Genomics and circulating tumor cells: promising tools for choosing and monitoring adjuvant therapy in patients with early breast cancer?

A high-throughput test enables specific detection of hepatocellular carcinoma

High-throughput tests for early cancer detection can revolutionize public health and reduce cancer morbidity and mortality. Here we show a DNA methylation signature for hepatocellular carcinoma (HCC) detection in liquid biopsies, distinct from normal tissues and blood profiles. We developed a classifier using four CpG sites, validated in TCGA HCC data. A single F12 gene CpG site effectively differentiates HCC samples from other blood samples, normal tissues, and non-HCC tumors in TCGA and GEO data repositories. The markers were validated in a separate plasma sample dataset from HCC patients and controls. We designed a high-throughput assay using next-generation sequencing and multiplexing techniques, analyzing plasma samples from 554 clinical study participants, including HCC patients, non-HCC cancers, chronic hepatitis B, and healthy controls. HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC. Implementing this assay for high-risk individuals could significantly decrease HCC morbidity and mortality.

The signature of liver cancer in immune cells DNA methylation

Background

The idea that changes to the host immune system are critical for cancer progression was proposed a century ago and recently regained experimental support.

Results

Herein, the hypothesis that hepatocellular carcinoma (HCC) leaves a molecular signature in the host peripheral immune system was tested by profiling DNA methylation in peripheral blood mononuclear cells (PBMC) and T cells from a discovery cohort (n = 69) of healthy controls, chronic hepatitis, and HCC using Illumina 450K platform and was validated in two validation sets (n = 80 and n = 48) using pyrosequencing.

Conclusions

The study reveals a broad signature of hepatocellular carcinoma in PBMC and T cells DNA methylation which discriminates early HCC stage from chronic hepatitis B and C and healthy controls, intensifies with progression of HCC, and is highly enriched in immune function-related genes such as PD-1, a current cancer immunotherapy target. These data also support the feasibility of using these profiles for early detection of HCC.

A Noninvasive and Real-Time Method for Circulating Tumor Cell Detection by In Vivo Flow Cytometry

The quantification of circulating tumor cells (CTCs) has been considered a potentially powerful tool in cancer diagnosis and prognosis, as CTCs have been shown to appear very early in cancer development. Great efforts have been made to develop methods that were less invasive and more sensitive to detect CTCs earlier. There is growing evidence that CTC clusters have greater metastatic potential than single CTCs. Therefore, the detection of CTC clusters is also important. This chapter is aimed to introduce a noninvasive technique for CTCs detection named in vivo flow cytometry (IVFC), which has been demonstrated to be capable of monitoring CTCs dynamics continuously. Furthermore, IVFC could be helpful for CTC cluster enumeration.

On the identification of circulating tumor cells in breast cancer

Breast cancer is a highly heterogeneous disease and very common among western women. The main cause of death is not the primary tumor but its metastases at distant sites, such as lymph nodes and other organs (preferentially lung, liver, and bones). The study of circulating tumor cells (CTCs) in peripheral blood resulting from tumor cell invasion and intravascular filtration highlights their crucial role concerning tumor aggressiveness and metastasis. Genomic research regarding CTCs monitoring for breast cancer is limited due to the lack of indicative genes for their detection and isolation. Instead of direct CTC detection, in our study, we focus on the identification of factors in peripheral blood that can indirectly reveal the presence of such cells. Using selected publicly available breast cancer and peripheral blood microarray datasets, we follow a two-step elimination procedure for the identification of several discriminant factors. Our procedure facilitates the identification of major genes involved in breast cancer pathology, which are also indicative of CTCs presence.

The challenge of gene expression profiling in heterogeneous clinical samples

Almost all samples used in tumor biology, such as tissues and bodily fluids, are heterogeneous, i.e., consist of different cell types. Evaluating the degree of heterogeneity in samples can increase our knowledge on processes such as clonal selection and metastasis. In addition, generating expression profiles from specific sub populations of cells can reveal their distinct functions. Tissue heterogeneity also poses a challenge, as it can confound the interpretation of gene expression data. This chapter will (1) give a brief overview on how heterogeneity may influence gene expression profiling data and (2) describe the methods that are currently available to assess transcriptional biomarkers in a heterogeneous cell population.

3D microfilter device for viable circulating tumor cell (CTC) enrichment from blood

Detection of circulating tumor cells has emerged as a promising minimally invasive diagnostic and prognostic tool for patients with metastatic cancers. We report a novel three dimensional microfilter device that can enrich viable circulating tumor cells from blood. This device consists of two layers of parylene membrane with pores and gap precisely defined with photolithography. The positions of the pores are shifted between the top and bottom membranes. The bottom membrane supports captured cells and minimize the stress concentration on cell membrane and sustain cell viability during filtration. Viable cell capture on device was investigated with scanning electron microscopy, confocal microscopy, and immunofluorescent staining using model systems of cultured tumor cells spiked in blood or saline. The paper presents and validates this new 3D microfiltration concept for circulation tumor cell enrichment application. The device provides a highly valuable tool for assessing and characterizing viable enriched circulating tumor cells in both research and clinical settings.

