Sequencing of patient tumor samples and cancer cell lines for endotype identification in multiple cancer types
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE138269 | GEO | 2019/10/02
REPOSITORIES: GEO
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Project description:MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis. In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling. Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling
2008-11-01 | GSE12458 | GEO
Project description:Mouse distal colons were preserved snap frozen in RNAlater, homogenized in Trizol Reagent. A total of 100 ng of RNA per sample were used for hybridization and run on the XT_PGX_MmV2_Inflammation_CSO 248 gene panel for multiplexed semi-quantitative analysis of colonic RNA markers of inflammation.
2021-09-02 | GSE181253 | GEO
Project description:Introduction: Effective predictive biomarkers for selection of patients benefiting from adjuvant platinum-based chemotherapy in non-small cell lung cancer (NSCLC) are needed. Based on a previously validated methodology, molecular profiles of predicted sensitivity in two patient cohorts are presented. Methods: The profiles are correlations between in vitro sensitivity to cisplatin and vinorelbine and baseline mRNA expression of the 60 cell lines in the National Cancer Institute panel. An applied clinical samples filter focused the profiles to clinically relevant genes. The profiles were tested on 1) snap-frozen tumors from 133 patients with completely resected stage 1B-2 NSCLC randomized to adjuvant cisplatin and vinorelbine (ACV, n=71) or no adjuvant treatment (OBS, n=62) [GSE14814] and 2) formalin-fixed paraffin-embedded (FFPE) pre-treatment tumors from 95 patients with completely resected stage 1A-3B NSCLC receiving adjuvant cisplatin and vinorelbine. Results: The combined cisplatin and vinorelbine profiles showed: 1) univariate Hazard Ratio (HR) for sensitive versus resistant of 0.265 (95% CI:0.079-0.889, p=0.032) in the ACV cohort and a HR of 0.28 in a multivariate model (95% CI:0.08-1.04, p=0.0573); 2) significant prediction at 3 year survival from surgery in univariate (HR=0.138 (95% CI:0.035-0.537), p=0.004) and multivariate analysis (HR=0.14 (95% CI:0.030-0.6), p=0.0081). No discrimination was found in the OBS cohort (HR=1.328, p=0.60). The cisplatin predictor alone had similar figures with 1) univariate HR of 0.37 (95% CI:0.12-1.15, p=0.09) in the ACV cohort and 2) univariate HR of 0.14 (95% CI:0.03-0.59, p=0.0076) to three years. Functional analysis on the cisplatin profile revealed a group of upregulated genes related to RNA splicing as a part of DNA damage repair and apoptosis. Conclusions: Profiles derived from snap-frozen and FFPE NSCLC tissue were prognostic and predictive in the patients that received cisplatin and vinorelbine but not in the cohort that did not receive adjuvant treatment.
2017-12-25 | GSE108492 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that repress gene expression at the post transcriptional level via an antisense RNA-RNA interaction. Generally, miRNAs derived from snap frozen or fresh samples are used for array based profiling. Since tissues in most pathology departments are available only in formalin fixed and paraffin embedded state, we sought to evaluate the miRNA derived from formalin fixed and paraffin embedded (FFPE) samples for microarray analysis. In this study, miRNAs extracted from matched snap frozen and FFPE samples were profiled using the Agilent miRNA array platform. Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. A total of seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results, as technical replicates showed high correlations (Kendall tau=0.722-0.853, Spearman rank correlation coefficient=0.891-0.954). Our results showed consistent high correlation between matched frozen and FFPE samples (Kendall tau=0.669-0.815, Spearman rank correlation coefficient=0.847-0.948), supporting the use of FFPE-derived miRNAs for profiling. Keywords: formalin-fixed and paraffin-embedded (FFPE) miRNA profiling 7 matched frozen and FFPE lymphoid hyperplasia tissues were profiled and compared. Triplicate arrays were performed for two pairs of hyperplasia samples and duplicate arrays for three pairs of hyperplasia samples.
