scholarly journals Expression of miR-127, miR-154, and miR-183 in Medullary Thyroid Carcinoma Tumors

2021 ◽  
Author(s):  
Mahsa RAHMANI SAMANI ◽  
Marjan ZARIF-YEGANEH ◽  
Atefeh MEHRABI ◽  
Amir Nader EMAMI RAZAVI ◽  
Sara SHEIKHOLESLAMI ◽  
...  
Keyword(s):  
Thyroid Cancer ◽  
Rna Extraction ◽  
Control Group ◽  
Tissue Samples ◽  
Altered Expression ◽  
Medullary Thyroid ◽  
Formalin Fixed Paraffin ◽  
Tumor Tissues ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues

Background: Medullary thyroid cancer (MTC) accounts for 5%–10% of all thyroid cancers, but causes 13% of all thyroid cancer related deaths. MicroRNAs (miRs) have key functions in the development and progression of MTC. Altered expression of some miRs has been reported in many human cancers, including Thyroid cancer. Therefore, we aimed to analyze the expression of miR-154, miR-183 and miR-127 in MTC tumor tissues. Methods: In this case-control study, 15 MTC Formalin-fixed, paraffin-embedded (FFPE) tissue samples and 15 adjacent normal thyroid FFPE tissues, as a control group, were collected from Taleghani, and Loghman Hakim Hospitals, Tehran, Iran since 2005 till 2015. After RNA extraction and cDNA synthesis, the expression of miR127, miR-154 and miR-183 was measured by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Results: Our data showed a significant increase in the expression of miR-127 in MTC samples in comparison with the control group (P<0.05). Although miR-154 and miR-183 expression levels had increase expression in MTC tumors, this change was not statistically significant. Conclusion: The miR-127 could be considered as a prognostic, diagnostic and therapeutic marker for the management of MTC, and it is proposed for further investigation to fully establish the role of this miRNA in MTC.

scholarly journals Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Tamara Sequeiros ◽  
Marta García ◽  
Melania Montes ◽  
Mireia Oliván ◽  
Marina Rigau ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Markers ◽  
Tumor Grade ◽  
Developed Countries ◽  
Response To Therapy ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

Prostate cancer (PCa) is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy.

scholarly journals Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2844 ◽  
Author(s):  
Susana Iraola-Guzmán ◽  
Anna Brunet-Vega ◽  
Cinta Pegueroles ◽  
Ester Saus ◽  
Hrant Hovhannisyan ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Transcriptional Profiling ◽  
Differentially Expressed ◽  
Specific Expression ◽  
Altered Expression ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
New Biomarkers

Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.

scholarly journals Graphene oxide-quenching-based fluorescence in situ hybridization (G-FISH) to detect RNA in tissue: simple and fast tissue RNA diagnostics

2017 ◽  
Author(s):  
Do Won Hwang ◽  
Yoo Ri Choi ◽  
Dohyun Kim ◽  
Hye Yoon Park ◽  
Kyu Wan Kim ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Hippocampal Neurons ◽  
Rna Detection ◽  
Formalin Fixed Paraffin ◽  
Tumor Tissues ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues

AbstractFISH-based RNA detection in paraffin-embedded tissue can be challenging, with complicated procedures producing uncertain results and poor image quality. Here, we developed a robust RNA detection method based on graphene oxide (GO) quenching and recovery of fluorescence in situ hybridization (G-FISH) in formalin-fixed paraffin-embedded (FFPE) tissues. Using G-FISH technique, the long noncoding BC1 RNA, β-actin mRNA, miR-124a and miR-21 could be detected in the cytoplasm of a mouse brain, primary hippocampal neurons, and glioblastoma multiforme tumor tissues, respectively. G-FISH showed the increased BC1 RNA level in individual hippocampal neurons of Alzheimer’s disease brain. The fluorescence recovered by G-FISH correlated highly with the amount of miR-21, as measured by real time RT-PCR. We propose G-FISH as a simple, fast, inexpensive, and sensitive method for RNA detection, with very low background, which could be applied to a variety of researches or diagnostic purposes.

scholarly journals Methods for restoration of ki67 antigenicity in aged paraffin tissue blocks