Phenotypic and genetic characterization of circulating tumor cells by combining immunomagnetic selection and FICTION techniques

The presence of circulating tumor cells (CTCs) in breast cancer patients has been proven to have clinical relevance. Cytogenetic characterization of these cells could have crucial relevance for targeted cancer therapies. We developed a method that combines an immunomagnetic selection of CTCs from peripheral blood with the fluorescence immunophenotyping and interphase cytogenetics as a tool for investigation of neoplasm (FICTION) technique. Briefly, peripheral blood (10 ml) from healthy donors was spiked with a predetermined number of human breast cancer cells. Nucleated cells were separated by double density gradient centrifugation of blood samples. Tumor cells (TCs) were immunomagnetically isolated with an anti-cytokeratin antibody and placed onto slides for FICTION analysis. For immunophenotyping and genetic characterization of TCs, a mixture of primary monoclonal anti-pancytokeratin antibodies was used, followed by fluorescent secondary antibodies, and finally hybridized with a TOP2A/HER-2/CEP17 multicolor probe. Our results show that TCs can be efficiently isolated from peripheral blood and characterized by FICTION. Because genetic amplification of TOP2A and ErbB2 (HER-2) in breast cancer correlates with response to anthracyclines and herceptin therapies, respectively, this novel methodology could be useful for a better classification of patients according to the genetic alterations of CTCs and for the application of targeted therapies.

Adjuvant chemotherapy--yes or no? Prognostic markers in early breast cancer

The question of whether to offer adjuvant chemotherapy to patients with early-stage breast cancer continues to challenge clinicians on a daily basis. Many patients with node-negative or low-risk breast cancer could be spared the trauma of receiving chemotherapy, but more reliable prognostic markers are still needed to aid our therapy decision making. Gene expression profiling is a welcome product of the 'omic' era and several multi-gene expression panels ('signatures') have now been developed that show promise in predicting which breast cancer patients are likely to develop metastatic disease if adjuvant chemotherapy is not administered. The value of gene expression profiling as a prognostic tool in clinical practice is currently being appraised more fully in two large, prospective, randomised studies--TAILORx and MINDACT. These studies should provide level I evidence of the prognostic power of gene expression profiling and will hopefully allow us to one day quantify risk of progression in the individual patient and tailor treatment accordingly. Genetic profiling of circulating tumour cells and micrometastases should further enhance our understanding of breast cancer biology and allow us to personalise therapy based on functional maps of critical tumour pathways. Close collaboration between clinicians and scientists will be essential to achieve this goal.

Silencing of prion protein sensitizes breast adriamycin-resistant carcinoma cells to TRAIL-mediated cell death

We investigated the relationship between the resistance to the proapoptotic action of tumor necrosis factor-related apoptosis inducing ligand (TRAIL) and cellular prion protein (PrPc) function, using the TRAIL-sensitive MCF-7 human breast adenocarcinoma cell line and two TRAIL-resistant sublines: 2101 and MCF-7/ADR. All of the cell lines tested expressed TRAIL-R1 and TRAIL-R2. TRAIL decoy receptors were not detected, suggesting that the resistance of 2101 and MCF-7/ADR cells, strongly expressing PrPc, to TRAIL-mediated cell death was independent from the expression of TRAIL receptors and death-inducing signaling complex formation. Down-regulation of PrPc by small interfering RNA increased the sensitivity of Adriamycin- and TRAIL-resistant cells to TRAIL, but not to epirubicin/Adriamycin. TRAIL-mediated apoptosis in PrPc knocked-down cells was associated with caspase processing, Bid cleavage, and Mcl-1 degradation. In addition, an increased sensitivity of apoptosis-resistant cells to TRAIL after PrPc silencing was not associated with the increased recruitment of receptors and intracellular signaling molecule to the death-inducing signaling complex. Bcl-2 expression was substantially decreased after PrPc knock-down but the levels of Bcl-X(L) and Mcl-1 were not affected. The down-regulation of Bcl-2 was concomitant with Bax delocalization. Our findings support the notion that silencing of PrPc facilitates the activation of proapoptotic Bax by down-regulation of Bcl-2 expression, thereby abolishing the resistance of breast cancer cells to TRAIL-induced apoptosis.

