Archive for the 'General' Category
Monday, November 3rd, 2008
Recently, NCI announced the launch of a clinical trial known as MARVEL (Marker Validation of Erlotinib in Lung Cancer) that hopes to find the biomarkers that may identify patient candidates for the class of EGFR tyrosine kinase small molecule inhibitors. EGFR FISH and KRAS mutations are among the biomarkers that will be evaluated in this trial. This study also hopes to provide guidance on how different EGFR biomarkers correlate to each other and their associations with clinical outcomes.
At TMD, we offer both the EGFR FISH and KRAS mutation assessment in a GLP and GCP laboratory. Recently, TMD completed the EGFR FISH assessment of a 480 patient Phase III lung cancer trial. We were able to complete the trial in a 30 day period (we think it’s a great turnarond time) and collected the data in the fashion prescribed by Dr. Fred Hirsch (University of Colorado Health Science Center). Specifically, EGFR positive specimens are defined as:
• EGFR gene to CEP 7 ratio ≥ 2
• Small gene cluster (4-10 copies) or innumerable tight gene cluster in > 10% of the tumor cells independent of the EGFR to CEP 7 ratio
• Larger and brighter EGFR signals than CEP 7 signals in >10% of the tumor cells while EGFR signals are smaller than the CEP 7 signals in the adjacent stromal and reactive cells independent of the EGFR to CEP 7 ratio
• > 15 copies of the EGFR signals in > 10% of the tumor cells independent of the EGFR to CEP 7 ratio
• Specimens with ≥ 40% of cells displaying ≥ 4 copies of the EGFR signal
We have found that the quality of tissue plays a critical role in the success of the EGFR FISH assay. Please contact us if you have an interest in the EGFR FISH testing on colon or other solid tumors.
The TMD website offers abundant information for KRAS testing. While the KRAS mutation story emerged out of colon cancer, the interest in lung cancers is rapidly growing. There are some significant differences. Colon biopsies tend to be easily available. Lung tumor material is much more challenging to obtain. Thus, the upfront assessment of the sufficiency of tumor for a KRAS mutation assay is very important. The DxS assay (CE-approved in Europe) detects 7 mutations that cover approximately 97% of the oncogenic KRAS mutations reported in colon cancer. This may not be the case with lung cancer where preliminary publications indicate these 7 mutations cover approximately 92% of the reported oncogenic mutations.
Stay tuned to our website and blogs for additional information on EGFR FISH and KRAS testing. We have several KRAS mutation trials kicking off at the end of the year and we look forward to solving further questions in this exciting arena with you.
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Friday, October 24th, 2008
In a recent blog, I noted that the CEO of ImClone said KRAS testing has grown substantially since the announcements earlier this summer linking mutations in KRAS with resistance to Erbitux and Vectibix therapies. We may now have to add mutations in BRAF as well, in order to get a more comprehensive view of whether a patient will benefit from these therapies.
A study presented this week at the annual EORTC meeting in Geneva showed that patients with a mutation in the BRAF gene also do not benefit Erbitux or Vectibix. So far, these clinical observations fit perfectly with what we know about the biology of the EGFR pathway. Because KRAS lies downstream of the EGFR, activating mutations in KRAS would be expected to override any inhibition of the EGFR that occurs upstream. Similarly, BRAF lies downstream of KRAS, so activating mutations in BRAF would also be expected to override any inhibition of the EGFR that occurs upstream as well. The study (of 113 patients) found that KRAS and BRAF mutations were mutually exclusive, suggesting that a BRAF mutation is as sufficient as a KRAS mutation in mediating resistance to these therapies, although larger studies would be needed to truly determine this. If these observations fit so well with the biology of EGFR – KRAS – BRAF signaling, you might wonder why it took so long to figure it out (given that we’ve understood these pathways for a quite a long time). To be sure, hindsight is always 20/20, but studies on patient specimens are immensely more challenging than pre-clinical studies, and only in the last several years have more sensitive methods of sequencing and mutation detection come about that can really pinpoint mutations in clinical specimens, where the DNA is generally of poor quality and also may be limiting if only small amounts of tumor are present in a specimen.
