scholarly journals RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens

Biomedicines ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 114
Author(s):  
Maxim Sorokin ◽  
Kirill Ignatev ◽  
Elena Poddubskaya ◽  
Uliana Vladimirova ◽  
Nurshat Gaifullin ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lung Cancer ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Correlation Study ◽  
Cancer Tissue ◽  
Transcriptional Level ◽  
Tissue Samples ◽  
Protein Levels ◽  
Formalin Fixed Paraffin Embedded

RNA sequencing is considered the gold standard for high-throughput profiling of gene expression at the transcriptional level. Its increasing importance in cancer research and molecular diagnostics is reflected in the growing number of its mentions in scientific literature and clinical trial reports. However, the use of different reagents and protocols for RNA sequencing often produces incompatible results. Recently, we published the Oncobox Atlas of RNA sequencing profiles for normal human tissues obtained from healthy donors killed in road accidents. This is a database of molecular profiles obtained using uniform protocol and reagents settings that can be broadly used in biomedicine for data normalization in pathology, including cancer. Here, we publish new original 39 breast cancer (BC) and 19 lung cancer (LC) RNA sequencing profiles obtained for formalin-fixed paraffin-embedded (FFPE) tissue samples, fully compatible with the Oncobox Atlas. We performed the first correlation study of RNA sequencing and immunohistochemistry-measured expression profiles for the clinically actionable biomarker genes in FFPE cancer tissue samples. We demonstrated high (Spearman’s rho 0.65–0.798) and statistically significant (p < 0.00004) correlations between the RNA sequencing (Oncobox protocol) and immunohistochemical measurements for HER2/ERBB2, ER/ESR1 and PGR genes in BC, and for PDL1 gene in LC; AUC: 0.963 for HER2, 0.921 for ESR1, 0.912 for PGR, and 0.922 for PDL1. To our knowledge, this is the first validation that total RNA sequencing of archived FFPE materials provides a reliable estimation of marker protein levels. These results show that in the future, RNA sequencing can complement immunohistochemistry for reliable measurements of the expression biomarkers in FFPE cancer samples.

scholarly journals Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Cheng-Liang Yuan ◽  
Xiang-Mei Jiang ◽  
Ying Yi ◽  
Jian-Fei E ◽  
Nai-Dan Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Luminal B ◽  
Ppi Networks ◽  
Tumor Tissues ◽  
Cancer Tumor

Abstract Background Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer. Methods Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100 kb window up- or down-stream of DElncRNAs were searched, which were defined as cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs. Results A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally. Conclusion This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer.

scholarly journals Overexpression of β-Arrestins inhibits proliferation and motility in triple negative breast cancer cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Saber Yari Bostanabad ◽  
Senem Noyan ◽  
Bala Gur Dedeoglu ◽  
Hakan Gurdal
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Cancer Cells ◽  
Cancer Cell ◽  
Breast Cancer Cells ◽  
Cell Function ◽  
Expression Profiles ◽  
Tissue Samples ◽  
Expression Levels ◽  
Cell Cycle Genes

Abstractβ-Arrestins (βArrs) are intracellular signal regulating proteins. Their expression level varies in some cancers and they have a significant impact on cancer cell function. In general, the significance of βArrs in cancer research comes from studies examining GPCR signalling. Given the diversity of different GPCR signals in cancer cell regulation, contradictory results are inevitable regarding the role of βArrs. Our approach examines the direct influence of βArrs on cellular function and gene expression profiles by changing their expression levels in breast cancer cells, MDA-MB-231 and MDA-MB-468. Reducing expression of βArr1 or βArr2 tended to increase cell proliferation and invasion whereas increasing their expression levels inhibited them. The overexpression of βArrs caused cell cycle S-phase arrest and differential expression of cell cycle genes, CDC45, BUB1, CCNB1, CCNB2, CDKN2C and reduced HER3, IGF-1R, and Snail. Regarding to the clinical relevance of our results, low expression levels of βArr1 were inversely correlated with CDC45, BUB1, CCNB1, and CCNB2 genes compared to normal tissue samples while positively correlated with poorer prognosis in breast tumours. These results indicate that βArr1 and βArr2 are significantly involved in cell cycle and anticancer signalling pathways through their influence on cell cycle genes and HER3, IGF-1R, and Snail in TNBC cells.

