Liquid biopsy by NGS: Differential presence of exons (DPE) is related to metastatic potential in a colon-cancer model in the rat

Differential presence of exons (DPE) is a method of interpretation of exome sequencing, which has been proposed to design a predictive algorithm with clinical value in patients with colorectal cancer (CRC). The goal of the present study was to examine the reproducibility in a rat model of metastatic colon cancer. DHD/K12-TRb cells were injected in syngenic immunocompetent BD-IX rats. Cells were from two stocks with low and normal metastatic potential, and injected into two separate groups of rats. Five to ten weeks after injection, blood samples were taken prior euthanasia and whole exome sequencing performed. Through DPE analysis, we identified a set of exons whose differential presence in plasma allowed us to compare both groups of tumor-bearing animals. A verification test was performed to confirm that the algorithm was able to classify extracted samples into their corresponding groups of origin. The highest mean probability was 0.8954. In conclusion, the DPE analysis in tumor-bearing animals was able to discriminate between different disease status, which fully supports previous results in CRC patients.

Potential clinical significance of perioperative levels of mRNA in plasma from patients with cancer of the larynx or hypopharynx

BACKGROUND

The use of plasma as a "liquid biopsy" has gained increasing attention. The purpose of the present study was to evaluate the diagnostic and prognostic utility of the perioperative detection and quantitation of mRNAs encoding human telomerase reverse transcriptase (hTERT) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in plasma from patients with cancer of the larynx or hypopharynx.

METHODS

We recruited 47 patients with laryngeal cancer and 2 patients with hypopharyngeal cancer, plus 27 healthy subjects. A blood sample was taken from each patient before and after surgical resection of the tumor. We quantified hTERT mRNA and GAPDH mRNA in plasma by real-time polymerase chain reaction (PCR).

RESULTS

Detection of hTERT mRNA before surgery had diagnostic value (sensitivity, 22%; specificity, 100%). Detection was more frequent in patients with supraglottic tumors than glottic tumors (p = .02) and was related to subsequent recurrence (p = .02). Preoperative levels of hTERT mRNA in plasma were higher in patients with subsequent recurrence (p = .046) and/or metastases (p = .047). The disease-free survival (DFS) and overall survival (OS) of patients with plasma samples positive for hTERT mRNA was poorer than that of patients with negative samples. Mean levels of plasma GAPDH mRNA in untreated patients were higher than in healthy subjects (p < .001).

CONCLUSION

Detection and quantitation of hTERT and GAPDH mRNA in patients' plasma might be clinically significant in cases of laryngeal and hypopharyngeal cancer. © 2017 Wiley Periodicals, Inc. Head Neck 39: 647-655, 2017.

Abstract P3-14-11: Gene-expression analyses identify altered transcription factors and supports the antitumor activity of novel bromodomain inhibitors in triple negative breast cancer

Introduction: Identification of novel therapeutic targets in triple negative breast cancer (TNBC) is a main goal. In silico evaluation of human tumors by gene expression analyses can identify functions that could be pharmacologically inhibited. BET bromodomain inhibitors are a new family of compounds that reduce activity of oncogenic transcription factors through the inhibition of bromodomains.

Material and methods: We performed gene expression and functional analyses comparing triple negative tumors with normal breast samples. RT-PCR was used to evaluate genes down-regulated by treatment with the BET bromodomain inhibitors JQ1 and OTOX15 at different time points in MDA-MB231 cells. Cell proliferation and colony growth was measured by MTT uptake and 3D growth in matrigel in a panel of cell lines including HS578T, BT549, MDA-MB231 and HCC3153 treated with JQ1 and OTOX15. Evaluation of apoptosis and cell cycle was performed by flow cytometry using Annexin V and propidium iodide, respectively. Western-blot was used for evaluation of protein expression. Xenografted animals were used for the assessment of the in vivo activity of JQ1.

Results: Gene expression analyses identified upregulated genes including a number of transcription factors. These genes were more expressed in MDA-MB231 compared with MCF-10A. Treatment with JQ1 reduced the expression of some transcription factors at different time points. JQ1 and OTX015 reduced proliferation and cell growth in a panel of triple negative cell lines. They also led to arrest at the G0/G1 phase in HS578T and MDA-MB231 at 12 and 24 hours; that was confirmed by the biochemical evaluation of cell cycle mediators. An induction of apoptosis was observed at 48 hours in HS578T. JQ1 at 50 mg/kg daily reduced tumor growth in MDA-MB231 xenografted in nude mice.