So it looks like we may need to test colon cancer patients for both KRAS and BRAF together. While the exact frequency of BRAF mutations in colorectal cancer is not yet known, it is probably at least 10% and perhaps as high as 25%. So even being conservative, we can probably say that almost half (and possibly more) of colon cancer patients will have either a KRAS or BRAF mutation. This is another step forward for personalized medicine since more patients can be put on therapies sooner that will have a real chance of helping them.
At TMD, we’ve been ahead of the curve, by providing the KRAS Mutation test since earlier this year, and also validating the BRAF Mutation test, as we expected that it was only a matter of time before BRAF was found to be important as well. The BRAF Mutation test we use employs the same highly sensitive technology as the KRAS Mutation test. Please contact us to find out how we can provide both KRAS and BRAF testing.
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Monday, October 6th, 2008
A new study of a large clinical trial, FOCUS, in patients with advanced colorectal cancer showed that patients with low expression of topoisomerase I (Topo I) did not benefit from irinotecan therapy (a Topo I inhibitor), while patients with intermediate to high expression of Topo I did show benefit from irinotecan therapy. This is an important finding for several reasons. First, although it may seem obvious that expression of the molecular target of a drug would be necessary for that drug to have an effect, this does not always seem to be the case. Although patients need to have HER2 overexpression in order to benefit from HER2 targeted therapies such as Herceptin and Tykerb, high expression of the HER2 family member EGFR has so far not shown a correlation between high expression of the protein and response to EGFR targeted therapy.
Second, topo I inhibitors have long been considered as chemotherapies which are generally given to cancer patients in a one size fits all approach. This new finding may indicate that our older chemotherapies, often seen as hatchets rather than scalpels, may in fact be more selective than previously thought. Although chemotherapies often cause toxicity in many patients, toxicity risks may be more worthwhile if a patient can be identified prior to therapy that is more likely to benefit, thus sparing patients who are not likely to benefit and helping them to find other therapies that they may have a better chance of benefiting from.
At TMD, we have a number of biomarker assays that could be used to assess the impact of chemotherapeutic drugs on relevant cancer associated pathways. We have a great deal of expertise in developing immunohistochemistry assays, such as the one used for the detection of Topo I in this study. We currently have a validated immunohistochemistry assay for the detection of Topo II. If you’re interested in developing an assay for the detection of Topo I, please contact us.
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Monday, September 29th, 2008
New data presented at the Molecular Diagnostics in Cancer Therapeutic Development meeting from investigators at Wyeth shows that the Src pathway may play a role in resistance to some breast cancer therapies. Src is an enigmatic player in cancer. Despite being one of the oldest known oncogenes and having potent transforming capabilities in chicken cells, Src’s exact role in human cancer has remained somewhat elusive. The new research indicates that high activation of the Src pathway is often seen in tumors that are estrogen receptor, progesterone receptor and HER2 negative (so called “triple negative breast cancer”). Patients with high levels of Src pathway biomarkers were generally correlated with lower overall survival.
Because there are now Src inhibitors in clinical trials, this finding raises the intriguing possibility that current breast cancer therapies could be combined with Src inhibitors to augment the action of breast cancer therapy or perhaps decrease the chance of a patient developing resistance. At TMD, we’ve been involved with the clinical development of Src inhibitors and have many bioamarkers to interrogate the activation state of the Src pathway such as phospho-Src, phospho-FAK and phospho-paxillin, to name just a few. These biomarkers can be performed in real time and used to guide patient therapy or can be part of larger biomarker strategy for a retrospective study analysis. Please see the biomarker section of website for a complete list of our validated biomarkers. We also offer a full range of clinical development services.