2010-05-17 | E-GEOD-12458 | biostudies-arrayexpress
Project description:We set out to investigate systematic changes in gene expression that may occur between surgical resection, routine processing in the histopathology department, frozen storage, and long term archiving in FFPE blocks. Lung carcinoma tissue samples were obtained from six patients during tumour resection surgery at the Royal Brompton Hospital, London.. When possible for each patient tissue samples were obtained at five collection points: viable tissue at the time of chest opening (T1a(CO)); immediately after resection (T1b(LR)); after transfer to histopathology (T2a(HP)); after transfer to histopathology and snap freezing (T2b(HP.SF)); and after transfer to histopathology and a week after being snap frozen and archived (T2c(HP.SFA)). FFPE samples of each patientM-^Rs tumour was obtained from histopathology after tissue had been fixed in 10% formalin and then embedded in paraffin blocks according to standard procedure.The T1a(CO), T1b(LR), and T2a(HP) tissues were immediately post sampling placed into RNAlater (Qiagen, USA) for 24 hrs and then frozen at -80oC until RNA extraction. No RNAlater was used for the T2b(HP.SF) and T2c(HP.SFA) samples as these were snap frozen. Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit (Qiagen, USA) for the majority of time points with the exception of the FFPE samples which were processed using the RecoverAllM-^Y Total Nucleic Acid Isolation Kit for FFPE (Ambion, USA). Illumina Human WG-6 v2 BeadChip microarrays were used to assess global gene expression for each sample.
2011-12-01 | E-MTAB-581 | biostudies-arrayexpress
Project description:Comparative proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies
2022-01-10 | E-PROT-41 | ExpressionAtlas
Project description:Purpose The heterogeneity of squamous cell carcinoma tissue complicates diagnosis and an individualized therapy to a great extent. Therefore it is of utmost importance to spatially characterize this tissue heterogeneity and to identify appropriate biomarkers. Matrix assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) can analyze spatially resolved tissue biopsies on a molecular level. Experimental design MALDI MSI of snap frozen tissues as well as of formalin-fixed and paraffin-embedded (FFPE) tissue samples from patients with head and neck cancer (HNC) were used to analyze m/z values localized in tumor and non-tumor regions. Peptide identification was performed by using liquid chromatography (LC)-MS/MS and immunohistochemistry (IHC). Results In both FFPE and frozen tissue specimen seven characteristic masses of the tumor epithelial region were found identified. Using LC-MS/MS, the peaks were identified as Vimentin, Keratin type II, Nucleolin, Heat shock protein 90, Prelamin-A/C, Junction plakoglobin and PGAM1. Finally, Vimentin, Nucleolin and PGAM1 were verified with IHC. Conclusions and Clinical Relevance The combination of MALDI MSI, LC-MS/MS and subsequent IHC is an appropriate tool to characterize the molecular heterogeneity of tissue as well as to identify new representative biomarkers for a more individualized therapy.
2018-11-14 | PXD009144 | Pride
Project description:Whole transcriptome and 850k mehylome profiling of human intraoperative or snap frozen and FFPE MBM.
| EGAD00001008508 | EGA
Project description:Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories as a cost-effective means of preserving invaluable specimens for subsequent study, including for clinical proteomics in translational medicine. With the rapid growth of spatial proteomics, FFPE tissue samples can serve as a more accessible alternative to commonly used fresh frozen tissues. However, extracting proteins from FFPE tissue for analysis by mass spectrometry has been challenging due to crosslinks formed between proteins and formalin, particularly when studying limited samples. We have previously demonstrated that nanoPOTS (Nanodroplet Processing in One Pot for Trace Samples) is an enabling technology for high-resolution and in-depth spatial and single-cell proteomics measurements, but only fresh frozen tissues had been previously analyzed. Here we have adapted the nanoPOTS sample processing workflows for proteome profiling of 10-µm-thick FFPE tissues with lateral dimensions as small as 50 µm. Following a comparison of extraction solvents, times, and temperatures, and under the most favorable conditions, we respectively identified an average of 1180 and 2990 proteins from FFPE preserved mouse liver tissues having dimensions of 50 µm and 200 µm. This was on average 87% of the coverage achieved for fresh frozen mouse liver samples analyzed with the same general procedure. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. These workflows provide the greatest depth of coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues.
2022-08-02 | PXD029729 | Pride
Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.
2009-02-18 | GSE14744 | GEO