Gene Expression Profiling & Whole Cell Profiling

gdpawel Member Posts: 523
edited March 2014 in Leukemia #1
Cell Culture Drug Resistance Testing (CCDRT) has a long history with a number of different technologies and many different tumor types tested. Almost all technologies used for hematological malignancies are identical in their logic and similar in their execution.

The concepts underlying cell death assays are relatively simple: if the drug kills tumor cells from an individual patient in a test tube, then the drug is more likely to be effective when administered to a patient. Conversely, a drug that does not kill the patient's cells, even at concentrations significantly higher than can be achieved in the patient, it is unlikely to be effective.

Total cell kill assay have almost exclusively been used for testing the drug sensitivity of leukemias and lymphomas. The DiSC assay and similar tests have some advantages over the other short term assays.

Cell Culture Drug Resistance Testing (CCDRT)

CCDRTs are laboratory tests in which fresh specimens of human neoplasms are cultured in the presence and absence of anti-cancer drugs. At the conclusion of the cell culture, measurements are made to determine whether the drugs are effective in either killing the neoplastic cells and in/or preventing their growth. Test results correlate with drug effects in the patient, with respect to both treatment response and patient survival.

The logic is that if the drug kills tumor cells from an individual patient in a test tube, then the drug is more likely to be effective when administered to a patient. Conversely, a drug that does not kill the patient's cancer cells, even at concentrations significantly higher than can be achieved in the patient, then it is unlikely to be effective.

The concept is to isolate cells from a fresh specimen obtained from a viable neoplasm. These cells are cultured in the continuous presence or absence of a drug, most often for 3 to 7 days. At the end of the culture period, a measurement is made of cell injury, which correlates directly with cell death (apoptosis).

The general measurements of cell death are the DISC assay method, the MTT assay method, the ATP assay method, and the flurescein diacetate assay method. These four endpoints produce valid and reliable measurements of cell death. They also correlate well with each other on direct comparisons of the different methods.

As with other laboratory tests, the determination of the efficacy of CCDRT is based on comparisons of laboratory tests with patient response (clinical correlations). The hypothesis to be tested with clinical correlations is that above-average drugs effects in the assays correlate with above-average drug effects in the patient, as measured by both response rates and patient survival.

Patients with test results in the "sensitive" range were more likely to respond than the total patient population as a whole. Conversely, patients with test results in the "resistant" range were less likely to respond than the patient population as a whole. On average, patients with assays in the "sensitive" range were 3.5-fold more likely to respond than patients with assays in the "resistant" range.

Gene Expression Profiling

Over the past few years, gene expression profiling has been suggested as the best or only way of determining ex vivo drug sensitivity. However, due to almost all patients being treated with combination chemotherapy, this methodology cannot even be calibrated without the use of CCDRT. CCDRTs can actually integrate all the gene expression into one convenient test result.

In obtaining information from gene mutations (DNA content assays) and/or gene expression (RNA content) it must be realized that DNA structure is only important insofar as it predicts for RNA content, which is only important insofar as it predicts for protein content, which is only important insofar as it predicts for protein function, which is important only insofar as it predicts for cell response, which is only important insofar as it predicts for tumor response and function. In other words, it correlates only with response and not survival, in entirely retrospective (not prospective) studies.

What are the data supporting the use of testing DNA, RNA and Protein expression? Two retrospective studies from two Harvard-affiliated hospitals, showing response, but not survival advantages, with a grand total of twenty six correlations. And a subsequent study, presented in the July 14, 2005 issue of the New England Journal of Medicine from another laboratory that did not show correlations between gene mutations and patient survival (Volume 353:133-144 Number 2).

Laboratory, Clinical and Radiographic Tests

The traditional criteria ever used to evaluate laboratory, clinical and radiographic tests have been the performance characteristics (predictive accuracy, sensitivity and specificity) and perceived utility in the judgement of the clinician who orders the tests.

None of the available tests used in clinical decisions regarding treatment selection have ever been tested for there 'efficacy.' This includes estrogen receptor, progesterone receptor, Her2/neu, Oncotype DX, EGFR amplification/mutation, immunohistochemical staining for tumor classification, bacterial culture and sensitivity testing, CT, MRI, FDG Pet Scans to measure tumor response to treatment.

The only data supporting any of them relate to test 'accuracy,' and there is a total lack of information regarding test 'efficacy' (randomized trials with outcome measurements for diagnostic tests).

New "Targeted" drugs

Several new "targeted" drugs have been introduced during the last few years. Most of them have been developed for use in solid tumors but some have also emerged for hematological maligancies. These new "targeted" drugs mostly need to be combined with active chemotherapy to provide any benefit and the need for predictive tests for individualized therapy selection has increased.

Unfortunately, the introduction of these new drugs has not been accompanied by specific predictive tests allowing for a rational and economical use of the drugs. Given the technical and conceptual advantages of CCDRTs together with their performance and the modest efficacy of therapy prediction based on analysis of genome expression as published so far, there is reason for a renewal in the interest for CCDRTs for optimized use of medical treatment of malignant disease.

Choices in Drug Selection

It is within each practitioner's prerogative to order CCDRT, providing that he/she specifies to the patient what the treatment would be in the absence of the assay and be clear if and how the information will be used to inform treatment decision making. Until the clinical trial approach has delivered curative results with a high success rate, the clinical autonomy to integrate promising insights and methods, like CCDRT, remains an essential component of patient advocacy.

One conservative application of the assays would be to identify the most active of the otherwise equally acceptable regimens. Another would be to eliminate the most inactive of the regimens and chose from among the rest on the basis of other clinical factors, including cost. In the setting of relapsed, refractory disease, CCDRT provides a mechanism for choosing from an even larger number of potential drug choices, many of which will not be tested in prospective, randomized trials for years to come.

If test results are used to assist in the selection of a regimen chosen from a series of otherwise reasonable alternatives, then patients will never be harmed by using the test result, and best available evidence strongly indicates that they will often be helped.

CCDRTS have been well proven to have predictive 'accuracy' with that of estrogen receptor, progesterone receptor, Her2/neu and the newer molecular tests. These are diagnostic tests and should be held to that criteria, and not to that of therapy.

In light of the precious little in the way of guidance from clinical trials with respect to best empiric therapy and the importance of basing cancer treatment at least in part on patient preferences, it is entirely reasonable to support judicious application of laboratory tests which have been well characterized with respect to test 'accuracy.'

There is a 35-year history of highly positive studies in hematologic neoplasms showing consistent, strong correlations between the results of cell death assays and clinical outcomes (both initial response and long-term patient survival).

There is strong scientific rationale and good documentation for these tests in a collectively large and diverse literature about hematologic neoplasms for the clinical relevance of the information provided by the tests.

Their use could improve the rationale of treatment choice as well as probability of response and survival.