2021 ◽  
Author(s):  
Federica Grillo ◽  
Michela Campora ◽  
Simona Pigozzi ◽  
Silvia Bonadio ◽  
Luca Valle ◽  
...  
Keyword(s):  
Central Area ◽  
Antigen Retrieval ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Prolonged Heat ◽  
Paraffin Tissue ◽  
Visual Colour ◽  
Formalin Fixed

AbstractPathology archives are a treasure trove of paraffin embedded tissue spanning many years and covering a wide variety of tissues and diseases. The possibility of using old archival formalin fixed paraffin embedded (FFPE) tissues for diagnostic updates and research projects is a widespread need and it requires archives of stable, well-preserved samples. Immunohistochemistry performed on old archival paraffin blocks may give unreliable results, in particular for some antigens, such as Ki67. In consideration of this phenomenon, our aim is to comprehensively test and identify methods which may be used to obtain Ki67 immunohistochemical reactions of good quality from old archival FFPE blocks. Various methods were tested in order to evaluate their possible efficacy in increasing Ki67 immunointensity in a collection of 40-year-old, archival blocks including re-embedding, with deeper sectioning of tissue from the block and increasing heat-based pretreatment times (20 cases) and re-processing (20 cases). All reactions were performed using an automated immunostainer and Ki67 stained immunosections compared using a visual colour-based scale (the first immunostained section was considered as baseline). The combination of deep sectioning (1000 µM) and prolonged heat-based pretreatment (64 min) markedly increased immunoreactivity for Ki67. Re-embedding and reprocessing did not have a significant effect. Large tissue samples showed heterogeneity of Ki67 immunoexpression between the periphery of the sample and the central area. In conclusion, the study defines a useful protocol to increase antigen retrieval applicable to dated archival tissues.

ROLE OF MICRORNA-155 AS A DIAGNOSTIC BIOMARKER FOR HUMAN PAPILLOMAVIRUS ASSOCIATED CERVICAL CANCER

2021 ◽  
Vol 74 (9) ◽  
pp. 2301-2304
Author(s):  
Noor A. Jihad ◽  
Yasir W. Issa
Keyword(s):  
Cervical Cancer ◽  
Control Group ◽  
Cancer Tissue ◽  
Diagnostic Biomarker ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Hpv Status ◽  
Formalin Fixed Paraffin Embedded ◽  
Cancer Tissues

The aim: This study was designed to investigate the potential role of miRNA-155 in the pathogenesis of HPV-induced cervical cancer. Materials and methods: A total of 42 formalin-fixed paraffin-embedded (FFPE) cervical cancer tissue samples and 38 FFPE normal cervical tissue samples were used (they were collected at the Department of Pathology, Baghdad teaching hospital, Baghdad, Iraq, between January 2019 to January 2021). Following HPV testing and genotyping, the expression of miRNA-155 were evaluated by real-time PCR (qPCR). Results: A statistically significant up-regulation of miRNA-155 expression was observed in cervical cancer tissues compared to results in control group, regardless of HPV status and clinical grading. Conclusions: These data suggest that overexpression of miRNA-155 can delineate cervical cancer tissues from normal and may be a useful diagnostic biomarker for early detection of cervical cancer.

scholarly journals Solitary Fibrous Tumor/Hemangiopericytoma Metastasizes Extracranially, Associated with Altered Expression of WNT5A and MMP9

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1142
Author(s):  
Jong-Hwan Hong ◽  
Myung-Giun Noh ◽  
Md Rashedunnabi Akanda ◽  
Yeong Jin Kim ◽  
Se Hoon Kim ◽  
...  
Keyword(s):  
Solitary Fibrous Tumor ◽  
Soft Tissues ◽  
Fusion Gene ◽  
Wnt Signaling Pathway ◽  
Tissue Samples ◽  
Altered Expression ◽  
Mmp9 Expression ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Fibrous Tumor

