Accurate breast cancer diagnosis through real-time PCR her-2 gene quantification using immunohistochemically-identified biopsies

Prospective Validation of a One-Step RT-qPCR-based Test for Quantifying HER2 Gene Expression in Breast Cancer

OBJECTIVE

To Validate a one-step RT-qPCR as a reliable diagnostic tool in HER-2 positive breast cancer. Further, establishing this tool as a standard procedure to quantify HER-2 expression in Breast cancer patient.

METHODS

Here we report a prospective validation study that shows the concordance of one-step RT-qPCR in assessing the HER2 levels in formalin-fixed paraffin-embedded (FFPE) tissue samples with the current paradigm of diagnosis such as Immunohistochemistry (IHC) and Fluorescence-in-situ Hybridization (FISH). We collected 275 FFPE samples from the Department of Pathology, Ibn Rochd University Hospital Center.  IHC was carried out in all the samples and those with a score of 2+ were also analyzed using FISH. We extracted mRNA from FFPE samples and performed RT-qPCR, and the results were compared with those obtained using IHC/FISH. HER2 mRNA levels were quantified and normalized using the reference genes RPL30 and RPL37, based on our earlier reports.

RESULTS

HER2 cut-off value was fixed at 11.954 corresponding to the combination of the best sensitivity and specificity (93.4% and 100%) respectively, and with positive predictive values PPV that reached 100% and a negative predictive value NPV that reached 89.4%. The results showed 100% concordance with FISH. The Kappa coefficient was 0.863 which indicated concordance with IHC. The area under the curve (AUC) which is an important parameter that determines the diagnostic accuracy of the test was calculated as AUC=0.955. The results were comparable to some of the recent studies published in a similar direction.

CONCLUSION

Our study shows that one-step RT-qPCR-based quantitation is an accurate and reproducible test to record HER2 gene expression for a better treatment orientation focusing on maximal therapeutic and survival outcome.

Prediction of Receptor Status in Radiomics: Recent Advances in Breast Cancer Research

Breast cancer is a multifactorial heterogeneous disease and the leading cause of cancer-related deaths in women; its diagnosis and treatment require clinical sensitivity and a comprehensive disciplinary research approach. The expression of different receptors on tumor cells not only provides the basis for molecular typing of breast cancer but also has a decisive role in the diagnosis, treatment, and prognosis of breast cancer. To date, immunohistochemistry (IHC), which uses invasive histological sampling, has been extensively used in clinical practice to analyze the status of receptors and to make an accurate diagnosis of breast cancer. As an invasive assay, IHC can provide important biological information on tumors at a single point in time, but cannot predict future changes (due to treatment or tumor mutations) without additional invasive procedures. These issues highlight the need to develop a non-invasive method for predicting receptor status. The emerging field of radiomics may offer a non-invasive approach to identification of receptor status without requiring biopsy. In this paper, we present a review of the latest research results in radiomics for predicting the status of breast cancer receptors, with potential important clinical applications.

Diverse applications and development of aptamer detection technology

Aptamers have received extensive attention in recent years because of their advantages of high specificity, high sensitivity and low immunogenicity. Aptamers can perform almost all functions of antibodies through the combination of spatial structure and target, which are called "chemical antibodies". At present, aptamers have been widely used in cell imaging, new drug development, disease treatment, microbial detection and other fields. Due to the diversity of modifications, aptamers can be combined with different detection technologies to construct aptasensors. This review focuses on the diversity of aptamers in the field of detection and the development of aptamer-based detection technology and proposes new challenges for aptamers in this field.

Clinical-radiomics nomogram for identifying HER2 status in patients with breast cancer: A multicenter study

Purpose

To develop and validate a clinical-radiomics nomogram based on radiomics features and clinical risk factors for identification of human epidermal growth factor receptor 2 (HER2) status in patients with breast cancer (BC).

Methods

Two hundred and thirty-five female patients with BC were enrolled from July 2018 to February 2022 and divided into a training group (from center I, 115 patients), internal validation group (from center I, 49 patients), and external validation group (from centers II and III, 71 patients). The preoperative MRI of all patients was obtained, and radiomics features were extracted by a free open-source software called 3D Slicer. The Least Absolute Shrinkage and Selection Operator regression model was used to identify the most useful features. The radiomics score (Rad-score) was calculated by using the radiomics signature-based formula. A clinical-radiomics nomogram combining clinical factors and Rad-score was developed through multivariate logistic regression analysis. The performance of the nomogram was evaluated using receiver operating characteristic (ROC) curve and decision curve analysis (DCA).