scholarly journals The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Marczyk ◽  
Chunxiao Fu ◽  
Rosanna Lau ◽  
Lili Du ◽  
Alexander J. Trevarton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Rna Extraction ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
The Impact ◽  
Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

Strategy for SRM-based Verification of Biomarker Candidates Discovered by iTRAQ Method in Limited Breast Cancer Tissue Samples

2012 ◽  
Vol 11 (8) ◽  
pp. 4201-4210 ◽  
Author(s):  
Satoshi Muraoka ◽  
Hideaki Kume ◽  
Shio Watanabe ◽  
Jun Adachi ◽  
Masayoshi Kuwano ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Tissue ◽  
Cancer Tissue ◽  
Tissue Samples

scholarly journals Diagonistic Value of ARFI in Breast Lesions

2021 ◽  
pp. 24-30
Author(s):  
J. Jayapriya ◽  
S. Arul Murugan
Keyword(s):  
Breast Cancer ◽  
Acoustic Radiation ◽  
Radiation Force ◽  
Acoustic Radiation Force Impulse ◽  
Stiffness Index ◽  
Cancer Tissue ◽  
Cancer Type ◽  
Tissue Samples ◽  
Biopsy Confirmation ◽  
Index Value

Breast cancer became the most prominent cancer type in women worldwide. Its prevalence increased in recent years due to changes in life style and relapse among the patients seemed to be higher. Acoustic radiation force impulse (ARFI) imaging in based on the principle of the ultrasonic elasticity and the elestography accurately predict and measure the changes in breast cancer tissue compared to the normal tissue. It is a technical alternative to the palpation and able to measure lesser than 10 mm size. In contrast to biopsy, where the reduced deformability would occur and lead to biopsy failing. In fibroadenoma, due to its complications, many false positives could be detected and the ARFI elastography serve as an effective alternative method for breast cancer confirmation. The tissue stiffness index value is used to differentiate the benign and malignant tissue samples. ARFI further, use B- mode elasticity and help in recommending the biopsy confirmation.

scholarly journals Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

Cell Systems ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 531 ◽  
Author(s):  
Daniel Schulz ◽  
Vito Riccardo Tomaso Zanotelli ◽  
Jana Raja Fischer ◽  
Denis Schapiro ◽  
Stefanie Engler ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Tissue ◽  
Cancer Tissue ◽  
Mass Cytometry ◽  
Tissue Samples ◽  
Multiplexed Imaging ◽  
Subcellular Resolution

scholarly journals Multi-Omics and Informatics Analysis of FFPE Tissues Derived from Melanoma Patients with Long/Short Responses to Anti-PD1 Therapy Reveals Pathways of Response

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3515
Author(s):  
Saurabh K. Garg ◽  
Eric A. Welsh ◽  
Bin Fang ◽  
Yuliana I. Hernandez ◽  
Trevor Rose ◽  
...  
Keyword(s):  
Antigen Processing ◽  
Expression Profiles ◽  
Stage Iii ◽  
Poor Responders ◽  
Tissue Samples ◽  
Immune Therapies ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Melanoma Patients ◽  
Pathway Analyses

Anti-PD-1 based immune therapies are thought to be dependent on antigen processing and presentation mechanisms. To characterize the immune-dependent mechanisms that predispose stage III/IV melanoma patients to respond to anti-PD-1 therapies, we performed a multi-omics study consisting of expression proteomics and targeted immune-oncology-based mRNA sequencing. Formalin-fixed paraffin-embedded tissue samples were obtained from stage III/IV patients with melanoma prior to anti-PD-1 therapy. The patients were first stratified into poor and good responders based on whether their tumors had or had not progressed while on anti-PD-1 therapy for 1 year. We identified 263 protein/gene candidates that displayed differential expression, of which 223 were identified via proteomics and 40 via targeted-mRNA analyses. The downstream analyses of expression profiles using MetaCore software demonstrated an enrichment of immune system pathways involved in antigen processing/presentation and cytokine production/signaling. Pathway analyses showed interferon (IFN)-γ-mediated signaling via NF-κB and JAK/STAT pathways to affect immune processes in a cell-specific manner and to interact with the inducible nitric oxide synthase. We review these findings within the context of available literature on the efficacy of anti-PD-1 therapy. The comparison of good and poor responders, using efficacy of PD-1-based therapy at 1 year, elucidated the role of antigen presentation in mediating response or resistance to anti-PD-1 blockade.

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