Membrane microfilter device for selective capture, electrolysis and genomic analysis of human circulating tumor cells

This paper presents development of a parylene membrane microfilter device for single stage capture and electrolysis of circulating tumor cells (CTCs) in human blood, and the potential of this device to allow genomic analysis. The presence and number of CTCs in blood has recently been demonstrated to provide significant prognostic information for patients with metastatic breast cancer. While finding as few as five CTCs in about 7.5mL of blood (i.e., 10(10) blood cells in) is clinically significant, detection of CTCs is currently difficult and time consuming. CTC enrichment is performed by either gradient centrifugation of CTC based on their buoyant density or magnetic separation of epithelial CTC, both of which are laborious procedures with variable efficiency, and CTC identification is typically done by trained pathologists through visual observation of stained cytokeratin-positive epithelial CTC. These processes may take hours, if not days. Work presented here provides a micro-electro-mechanical system (MEMS)-based option to make this process simpler, faster, better and cheaper. We exploited the size difference between CTCs and human blood cells to achieve the CTC capture on filter with approximately 90% recovery within 10 min, which is superior to current approaches. Following capture, we facilitated polymerase chain reaction (PCR)-based genomic analysis by performing on-membrane electrolysis with embedded electrodes reaching each of the individual 16,000 filtering pores. The biggest advantage for this on-membrane in situ cell lysis is the high efficiency since cells are immobilized, allowing their direct contact with electrodes. As a proof-of-principle, we show beta actin gene PCR, the same technology can be easily extended to real time PCR for CTC-specific transcript to allow molecular identification of CTC and their further characterization.

Molecular screening for breast cancer prevention, early detection, and treatment planning: combining biomarkers from DNA, RNA, and protein

The completion of the human genome project, along with the ancillary technologies derived from this effort, provides the ability to comprehensively analyze patient tumors as well as the individual patient's own genetic make-up at the DNA, RNA, and protein level. As a result, novel molecular screening techniques have the potential to push the boundaries of detection to even smaller tumors and also to allow accurate risk assessment, cancer prevention, and treatment planning in individual women. This review focuses on advances over the past 2 years in the use of molecular signatures and circulating tumor cells for early breast cancer detection and for prediction of response to therapy.

The utility of peripheral thyrotropin mRNA in the diagnosis of follicular neoplasms and surveillance of thyroid cancers

BACKGROUND

Thyroid cells in peripheral circulation express uniquely thyrotropin receptor (TSHR) mRNA, and their detection may aid thyroid cancer management.

METHODS

Since 2002, 258 patients had prospective TSHR mRNA measurement by quantitative RT-PCR from peripheral blood before and/or after thyroidectomy. Thyroid cancer detection was assessed from known clinical diagnostic criteria and mRNA for patients with follicular neoplasms (n = 64) and long-term cancer follow-up (n = 13).

RESULTS

Adding TSHR mRNA to fine-needle aspiration biopsy (FNAB) maintained high sensitivity (90%) but improved specificity (73%) for thyroid cancer diagnosis. When FNAB specimens indicated follicular neoplasm, a decision algorithm combining TSHR mRNA and abnormal thyroid ultrasound features correctly diagnosed all cancer patients (100% sensitivity) and would have spared operation for benign disease in 38%. Elevated TSHR mRNA on postoperative day 1 predicted persistent/recurrent cancer. During long-term thyroid cancer surveillance, TSHR mRNA had a 91% concordance with radioactive iodine whole body scan (WBS)-detectable disease, agreed with thyroglobulin (Tg) levels in 64% of patents, missed disease in 5%, but was more sensitive to detecting disease than Tg levels in 31% of patients, including all patients with Tg antibodies.

CONCLUSIONS

Detecting circulating thyroid cancer cells is useful for initial thyroid cancer diagnosis and postoperatively predicts recurrent cancer. This novel test promises to enhance thyroid cancer patient care by management algorithms that combine histologic, genomic, and clinical criteria.

Prognostic Significance of Disseminated Tumor Cells as Detected by Quantitative Real-Time Reverse-Transcriptase Polymerase Chain Reaction in Patients with Breast Cancer

BACKGROUND

In this study we have validated the feasibility of detecting disseminated tumor cells (DTC) by real-time reverse-transcriptase polymerase chain reaction (RT-PCR) analysis. Bone marrow samples from a large cohort of patients with breast cancer were analyzed for the presence of DTC by immunocytochemistry (ICC) or a molecular-based method.

PATIENTS AND METHODS

Bone marrow samples were collected from 170 patients with breast cancer with stage I-IV disease before the initiation of any local or systemic treatment. Staining for cytokeratin (CK)-positive cells was performed with the Epimet kit. Disseminated tumor cells were also quantified by measuring relative gene expression for CK19 and mammaglobin (MAM) using a quantitative RT-PCR detection method. The mean follow-up time was 30 months. Kaplan-Meier analysis was used for predicting overall survival.

RESULTS

Despite an excellent quantitative correlation and qualitative concordance between ICC and RT-PCR, survival analysis suggested an improved prognostic significance of DTC as detected by quantitative RT-PCR. Univariate survival analysis computed a relative risk of death of 2.87 for women with ICC-positive cells in the bone marrow, as compared with those without positive cells. The relative risk for women with RT-PCR-positive bone marrow was even higher: 3.5 (CK19) and 3.39 (MAM). In multivariate analysis, bone marrow CK19 was a stronger prognostic factor than bone marrow ICC.

CONCLUSION

Reverse-transcriptase polymerase chain reaction-detected DTC is shown to be prognostically significant in untreated patients with breast cancer. Furthermore, it seems to be a more sensitive method for detecting DTC in bone marrow samples when compared with ICC.