Results

A total of 2,553 radiomics features were extracted, and 21 radiomics features were selected as the most useful radiomics features. Multivariate logistic regression analysis indicated that Rad-score, progesterone receptor (PR), and Ki-67 were independent parameters to distinguish HER2 status. The clinical-radiomics nomogram, which comprised Rad-score, PR, and Ki-67, showed a favorable classification capability, with AUC of 0.87 [95% confidence internal (CI), 0.80 to 0.93] in the training group, 0.81 (95% CI, 0.69 to 0.94) in the internal validation group, and 0.84 (95% CI, 0.75 to 0.93) in the external validation group. DCA illustrated that the nomogram was useful in clinical practice.

Conclusions

The nomogram combined with Rad-score, PR, and Ki-67 can identify the HER2 status of BC.

Investigation of promoter methylation patterns association with genes expression profile of ISL1, MGMT and DMNT3b in tissue of breast cancer patients

BACKGROUND AND OBJECTIVES

Cancer initiation and progression could influenced by both genetic and epigenetic events revealing of the overlap between epigenetic and genetic alteration can give important insights into cancer biology.

METHODS AND RESULTS

In this experiment ISL1, MGMT, DMNT3b genes were candidate to investigate both methylation status and expression profile by using methylation-specific PCR and real time PCR in 40 breast cancer patients, respectively, also we have assessed relation of the promoter methylation status and expression variation of the target genes. The mean level of methylation of ISL1 and MGMT in tumor tissues were significantly greater than normal tissues. In Contrast, DMNT3b gene was showed lower mean level of methylation in tumor tissue compared to normal tissues, however, this was not statistically significant. Relative expression analysis was displayed a significant reduction in expression level of ISL1 and MGMT in tumor tissues. Furthermore, there was a meaningful association between down expression of ISL1 with histological grade, Her2 and ER status. Moreover, MGMT down expression was significantly associated with tumor sizes. Any remarkable relation was not observed between DMNT3b expression level and clinic pathological features. At the end, significant relation between methylation status and expression level has been revealed.

CONCLUSIONS

In this study all observed results were exactly in line with the results were obtained from articles which were based on the methylation research and illustrate that the real-time PCR and methylation methods are in correlated with each other, furthermore, selected genes are capable to use as a potential biomarkers, however, more research on extended cases are needed.

Combined diagnosis of breast cancer in the early stage by MRI and detection of gene expression

Breast cancer is one of the most common cancer types in humans. Magnetic resonance imaging (MRI) is an efficient method for the detection of human breast cancer. However, the efficacy of MRI in detecting breast cancer in the early stage requires to be improved. The present study investigated the diagnostic efficacy of a combination of MRI and detection of gene expression in patients with breast cancer in the early stage. The gene expression levels of Ki-67, BCL11A, FOXC1, HOXD13, PCDHGB7 and her-2 were used as an auxiliary diagnostic index for patients with breast cancer in the early stage. Higher expression levels of TPA and C2erbB22 were observed in tumor tissue obtained from diagnostic biopsy and determined by immunohistochemistry, which indicated a higher risk of breast cancer in a total of 84 participants. Diagnostic data revealed that combination MRI and detection of gene expression had a significantly higher diagnostic rate (66/84) in diagnosing breast cancer in an early stage compared with either MRI (78/360) or detection of gene expression (72/84; P<0.01). It was indicated that the combination of MRI and detection of gene expression had a higher diagnostic rate (94.5%) than either MRI (81.4%) or detection of gene expression (75.5%). Histological analysis confirmed the diagnosis determined by MRI and detection of gene expression. These results suggest that the combination of MRI and detection of gene expression may be a potential diagnostic method for assessing patients with early-stage breast cancer.

Black rice-derived anthocyanins inhibit HER-2-positive breast cancer epithelial-mesenchymal transition-mediated metastasis in vitro by suppressing FAK signaling

This study aimed to investigate the role of focal adhesion kinase (FAK) signaling in the inhibitory effects of black rice anthocyanins (BRACs) on human epidermal growth factor receptor-2 (HER-2)-positive human breast cancer cell metastasis, using the MCF-10A, MCF-7 and MDA-MB-453 cells. BRACs exerted an anti-metastatic effect on the HER-2-positive breast cancer cells. The effects of BRACs on the proliferation of the MDA-MB-453 cells were examined by cell counting kit-8 assay. A wound-healing assay was used to examine the effects of BRACs on the migration of the breast cancer cells. BRACs interrupted migration and invasion. BRACs decreased the migration distance of the HER-2-positive human breast cancer cells, MDA-MB-453, by 37% compared with the cells in the untreated group. They also reduced the number of invading MDA-MB-453 cells by 68%. In addition, BRACs exerted an inhibitory effect on epithelial-mesenchymal transition. Western blot analysis revealed that BRACs decreased the phosphorylation of FAK, cSrc and p130^Cas. The FAK inhibitor, Y15, was also used to further evaluate the role of FAK signaling in the anti-metastatic effects of BRACs on MDA-MB-453 cells. The results of western blot analysis revealed that BRACs increased the expression of the epithelial marker, E-cadherin, and decreased the expression of the mesenchymal markers, fibronectin and vimentin, in the MDA-MB-453 cells. In addition, BRACs decreased the interaction between HER-2 and FAK, FAK and cSrc, cSrc and p130^Cas, and between FAK and p130^Cas. These results suggest that BRACs suppress the metastasis of HER-2-positive breast cancer in vitro, and that the cSrc/FAK/p130^Cas pathway plays a vital role in this inhibitory effect.

