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Feasibility of global microRNA analysis from fine-needle biopsy FFPE material in patients with hepatocellular carcinoma treated with sorafenib

ABSTRACT: Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. micro RNA expression were correlated to clinical outcome and sorafenib-therapy. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE56059 | GEO | 2014/07/29

SECONDARY ACCESSION(S): PRJNA242315

REPOSITORIES: GEO

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Feasibility of global microRNA analysis from fine-needle biopsy FFPE material in patients with hepatocellular carcinoma treated with sorafenib

Project description:Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. micro RNA expression were correlated to clinical outcome and sorafenib-therapy. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit 20 microdissected hepatocellular carcinoma samples with detailed clinical data

2014-07-29 | E-GEOD-56059 | biostudies-arrayexpress

Targeted DNA and RNA sequencing of fine-needle biopsy FFPE specimens in patients with unresectable hepatocellular carcinoma treated with sorafenib.

Project description:The multi-kinase inhibitor sorafenib is now used as standard therapy for advanced hepatocellular carcinoma (HCC). Predictive biomarkers of response to sorafenib are thus necessary. The purpose of this study was to assess the feasibility of using targeted DNA and RNA sequencing to elucidate candidate biomarkers of sorafenib response using fine-needle biopsy, formalin-fixed paraffin-embedded (FFPE) specimens in patients with HCC. Targeted DNA and RNA deep sequencing were feasible for the evaluation of fine-needle biopsy FFPE specimens obtained from 46 patients with HCC treated with sorafenib. Frequent mutations of suppressor genes, such as CTNNB1 (34.8%) and TP53 (26.1%), were detected in the HCC tumors. After excluding these suppressor genes, the average numbers of detected oncogene mutations differed significantly between the non-PD and PD groups (P = 0.0446). This result suggests that the oncogene mutational burden in the tumor might be associated with the clinical response to sorafenib. We have identified candidate gene expression (TGFa, PECAM1, and NRG1) in tumor for the prediction of sorafenib response and PFS by RNA sequencing. Our findings provide new insights into biomarkers for sorafenib therapy and allow us to discuss future therapeutic strategies.

| S-EPMC4673292 | biostudies-literature

MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule

Project description:Tumor cells were microdissected from FFPE sections of hepatocellular carcinoma (HCC) samples. Samples were compared between different localisations either within or around the tumor. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2015-01-14 | GSE54537 | GEO

EUS-guided fine-needle biopsy of gallbladder polypoid lesions.

Project description: Not available

| S-EPMC7125392 | biostudies-literature

EUS-Guided Biopsy with a Novel Puncture Biopsy Forceps Needle-Feasibility Study.

Project description:Endoscopic ultrasound (EUS) with fine needle aspiration (FNA) or biopsy (FNB) to diagnose lesions in the gastrointestinal tract is common. Demand for histology sampling to identify treatment-specific targets is increasing. Various core biopsy FNB needles to obtain tissue for histology are currently available, however, with variable (37-97%) histology yields. In this multicenter study, we evaluated performance, safety, and user experience of a novel device (the puncture biopsy forceps (PBF) needle). Twenty-four procedures with the PBF needle were performed in 24 patients with a suspected pancreatic lesion (n = 10), subepithelial lesion (n = 10), lymph node (n = 3), or pararectal mass (n = 1). In 20/24 (83%) procedures, the PBF needle yielded sufficient material for interpretation (sample adequacy). In 17/24 (71%), a correct diagnosis was made with the material from the PBF needle (diagnostic accuracy). All participating endoscopists experienced a learning curve. (Per)procedural technical issues occurred in four cases (17%), but there were no adverse events. The PBF needle is a safe and potentially useful device to obtain an EUS-guided biopsy specimen. As the design of the PBF needle is different to core biopsy FNB needles, specific training will likely further improve the performance of the PBF needle. Furthermore, the design of the needle needs further improvement to make it more robust in clinical practice.

| S-EPMC8466864 | biostudies-literature

Comparison of tissue and molecular yield between fine-needle biopsy (FNB) and fine-needle aspiration (FNA): a randomized study.

Project description:Background and study aims Recently, a new Franseen design endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) needle was developed with the goal of providing more tissue for histology. We compared the tissue adequacy rate and nucleic acid yield of 22G EUS-FNB vs. 22G endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA), in solid gastrointestinal and extra-intestinal lesions. Patients and methods We conducted a randomized crossover study and recruited 36 patients. We performed three passes for pancreatic lesions and two passes for other lesions, using each needle. We blinded the pathologist to needle assignment. We assessed the diagnostic tissue adequacy rate and compared the total tissue area, diagnostic tissue area, and desmoplastic stroma (DS) area in cases of carcinoma. We also examined the nucleic acid yield of the two needles in pancreatic lesions. Results The lesions included 20 pancreatic masses (55 %), six gastric subepithelial lesions (17 %), five lymph nodes (14 %) and five other abdominal masses (14 %). Mean ± SD lesion size was 3.8 ± 2.0 cm. The final diagnosis was malignant in 27 lesions (75 %) and benign in nine lesions (25 %). We found EUS-FNB procured significantly more median total tissue area (5.2 mm 2 vs. 1.9 mm 2 , P < 0.001), diagnostic tissue area (2.2 mm 2 vs. 0.9 mm 2 , P = 0.029), and DS area (2 mm 2 vs. 0.1 mm 2 , P = 0.001) in lesions diagnosed as carcinoma (n = 23), as compared to EUS-FNA. In pancreatic lesions, EUS-FNB obtained significantly more nucleic acid than EUS-FNA (median; 4,085 ng vs. 2912 ng, P = 0.02). There was no difference in the cellblock or rapid on-site cytological evaluation (ROSE) diagnostic yield between the needles. Conclusion The 22G EUS-FNB provides more histological core tissue and adequate nucleic acid yield compared to 22G EUS-FNA. In this study, the diagnostic performance was similar between the needles.

