effect on the microbial flora of the gut. Further, modulation of gut microbiome has been seen to contribute to effects of intensive insulin therapy in mice on high fat diet. In another study, abnormal gut microbiota was reported to contribute to development of diabetes in Db/Db mice. Recent studies indicate that microbiome and microbial dysbiosis plays a role in not only the onset of disease but also in its outcome. In colorectal cancer, Fusobacterium has been reported to promote therapy resistance. Certain intra-tumoral bacteria have also been shown to elicit chemo-resistance by metabolizing anti-cancerous agents. In pancreatic cancer, studies on altered gut microbiome have been relatively recent. Microbial dysbiosis has been observed to be associated with pancreatic tumor progression. Modulation of microbiome has been shown to affect response to anti-PD1 therapy in this disease as well. However, most of the studies in pancreatic cancer and microbiome have remained focused om immune modulation. In the current study, we observed that in a T2D mouse model, the microbiome changed significantly as the hyperglycemia developed in these animals. Our results further showed that, tumors implanted in the T2D mice responded poorly to Gemcitabine/Paclitaxel (Gem/Pac) standard of care compared to those in the control group. A metabolomic reconstruction of the WGS of the gut microbiota further revealed that an enrichment of bacterial population involved in drug metabolism in the T2D group.
2020-11-30 | E-MTAB-8739 | biostudies-arrayexpress