Solitary fibrous tumor/hemangiopericytoma (SFT/HPC) is a mesenchymal tumor originating from various soft tissues and meninges, which carries the NAB2-STAT6 fusion gene. Meningeal/intracranial SFT/HPCs (icSFT/HPC) have a poor clinical outcome with metastatic behavior compared to soft tissue/extracranial SFT/HPCs (exSFT/HPC), but the underlying genetic factors are unclear. Differentially expressed genes (DEGs) were analyzed by NanoString nCounter assay using RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue samples. Additionally, immunohistochemistry (IHC) was performed on 32 cases of exSFT/HPC, 18 cases of icSFT/HPC, and additional recurrent or metastatic cases to verify the findings. Pathway analysis revealed that the WNT signaling pathway was enriched in exSFT/HPC. Analysis of DEGs showed that expression of WNT5A was lower and that of MMP9 was higher in icSFT/HPC than in exSFT/HPC (p = 0.008 and p = 0.035, respectively). IHC showed that WNT5A and CD34 expression was high in exSFT/HPC (p < 0.001, both), while that of MMP9 was high in icSFT/HPC (p = 0.001). Expression of CLDN5 in tumoral vessels was locally decreased in icSFT/HPC (p < 0.001). The results suggested that decreased WNT5A expression, together with increased MMP9 expression, in icSFT/HPC, may affect vascular tightness and prompt tumor cells to metastasize extracranially.

scholarly journals Z Probe, an Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues

2018 ◽  
Author(s):  
Manish Tripathi ◽  
Chidi Zacheaus ◽  
Kyle Doxtater ◽  
Fatemeh Keramatnia ◽  
Lani Gao ◽  
...  
Keyword(s):  
Tissue Samples ◽  
Protein Coding ◽  
Dna And Rna ◽  
Non Coding Rna ◽  
Formalin Fixed Paraffin ◽  
Lncrna Malat1 ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Single Transcript ◽  
Long Non Coding Rna

Formalin-Fixed Paraffin Embedded (FFPE) tissues are a valuable resource in studying different markers and mechanistic molecules (protein, DNA and RNA) in order to understand the etiology of different cancers as well as many other diseases. Degradation and modification of RNA is the major challenge in utilizing FFPE tissue samples in medical research. Recently, non-protein coding transcripts long non-coding RNAs (lncRNAs), have gained significant attention due to their important biological actions and potential involvement in cancer. There is no validated method except qRTPCR or RNAseq to evaluate and study lncRNA expression. We have standardized and are reporting a sensitive Z probe based in situ hybridization method to identify, localize and quantitate lncRNA in FFPE tissues. This assay is sensitive to single transcript and localizes lncRNA in individual cells within tumor. We have characterized a tumor suppressor lncRNA-NRON (non coding repressor of NFAT), which is scarcely expressed, a moderately expressed oncogeneic lncRNA UCA1 (urothelial cancer associated 1), and a highly studied and expressed lncRNA MALAT1 (metastasis associated lung adenocarcinoma transcript1) in different cancers. High MALAT1 staining was found in colorectal, breast and pancreatic cancer. MALAT1 expression increased with the progression of the stage in colorectal cancer and invasiveness in breast cancer.

scholarly journals Comparison between immunofluorescence and immunohistochemistry for Listeria monocytogenes detection in formalin-fixed paraffin-embedded tissues

2022 ◽  
Vol 52 (3) ◽  
Author(s):  
Kelen Regina Ascoli Baldi ◽  
Jéssica Line Farias de Lima ◽  
Isabela Gimenes da Silva ◽  
Fernanda Felicetti Perosa ◽  
Ricardo Evandro Mendes ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Primary Antibody ◽  
Economic Losses ◽  
Secondary Antibody ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Rabbit Igg ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

ABSTRACT: Listeria monocytogenes is a bacterium that infect humans and animals and causes a zoonotic disease characterized by encephalitis, septicemia or abortion. In addition, listeriosis leads to significant economic losses due to animal death and sacrifice. This research compared the technique of immunofluorescence (IF) and immunohistochemistry (IHC) for the diagnosis of L. monocytogenes in formalin-fixed and paraffin-embedded (FFPE) tissues. A total of 30 tissue blocks from 15 animals with history and/or lesions compatible with listeriosis were selected. For both IHC and IF, the same diluted (1:200) polyclonal primary antibody was used against L. monocytogenes serotypes 1 and 4. For IHC, a polymer secondary antibody conjugated to peroxidase (HRP) was used. For IF, samples were incubated with a fluorescein-labeled anti-rabbit IgG secondary antibody. Each sample was classified according to the presence and percentage of immunolabeling area. From 30 samples, 10 were positive at least for one technique, whereas eight samples were positive for both IHC and IF with similar score. There was strong immunolabeling in tissue samples from bovines experimentally infected with L. monocytogenes ATCC 7644, as well as in nervous tissues from naturally infected ruminants. Additionally, IF did not show any difference in sensitivity when compared to IHC. Using processed biological materials for IF, instead of fresh tissues, is a quite unique technique, since there are few protocols described. Therefore, this study demonstrated that both techniques are efficient to detect L. monocytogenes in FFPE tissues.