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Thursday, September 18th, 2008
A recent study published in Molecular Cancer Research found an association between the expression of a histone deacetylase, SIRT1, and resistance to cisplatin. Cells that were initially sensitive to cisplatin were made resistant to the drug by continuous exposure. The researchers found high levels of SIRT1 in the resistant lines. Reducing the levels of SIRT1 made the cells more sensitive to cisplatin again. This study was conducted at the NCI. Although this is an early study performed in cell lines in the laboratory, it is important because while a great deal of effort goes into discovering biomarkers for targeted therapies, there has not been a lot of focus on finding biomarkers for traditional chemotherapies, like cisplatin-based drugs.
TMD has validated immunohistochemistry (IHC) assays for the detection and measurement of SIRT1 and SIRT2 in tissue. They can be used for pre-clinical development work such as xenograft studies or for clinical development in human tissue. Please contact us for more information about our SIRT1 or SIRT2 assays.
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Wednesday, August 13th, 2008
A recent study published in the Lancelet showed that patients with metastatic kidney cancer that had failed prior sunitinib (Sutent) or sorafenib (Nexavar), had longer progression free survival when treated with a new class of drug, called mTOR inhibitors, than patients receiving placebo. The drug, called everolimus, disrupts a molecular complex called TORC1, thought to be over-active in many cancers. TORC1 is comprised of several molecules, most notably mTOR (mammalian target of rapamycin) which is known to control cell growth in response to nutrient levels and growth factor signals.
The TORC1 complex signals to a number of downstream molecules such as p70S6 Kinase and 4E-BP1 by phosphorylating these molecules. The phosphorylation state of these molecules may therefore be important to monitor mTOR inhibitor efficacy. In addition, the expression of upstream molecules such as Akt and mutations in PI3KCA, KRAS and PTEN will also have an impact on mTOR signaling because they may provide information about which patients are likely to respond to mTOR inhibitors. TMD has validated assays for many upstream and downstream molecules in the mTOR pathway, such as phospho-p70S6 Kinase and phospho-4E-BP1. TMD offers KRAS mutation testing using the only kit approved by a regulatory agency. TMD also has an immunohistochemistry assay that is highly specific for PTEN and will soon offer PI3KCA mutation testing as well.
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Monday, August 4th, 2008
The CEO of ImClone recently said in an article that the company viewed KRAS testing as favorable for the future of Erbitux, despite the fact that it may limit the drug’s market in colorectal cancer (CRC) by almost 40%, the percentage of CRC patients who harbor a KRAS mutation. This is great news for the future support of predictive biomarkers and personalized medicine in general. Hopefully, more pharmaceutical and biotechnololgy companies will take ImClone’s view that further delineation of the molecular biomarkers that can help select patients will actually help their drugs. Why? There are several compelling reasons. The more a drug’s mechanism is understood, the greater confidence a physician may have in prescribing the drug for a patient whose profile matches well with the drug’s mechanism of action. This may be significant if other therapy options are available. This is the case for Erbitux, since Avastin is also been approved in metastatic CRC and has been shown to increase overall survival. Another reason, stated by ImClone’s CEO, is that knowing a patient’s KRAS mutation status may encourage earlier screening for the mutation, which in turn could lead to patients with wild-type KRAS being on the drug longer.
Many laboratories have announced the availability of a KRAS mutation test in the last few months, but not all perform the test the same way. TMD uses the only KRAS mutation kit that has been approved by a governmental organization, the CE marked kit manufactured by DxS. The DxS KRAS Mutation Test Kit is manufactured to high standards so reagent stability and consistency will be greater than homebrew kits that some laboratories employ. Also, the patented Real-Time PCR based technology utilized in the kit is highly sensitive and can detect KRAS mutations even in a large background of non-mutated DNA from normal cells and tissue, such as often occurs when analyzing DNA from formalin fixed paraffin embedded specimens.
ImClone’s CEO said that KRAS testing has grown from 5% to 20%, just since the relatively recent developments linking KRAS status with response to Erbitux and Vectibix. At TMD, we’re trying to make KRAS testing easy for physicians and clinical trial managers by providing all of the information and documents necessary to submit samples to TMD for KRAS testing. Please visit the KRAS section of TMD’s website for more information about our KRAS test and services.