Conclusion: Gene-expression profiling identified upregulated transcription factors in triple negative tumors compared with normal breast human samples. BET bromodomain inhibitors reduced the expression of some of these genes in cellular models. JQ1 shows clear antitumor activity in vitro and in vivo.

Citation Format: Ocana A, Perez-Peña J, Serrano-Heras G, Corrales-Sanchez V, Montero JC, Gascón-Escribano MJ, Picazo MG, García-Olmo DC, Martin M, Pandiella A. Gene-expression analyses identify altered transcription factors and supports the antitumor activity of novel bromodomain inhibitors in triple negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-14-11.

Quantitation of cell-free DNA and RNA in plasma during tumor progression in rats

BACKGROUND

To clarify the implications of cell-free nucleic acids (cfNA) in the plasma in neoplastic disease, it is necessary to determine the kinetics of their release into the circulation.

METHODS

To quantify non-tumor and tumor DNA and RNA in the plasma of tumor-bearing rats and to correlate such levels with tumor progression, we injected DHD/K12-PROb colon cancer cells subcutaneously into syngenic BD-IX rats. Rats were sacrificed and their plasma was analyzed from the first to the eleventh week after inoculation.

RESULTS

The release of large amounts of non-tumor DNA into plasma was related to tumor development from its early stages. Tumor-specific DNA was detected in 33% of tumor-bearing rats, starting from the first week after inoculation and at an increasing frequency thereafter. Animals that were positive for tumor DNA in the plasma had larger tumors than those that were negative (p = 0.0006). However, the appearance of both mutated and non-mutated DNA fluctuated with time and levels of both were scattered among individuals in each group. The release of non-tumor mRNA was unaffected by tumor progression and we did not detect mutated RNA sequences in any animals.

CONCLUSIONS

The release of normal and tumor cfDNA into plasma appeared to be related to individual-specific factors. The contribution of tumor DNA to the elevated levels of plasma DNA was intermittent. The release of RNA into plasma during cancer progression appeared to be an even more selective and elusive phenomenon than that of DNA.

Pneumonectomy in isoflurane-anesthetized rats without tracheal intubation: an experimental model

INTRODUCTION

A few models for pneumonectomy in rats have been described, and in most of these, anesthesia includes orotracheal intubation, which increases morbidity and mortality and also adds technical complexity. Models without tracheal intubation but with injectable anesthesia are difficult to reproduce, however, and lead to a lengthy postoperative-recovery period with high morbidity and mortality rates.

OBJECTIVE

The objective of this study was to describe a simple, safe, and effective experimental model for pneumonectomy in rats without tracheal intubation.

MATERIALS AND METHODS

A left-sided pneumonectomy was performed on 26 Sprague-Dawley rats anesthetized by isoflurane applied via a mask without tracheal intubation. To avoid dangerous traction movements, the lung pedicle was ligated en bloc using clips.

RESULTS AND DISCUSSION

No rat demonstrated cardiorespiratory depression. Of the 26 rats, 1 was dehydrated and had lost more than 10% of its body weight, resulting in death on the third day after surgery. Total mortality was therefore 3.8%. Mean (standard deviation [SD]) anesthesia duration was 9.8 (1.0) minutes, surgery time was 3.0 (0.6) minutes, and open pneumothorax time was 1.2 (0.3) minutes. Mean (SD) weight loss during the early postoperative period was 4.5% (3.5%). These results were more satisfactory than results obtained using ketamine mixtures as anesthetic agents (ketamine plus xylacine, and ketamine plus diazepam).

CONCLUSION

Our model for left-sided pneumonectomy in isoflurane-anesthetized rats does not require endotracheal intubation and is effective, safe, quick, and easily reproducible.

Transformation of non-tumor host cells during tumor progression: theories and evidence

INTRODUCTION

Most cancer deaths are due to the development of metastases and this phenomenon is still a hard challenge for researchers. A number of theories have tried to unravel the metastatic machinery, but definitive results that link the evidence with conventional concepts of metastatic disease remain to be reported.