scholarly journals Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues

2018 ◽  
Vol 4 (3) ◽  
pp. 20 ◽  
Author(s):  
Manish Tripathi ◽  
Chidi Zacheaus ◽  
Kyle Doxtater ◽  
Fatemeh Keramatnia ◽  
Cuilan Gao ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Cell Types ◽  
Rna Degradation ◽  
Activated T Cells ◽  
Tissue Samples ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues

Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge in these tissue samples. Recently, non-protein coding transcripts, long non-coding RNAs (lncRNAs), have gained significant attention due to their important biological actions and potential involvement in cancer. RNA sequencing (RNA-seq) or quantitative reverse transcription-polymerase chain reaction (qRT-PCR) are the only validated methods to evaluate and study lncRNA expression and neither of them provides visual representation as immunohistochemistry (IHC) provides for proteins. We have standardized and are reporting a sensitive Z probe based in situ hybridization method to visually identify and quantify lncRNA in FFPE tissues. This assay is highly sensitive and identifies transcripts visible within different cell types and tumors. We have detected a scarcely expressed tumor suppressor lncRNA NRON (non-coding repressor of nuclear factor of activated T-cells (NFAT)), a moderately expressed oncogenic lncRNA UCA1 (urothelial cancer associated 1), and a highly studied and expressed lncRNA MALAT1 (metastasis associated lung adenocarcinoma transcript 1) in different cancers. High MALAT1 staining was found in colorectal, breast and pancreatic cancer. Additionally, we have observed an increase in MALAT1 expression in different stages of colorectal cancer.

scholarly journals Application of the 3′ mRNA-Seq using unique molecular identifiers in highly degraded RNA derived from formalin-fixed, paraffin-embedded tissue

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jin Sung Jang ◽  
Eileen Holicky ◽  
Julie Lau ◽  
Samantha McDonough ◽  
Mark Mutawe ◽  
...  
Keyword(s):  
Bias Correction ◽  
Exome Capture ◽  
Sequencing Data ◽  
Tissue Samples ◽  
Paired Samples ◽  
Pcr Bias ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Formalin Fixed

Abstract Background Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis remains challenging with standard mRNA-seq methods as FFPE derived-RNA samples are often highly modified and fragmented. The recently developed 3′ mRNA-seq method sequences the 3′ region of mRNA using unique molecular identifiers (UMI), thus generating gene expression data with minimal PCR bias. In this study, we evaluated the performance of 3′ mRNA-Seq using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD with UMI, comparing with TruSeq Stranded mRNA-Seq and RNA Exome Capture kit. The fresh-frozen (FF) and FFPE tissues yielded nucleotide sizes range from 13 to > 70% of DV200 values; input amounts ranged from 1 ng to 100 ng for validation. Results The total mapped reads of QuantSeq 3′ mRNA-Seq to the reference genome ranged from 99 to 74% across all samples. After PCR bias correction, 3 to 56% of total sequenced reads were retained. QuantSeq 3′ mRNA-Seq data showed highly reproducible data across replicates in Universal Human Reference RNA (UHR, R > 0.94) at input amounts from 1 ng to 100 ng, and FF and FFPE paired samples (R = 0.92) at 10 ng. Severely degraded FFPE RNA with ≤30% of DV200 value showed good concordance (R > 0.87) with 100 ng input. A moderate correlation was observed when directly comparing QuantSeq 3′ mRNA-Seq data with TruSeq Stranded mRNA-Seq (R = 0.78) and RNA Exome Capture data (R > 0.67). Conclusion In this study, QuantSeq 3′ mRNA-Seq with PCR bias correction using UMI is shown to be a suitable method for gene quantification in both FF and FFPE RNAs. 3′ mRNA-Seq with UMI may be applied to severely degraded RNA from FFPE tissues generating high-quality sequencing data.

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