| S-EPMC6656554 | biostudies-literature

miRNA expression profiling divides follicular dendritic cell sarcomas into two groups, related to fibroblasts and myopericytomas or Castleman's disease

Project description:miRNA expression profiling divides 31 follicular dendritic cell (FDC) sarcomas into two subgroups, one group closely related to microdissected FDCs from Castleman´s disease, the other group closely related to fibroblasts and myopericytomas. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2017-06-21 | GSE83994 | GEO

Differential expression of miRNA in Tax1BP1 knock-out mice [miRNA]

Project description:To further characterize differential expression of miRNA and mRNA levels in livers of 12 weeks old male Tax1BP1 wildtype and knock-out mice, the untreated mice were sacrificed and miRNA and mRNA levels were determined miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2020-10-06 | GSE98907 | GEO

Sorafenib resistance related circRNAs

Project description:Sorafenib resistance up-regulated circRNA_104797 could be transmitted by exosomes and responsible for the spread of Sorafenib resistance among HCC cells. CircRNA_104797 was critical for Sorafenib resistance maintenance and silencing circRNA_104797 could substantially increase the efficacy of Sorafenib by inducing apoptosis. Mechanism dissection unveiled that circRNA_104797 could specifically sponge miR-103a-2-5p and miR-660-3p and act as a competing endogenous RNA (ceRNA), thus competitively activated wnt/β-catenin pathway and induced Sorafenib resistance. Meanwhile, LC-MS/MS also revealed that circRNA_104797 could specifically bind to translation related proteins, which might regulate downstream glycan biosynthesis and lipid metabolism, and finally induce Sorafenib resistance. In vivo experiments portrayed a promising clinical application by locally injection of in vivo-grade siRNA for circRNA_104797 by TACE or other manners, which could intensively enhance Sorafenib efficacy in HCC patients. The clinical application of in vivo-grade siRNA for circRNA_104797 in Sorafenib treated HCC patients might shed bright future for the management of advanced HCC.

2020-07-25 | GSE101850 | GEO

Endoscopic ultrasound fine-needle biopsy vs fine-needle aspiration for lymph nodes tissue acquisition: a systematic review and meta-analysis.

Project description:BackgroundEndoscopic ultrasound (EUS)-guided tissue acquisition represents the choice of methods for suspected lymph nodes (LNs) located next to the gastrointestinal tract. This study aimed to compare the pooled diagnostic performance of EUS-guided fine-needle biopsy (EUS-FNB) and fine-needle aspiration (EUS-FNA) for LNs sampling.MethodsWe searched PubMed/MedLine and Embase databases through August 2021. Primary outcome was diagnostic accuracy; secondary outcomes were sensitivity, specificity, sample adequacy, optimal histological core procurement, number of passes, and adverse events. We performed a pairwise meta-analysis using a random-effects model. The results are presented as odds ratio (OR) or mean difference along with 95% confidence interval (CI).ResultsWe identified nine studies (1,276 patients) in this meta-analysis. Among these patients, 66.4% were male; the median age was 67 years. Diagnostic accuracy was not significantly different between the two approaches (OR, 1.31; 95% CI, 0.81-2.10; P = 0.270). The accuracy of EUS-FNB was significantly higher when being performed with newer end-cutting needles (OR, 1.87; 95% CI, 1.17-3.00; P = 0.009) and in abdominal LNs (OR, 2.48; 95% CI, 1.52-4.05; P < 0.001) than that of EUS-FNA. No difference in terms of sample adequacy was observed between the two approaches (OR, 1.40; 95% CI, 0.46-4.26; P = 0.550); however, histological core procurement and diagnostic sensitivity with EUS-FNB were significantly higher than those with EUS-FNA (OR, 6.15; 95% CI, 1.51-25.07; P = 0.010 and OR, 1.87; 95% CI, 1.27-2.74, P = 0.001). The number of needle passes needed was significantly lower in the EUS-FNB group than in the EUS-FNA group (mean difference, -0.54; 95% CI, -0.97 to -0.12; P = 0.010).ConclusionsEUS-FNA and EUS-FNB perform similarly in LN sampling; however, FNB performed with end-cutting needles outperformed FNA in terms of diagnostic accuracy.

| S-EPMC9632631 | biostudies-literature

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