AREAS COVERED

Considerable evidence suggests interactions between tumor cells and host cells that might be essential for tumor progression and metastasis. Most such evidence is suggestive of fusion phenomena, but some suggest the transfer of cell-free DNA (cfDNA). Such evidence is often ignored or overlooked in the assessment and management of malignancy. In this article, we review the available evidence for the importance of cell fusion and cfDNA in metastasis, and we present some preliminary data that support the hypothesis that tumor progression might be based not only on the division of tumor cells but also on the transformation of normal cells.

EXPERT OPINION

Future success in the search for cancer therapies will surely require advances in our knowledge of the pathways of tumor invasion by unexpected mechanisms. Thus, no well supported evidence for roles of cell-free nucleic acids and fusion of cells or of cells with vesicles should be ignored.

Efficiency and safety of a technique for drawing blood from the hamster cranial vena cava

The authors evaluated the efficiency and safety of a technique for drawing blood from the cranial vena cava of the hamster (Mesocricetus auratus). They collected blood from Golden Syrian hamsters (n = 15) and from epileptic hamsters (GASH/Sal strain; n = 10) that were anesthetized with isoflurane. Four epileptic hamsters constituted a control group that underwent anesthesia but not blood collection. For blood sampling, a needle connected to a syringe was inserted at a site between 0.2 and 0.6 cm from the manubrium; the depth of insertion was 0.3-1.0 cm. Blood collection was successful in all hamsters except one, and the volume of collected blood ranged from 0.2 ml to 1.5 ml. All hamsters recovered quickly from the procedure, and none showed obvious signs of pain or stress. At necropsy (24 h after the procedure), six subjects showed small local hematomas, and eight showed vascular lacerations of limited severity. Lungs and hearts did not show any damage related to vein puncture. This relatively simple blood collection technique seems to be efficient and safe in hamsters.

Loss of a reporter gene for green fluorescent protein during tumor progression suggests the recruitment of host cells in rats with experimentally induced colon cancer

The interactions between a host's normal cells and tumor cells appear to be of significant importance during the development of tumors. In the present study, we examined this issue using a cancer model in vivo in which tumor cells were tagged with a reporter gene for green fluorescent protein (GFP). We used a model of colon cancer in immunocompetent rats, which were given a subcutaneous injection of tumor cells that had been transfected with a gene for GFP. We found that the number of fluorescent cells decreased with the progression of the primary tumors and that lymph node and lung metastases were never macroscopically fluorescent. No GFP-encoding sequences were detected by PCR in many of the long-term primary tumors, in most lymph node metastases (86%) and in all lung metastases, whereas the detection of mutated k-ras, which identified such cells as tumor cells, was always positive. To explain these findings, we present a brief review of the literature and postulate that tumor growth did not occur exclusively as a result of the division of the injected cells, but also involved recruitment of host cells.

Release of cell-free DNA into the bloodstream leads to high levels of non-tumor plasma DNA during tumor progression in rats

To examine the implications of cell-free DNA in the plasma in neoplastic disease, it is necessary to clarify various features of this DNA, such as the contribution of DNA from the host's normal cells and the kinetics of the release of this latter DNA. To quantify non-tumor DNA in the plasma of tumor-bearing rats and to correlate levels of this DNA with tumor progression, we injected DHD/K12-PROb colon cancer cells subcutaneously into BD-IX rats and recorded tumor diameters weekly. After euthanasia, we collected plasma from each rat and quantified non-mutated and mutated DNA in the plasma. Overall, levels of non-mutated (non-tumor) DNA in plasma of tumor-bearing animals were significantly higher than those in healthy animals measured by real-time PCR (p=0.001). However, 5 weeks after inoculation, levels were similar to those in healthy animals. As a whole, levels of non-mutated DNA were not significantly related to tumor size or to metastasis. However, when we excluded animals that were analyzed earliest, we found a positive and statistically significant correlation between levels of non-mutated DNA and tumor diameter (p=0.002). Release of cell-free DNA into the plasma during tumor progression appears to follow a predictable time course in a homogeneous population. In addition, large amounts of non-tumor DNA are released during tumor progression and, in particular, at early stages. Our findings support the hypothesis that interactions between tumor cells and host cells result in release of cell-free DNA.