Chromogenic in situ Hybridization Compared with Real time Quantitative Polymerase Chain Reaction to Evaluate HER2/neu Status in Breast Cancer

BACKGROUND AND OBJECTIVE

The assessment of human epidermal growth factor receptor 2 (HER2) status has become of great importance in the diagnosis of breast cancer. The aim of this study was to investigate the diagnostic value of quantitative Polymerase Chain Reaction (qPCR) and Chromogenic In Situ Hybridization (CISH) to assess HER2 status of biopsy specimens.

METHODS

To elucidate the status of HER2 gene amplification, biopsies of breast carcinoma from 120 patients with 2+ IHC status were analyzed by qPCR and CISH.

RESULTS

The results of the two experiments were compared, and it was depicted that the concordance rate between CISH and qPCR assays was 88.1%.The quantification of HER2 gene with CISH and qPCR showed that there was a significant correlation (p value= 0.0001 and r= 0.808).

CONCLUSION

The results of this research support the idea that qPCR is a precise and reproducible technique, which can be employed as a supplementary method to evaluate HER2 status.

Quantitative real-time polymerase chain reaction is an alternative method for the detection of HER-2 amplification in formalin-fixed paraffin-embedded breast cancer samples

Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) are the most common methods that are used to quantify HER-2 gene and protein levels, respectively, in human breast cancer. However, due to bad sample quality, some samples are unable to be subjected to a FISH assay. We evaluated 71 formalin-fixed paraffin-embedded (FFPE) breast carcinoma specimens by quantitative real-time polymerase chain reaction (qPCR), IHC, and FISH. We also performed qPCR and FISH assays on delayed formalin-fixed (DDF) samples. The qPCR results were in complete concordance with the results of IHC and FISH. In regards to the DDF samples, the HER-2 fluorescent signal seemed decayed compared with that of the DDF samples after 1 h. However, the qPCR method still works well up to 12 hours. Our results indicated that qPCR was obviously superior to FISH in cases that were not fixed in a reasonable amount of time. However, qPCR can be an alternative method by which to perform HER2 amplification assays in breast cancer.

FGFR2 Assessment in Gastric Cancer Using Quantitative Real-Time Polymerase Chain Reaction, Fluorescent In Situ Hybridization, and Immunohistochemistry

OBJECTIVES

Fibroblast growth factor receptor 2 (FGFR2) amplification has been reported to be a target for treatment in gastric cancer. However, an optimal tissue source and method for evaluating FGFR2 have yet to be established.

METHODS

Copy numbers were compared by quantitative polymerase chain reaction (qPCR) using frozen vs formalin-fixed, paraffin-embedded (FFPE) tissue and biopsy vs surgical specimens. We correlated the results of qPCR and immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) using stage IV gastric cancer biopsy specimens and validated the results in surgical specimens.

RESULTS

FFPE tissues were suitable for qPCR, and biopsy specimens were equivalent to or better than surgical specimens. qPCR and IHC results exhibited an excellent correlation with FISH at eight or more copies by qPCR in any kind of tissue, 5% or more by IHC in biopsy specimens, and 10% or more by IHC in surgical specimens. FGFR2 amplification was 6.6% in stage IV gastric cancers, and 42% of these showed heterogeneous amplification and overexpression. IHC indicated a good correlation with FISH even in the heterogeneous cases.

CONCLUSIONS

FFPE biopsy tissues are an adequate source for FGFR2 evaluation in gastric carcinomas, and a qPCR-based copy number assay can be used for screening. IHC is also a valid and practical method for evaluating FGFR2, considering frequent heterogeneity.

Clinicopathological variables predicting HER-2 gene status in immunohistochemistry-equivocal (2+) invasive breast cancer

BACKGROUND AND OBJECTIVE

Human epidermal growth factor receptor-2 (HER-2) gene status is crucial to guide treatment decisions regarding the use of HER-2-targeted therapies in breast cancer. An invasive breast cancer with HER-2 2+ score is regarded as HER-2 status equivocal and should further determine by fluorescent in situ hybridization (FISH), which is considered the standard test for HER-2 status. Here, we aimed to establish a risk score to allow for prediction of the presence of HER-2 gene status.