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Monday, July 28th, 2008
A recent survey of key opinion leaders (KOLs) in breast cancer treatment identified a lack of progress and treatment options for “triple negative” breast cancers as a major stumbling block for the field. Triple negative breast cancer is defined as those tumors that do not express HER2, estrogen receptor (ER) or progesterone receptor (PgR). There have been a number of notable breakthroughs for the treatment of HER2 positive and ER/PgR positive cancers in recent decades. Patients with ER and/or PgR positive cancers have a number of therapy options including anti-estrogens (eg. tamoxifen) and aromatase inhibitors (eg. Arimidex). Patients with HER2 positive breast cancers have had Herceptin for the past decade and more recently lapatinib (Tykerb), with a slew of new HER2 targeted antibodies and small molecules in late phase clinical studies.
There is a dearth of information however about the molecular underpinnings of what drives triple negative breast cancers. This is one reason that cytotoxic chemotherapies are still the only options for this type of disease. There may be some cause for optimism on the horizon though, as early studies have indicated a relatively new class of compound, histone deacetylase (HDAC) inhibitors, has shown promise against triple negative breast tumor cell lines. One reason that may explain why HDAC inhibitors have activity against triple negative breast tumor cell lines is because they reactivate the expression of ER-alpha, thus making the tumors more amenable to anti-estrogen or aromatase inhibitor therapies. TMD has a number of biomarkers relevant to the pre-clinical or clinical development of HDAC inhibitors, such as those listed above (HER2, ER, PgR) and many others. Please see our validated biomarker menu for a complete list.
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Wednesday, July 16th, 2008
A new study in leukemia tumor cells combining two targeted therapies was able to not only destroy the mature tumor cells but also the leukemia stem cells. The tyrosine kinase inhibitor Gleevec has been very successful in treating patients with chronic myelogenous leukemia (CML) by inhibiting the BCR-ABL oncogene. However, many patients eventually relapse because their cancer becomes resistant to the inhibitory effect of Gleevec, often by acquiring new mutations in the BCR-ABL gene. One reason for this may be that leukemia stem cells are not affected by Gleevec while they are still in an immature state in the bone marrow but then one day emerge with new mutations that make them resistant to the drug. Ravi Bhatia, M.D., director of the City of Hope Department of Hematopoietic Stem Cell and Leukemia Research found that treating leukemia tumor cells in pre-clinical studies with Gleevec and a histone deacetylase (HDAC) inhibitor killed both mature CML cells and leukemia stem cells (click here for the full story). If HDAC inhibitors have the ability to eliminate stem cells in multiple types of cancers, they could prove particularly valuable in combination with many other targeted therapies. We have experience working with HDAC inhibitors at TMD, and have a number of validated biomarkers to support the pre-clinical and clinical development of these agents. Please visit our website to see a menu of our validated biomarkers.
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Tuesday, July 15th, 2008
A study led by Dr. Kimberly Blackwell at Duke University explored why breast cancer in younger women is often more aggressive than in older women. The authors looked at gene activity in nearly 800 early stage breast tumors from women under 45 and over 65 years of age. Breast tumors in younger women shared over 350 similar sets of gene activation, while in breast tumors from older women no consistent patterns of gene activity were found. In general, breast tumors from younger women tended to have less estrogen receptor positivity, higher frequency of HER2/neu overexpression, higher grade tumors and were more likely to have positive lymph nodes.
The study was published in the July 10th issue of the Journal of Clinical Oncology and a summary can be found here. Studies like these continue to expand our understanding of what drives cancer progression in different patient populations and will ultimately lead to better and more efficacious treatment strategies. At TMD, we’ve also used microarray analysis to analyze gene expression profiles of tumor cells in vitro to explore the effect that targeted therapies have on gene activity and signaling pathways. These studies help elucidate mechanisms and profiles of response and resistance to a particular therapy (or to compare similar agents). Our pre-clinical biomarker identification program can help understand how a drug works which can generate hypotheses that will help guide early clinical studies including identification of appropriate cancer types or patient populations and efficacious drug combinations.
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