Circulating nucleic acids in plasma/serum and tumor progression: are apoptotic bodies involved? An experimental study in a rat cancer model

The "genometastasis hypothesis" proposes that cell-free tumor nucleic acids might be able to transform host stem cells, and that this might be a pathway for the development of metastases. This theory is supported by previous experimental findings and is consistent with observations of other authors. It has been suggested that tumor DNA might be horizontally transferred by the uptake of apoptotic bodies and initiate the genetic changes that are necessary for tumor formation. In addition, apoptotic bodies have been proposed as possible vehicles that protect the nucleic acids circulating in the plasma from enzymatic degradation. In the present study, we analyzed the presence of apoptotic bodies in serum and its relationship with tumor progression in a heterotopic model of colon cancer in the rat. We injected DHD/K12-PROb cancer cells subcutaneously into BD-IX rats and divided the animals into three groups according to the time between the injection of tumor cells and euthanasia. A control group of healthy animals was included (n = 6). After euthanasia, macroscopic metastases were assessed and samples of blood were collected. To detect apoptotic bodies in the sera, each sample was mixed with FITC-conjugated annexin V antibody in combination with propidium iodide and then analyzed by flow cytometry. Detection of apoptotic bodies was only significantly increased in the sera of a few tumor-bearing animals in late stages of tumor development. Thus, such particles appear not to be the vehicle of the cell-free tumor nucleic acids that are detected at early stages of cancer.

Surgery and Hematogenous Dissemination: Comparison Between the Detection of Circulating Tumor Cells and of Tumor DNA in Plasma Before and After Tumor Resection in Rats

BACKGROUND

To examine the effects of the surgical manipulation of tumors on the hematogenous dissemination of tumors, we compared rates of detection of tumor-derived DNA in the buffy coat and in plasma from tumor-bearing rats before and after tumor resection.

METHODS

We injected DHD/K12-PROb cells subcutaneously into BD-IX rats. Three weeks later, we removed the tumors surgically. Group PERI was sacrificed 3 hours after surgery, group POST-2 was sacrificed 2 weeks later, group POST-4 was sacrificed another 2 weeks later, and group POST-LONG was sacrificed when rats were close to death. In group PERI, four perioperative blood samples were taken. In the other groups, only one blood sample was taken per rat, immediately before euthanasia. We used polymerase chain reaction to detect tumor-derived DNA in buffy-coat, plasma, and lung samples.

RESULTS

In group PERI, tumor DNA in plasma was more frequent than circulating tumor cells at all perioperative time points. The difference was statistically significant 3 hours after surgery (P = .035). In group POST-2, there was no detectable metastasis or tumor DNA in blood samples. There were lymphatic and lung metastases in most animals in group POST-4 and in all animals in group POST-LONG. In the last two groups, the frequencies of tumor DNA in the buffy coat and in plasma were similar.

CONCLUSIONS

In our animal model, the hematogenous dissemination of tumors due to surgery seemed to be more closely related to tumor-derived cell-free DNA than to circulating tumor cells. In addition, the surgical resection of primary tumors did not inhibit the development of metastases.

Detection of circulating tumor cells and of tumor DNA in plasma during tumor progression in rats

The role and clinical significance of circulating tumor cells and of tumor DNA in the plasma have not yet been clarified. In the present study, we compared rates of detection of tumor-derived DNA in the buffy coat to those in plasma from tumor-bearing rats, and we attempted to correlate these rates with the progression of tumors. We injected DHD/K12-PROb cancer cells subcutaneously into BD-IX rats and divided the animals into six groups according to the time between the injection of tumor cells and euthanasia. After euthanasia, macroscopic metastases were assessed and samples of blood and lung were collected. We used mutant allele-specific amplification by PCR to detect tumor-derived DNA. We detected tumor DNA in lung samples from the first week after inoculation, in plasma from the third week and in the buffy coat from the fifth week. All animals analyzed on the 11th week had macro- or micrometastases in their lungs. Regardless of group, the rate of PCR-positive plasma samples was significantly higher than that of circulating tumor cells (P=0.005). In animals with metastases, this difference was also statistically significant (P=0.008). However, neither the detection of tumor DNA in the plasma nor the presence of circulating tumor cells was strongly correlated with the presence of metastases. Thus, cell-free tumor DNA was detected sooner and more frequently than circulating tumor cells and the dissemination of tumor DNA in the plasma seems to be much more common than detectable hematogenic tumor cells during the spread of colorectal cancer.