METHODS

A total of 182 HER-2 2+ by immunohistochemistry (IHC) invasive breast cancer cases were enrolled in this study. The association between clinicopathological variables like age, sex, tumor grade, hormone receptor (HR) status, P53 and proliferation index (Ki67), and FISH result using US Food and Drug Administration (FDA) criteria was evaluated. Also, we compared the HER-2 FISH results using FDA criteria and 2013 American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guideline.

RESULTS

The study population had a median age of 48 years (range, 29-78 years). Estrogen receptor (ER) was expressed in 131 (72.0%) patients. 73.1% of patients (133/182) were progesterone receptor (PR) positive. The median Ki67 value was 20% (range, 3-90%). There was good agreement between the FDA and 2013 ASCO/CAP guideline. Sixty-three of all patients were HER-2 FISH amplified (positive) based on FDA criteria. Tumors with HER-2 amplified were more likely to harbor ER negative (58.8% vs. 25.2%, P<0.001) or PR negative (57.1% vs. 26.3%, P<0.001) or P53 negative (44.8% vs. 29.8%, P=0.048). A significant high level of Ki67 was detected in HER-2 amplified groups (P=0.006). We created a risk score that comprised HR, P53 and Ki67. A significant association between risk score and HER-2 FISH amplification was observed (χ(2)=30.41, P<0.001).

CONCLUSIONS

This novel immunohistochemical risk score could be highly useful to predict the presence of HER-2 gene status in invasive breast cancer.

Expression of PIK3CA, PTEN mRNA and PIK3CA mutations in primary breast cancer: association with lymph node metastases

Purpose

High activity of the intracellular phosphatidylinositol-3 kinase (PI3K) pathway is common in breast cancer. Here, we explore differences in expression of important PI3K pathway regulators: the activator, phosphatidylinositol-3-kinase catalytic subunit alpha (PIK3CA), and the tumour suppressor, phosphatase and tensin homolog (PTEN), in breast carcinoma tissue and normal breast tissue. Furthermore, we examine whether expression of PIK3CA and PTEN mRNA and occurrence of PIK3CA mutations are associated with lymph node metastases in patients with primary breast cancer.

Methods

Paired tissue samples of breast carcinoma and normal breast tissue were obtained from 175 breast cancer patients at the time of primary surgery, of these 105 patients were lymph node positive. Expression of PIK3CA and PTEN mRNA was quantified with Quantitative Real Time PCR. Somatic mutations in exon 9 and exon 20 of the PIK3CA gene were identified by genotyping.

Results

Both PIK3CA and PTEN mRNA expression was significantly increased in breast carcinoma tissue compared to normal breast tissue (p = 2 × 10^-11) and (p < 0.001), respectively. PIK3CA mutations were present in 68 out of 175 patients (39%), but were not associated with PIK3CA expression (p = 0.59). Expression of PIK3CA and PTEN mRNA, and PIK3CA mutations in breast carcinomas were not associated with presence of lymph node metastases.

Conclusions

The expression of PTEN and PIK3CA mRNA is increased in breast carcinoma tissue compared to normal breast tissue, and PIK3CA mutations are frequent in primary breast carcinoma, however these factors were not associated with lymph node metastases.

Electronic supplementary material

The online version of this article (doi:10.1186/2193-1801-2-464) contains supplementary material, which is available to authorized users.

Detection of tumor cell-specific mRNA in the peripheral blood of patients with breast cancer—evaluation of several markers with real-time reverse transcription-PCR

It is widely known that cells from epithelial tumors, e.g., breast cancer, detach from their primary tissue and enter blood circulation. We show that the presence of circulating tumor cells (CTCs) in samples of patients with primary and metastatic breast cancer can be detected with an array of selected tumor-marker-genes by reverse transcription real-time PCR. The focus of the presented work is on detecting differences in gene expression between healthy individuals and adjuvant and metastatic breast cancer patients, not an accurate quantification of these differences. Therefore, total RNA was isolated from blood samples of healthy donors and patients with primary or metastatic breast cancer after enrichment of mononuclear cells by density gradient centrifugation. After reverse transcription real-time PCR was carried out with a set of marker genes (BCSP, CK8, Her2, MGL, CK18, CK19). B2M and GAPDH were used as reference genes. Blood samples from patients with metastatic disease revealed increased cytokine gene levels in comparison to normal blood samples. Detection of a single gene was not sufficient to detect CTCs by reverse transcription real-time PCR. Markers used here were selected based on a recent study detecting cancer cells on different protein levels. The combination of such a marker array leads to higher and more specific discovery rates, predominantly in metastatic patients. Identification of CTCs by PCR methods may lead to better diagnosis and prognosis and could help to choose an adequate therapy.