LMTK3: a Novel Therapeutic Target for Breast Cancer
UK researchers discover that blocking a protein kinase in human cancer cells improves response to tamoxifen and leads to a significant decrease in the size of breast tumors.
The study performed at Imperial College London, UK, found that the abundance and intronic polymorphisms of lemur tyrosine kinase-3, LMTK3, are significantly associated with disease-free and overall survival and predicted response to endocrine therapies. The findings, which are published in the May issue of the journal Nature Medicine, are the first to assign a role to the kinase.
“Antiestrogen drugs have been very successful at allowing women with breast cancer to live longer, but resistance to these drugs is a common problem”, commented senior author of the study Professor Justin Stebbing, from the Department of Surgery and Cancer at Imperial College London.
Indeed, over 70% of breast cancer patients are ERα positive and are treated with antihormonal drugs (i.e., tamoxifen); however, almost half of these patients eventually relapse after sometime and become resistant to tamoxifen, highlighting the need for the discovery of new regulators of ERα activity.
Speaking to Pharmacogenomics about the significance of this study, Dr Georgios Giamas, Research Associate at the Department of Surgery and Cancer explains: “In this study we identified a novel protein kinase that is able to regulate the activity of ERα and most importantly our data demonstrate that inhibition of the expression of LMTK3 could desensitize cells (that are normally tamoxifen resistant) to tamoxifen treatment. These results are very important as they suggest that LMTK3 is implicated in the mechanisms of developing resistance in breast cancer”.
The study was performed in a mouse model of the disease and employed genetic techniques to block the production of LMTK3. The concept and design of the screening and the readout assay (RT-PCR analysis) was not only time consuming and expensive, but ‘risky‘ and not the type of assay that is routinely used in such cases (cell proliferation).
Giamas, who designed and led the study, went on to explain that the London researchers decided to focus on the most ‘challenging‘ kinase (of the ~15–20 new ones identified); LMTK3 had not been previously described before and its role and function were completely unknown. He stressed however that “in the end, the results justified all this effort and risk”.
An additional finding of interest to come from the study was that of substantial disparity between the LMTK3 gene sequence in humans and chimpanzees (as chimpanzees are not susceptible to ERα-positive breast cancer).
“It‘s quite intriguing that humans and chimps have evolved these differences in the LMTK3 gene, since related genes are very similar between the two species”, commented Dr Georgios Giamas.
“We could speculate that evolutionary changes in this gene might have given humans some unknown advantage, but also have made us more susceptible to breast cancer”.
Asked how the results of this study should be carried forward, Giamas speculates: “We are currently trying to understand more about the mechanism of action and the regulation of LMTK3 and eventually our main goal is to design a specific inhibitor against LMTK3 that can be used primarily in cell line experiments followed by animal breast cancer models in order to examine if inhibition of LMTK3 is able to resensitize them to hormonal treatments. If so, then obviously the next step would be to try it in humans”.
Speculating on how far away we are from this next step, Stebbing comments: “It will probably take at least 5–10 years to develop new treatments that are safe to be used in humans”.
Source: Giamas G, Filipović A, Jacob J et al. Kinome screening for regulators of the estrogen receptor identifies LMTK3 as a new therapeutic target in breast cancer. Nat. Med. 17(6), 715–719 (2011).
Acknowledgements
Georgios Giamas would like to acknowledge the help of collaborators in the UK and the USA and the support of Richard and Evelina Girling and friends for financially supporting this research work.
HeliScopeCAGE: from Nanograms to High-Precision Gene-Expression Analysis
A new technique developed by researchers at the Japanese research institute, RIKEN Omics Science Center (OSC), boasts the ability to quantitatively measure gene-expression levels using as little as 100 ng of total RNA. This technical breakthrough paves the way for the detailed analysis of gene-expression networks and rare cell populations.
HeliScopeCAGE, which pairs one of the most powerful methods for analyzing RNA transcripts; RIKEN‘s Cap Analysis of Gene Expression (CAGE) protocol with the Helicos® Genetic Analysis System, was used to compare a leukemia cell line (THP-1) and a human cervical cancer cell line (HeLa) demonstrating results similar to those obtained from a traditional microarray analysis.
However, this technique marks a big step forward from previous microarray-based studies as the HeliScope Sequencer offers a digital count of the transcripts rather than a relative expression level. In addition, it avoids biases introduced by PCR amplification, ligation and digestion, instead actually sequencing the DNA strand itself, enabling direct, high-precision measurement.
The technique is currently being used as the platform technology for the FANTOM5 project; the fifth installment of the Functional Annotation of Mammals (FANTOM) Project comprising over 120 collaborators from 17 countries. This collective group is providing in-depth biological knowledge, access to rare cell types, novel bioinformatic strategies and new ideas, which collectively are pushing the project forward.
Speaking to Pharmacogenomics about the application of this technique in FANTOM5, Dr Alistair Forrest, leader of the genome profiling technology unit at OSC, highlights: “We have applied this [HeliScopeCAGE] to a very large panel of human samples – primary cells, tissues and cancer cell lines – to map the expression of transcripts and location of promoters used to regulate each cellular state”. He goes on: “This will be the starting point for building large-scale regulatory network models defining each cellular state. This will also be one of the first large-scale projects using single molecule sequencing”.
Asked what the implications of this technique could be on the field of pharmacogenomics, Forrest speculates: “I could see that the expression atlas we have collected will be useful in mapping which cell types and tissues express particular drug targets. This will be important for assessing off-target effects. Similarly the expression patterns can give us a greater understanding of diseases with tissue specific presentations. We can distinguish whether the tissue-specific pathology is a tissue-specific presentation of a system-wide disorder (expressed everywhere), or a tissue-specific disorder (expressed just in the target tissue). This can be important in designing drug targets and diagnostic strategies”.
Looking ahead, the OSC researcher believes that expanding their collection into disease states marks the next step.
Source: Kanamori-Katayama M, Itoh M, Kawaji H et al. Unamplified cap analysis of gene expression on a single molecule sequencer. Genome Res. 21(7), 1150–1159 (2011).
Genome-Wide Population-Based Study Could Lead to Early Detection of Common Variable Immunodeficiency Disease
Common variable immunodeficiency disease (CVID) is a serious immunodeficiency disorder for which there is currently no predictive diagnostic test. It is hoped that a genome-wide association study carried out by Center for Applied Genomics at The Children‘s Hospital of Philadelphia (PA, USA) will facilitate the development of a potentially life-saving diagnostic test.
Common variable immunodeficiency disease can occur at any stage of life and presents a disparate range of symptoms in different patients; the complexity of the disease has also prevented researchers from establishing a cause for the disease. Individuals with CVID have hypogammaglobulinemia and a failure of specific antibody production, resulting in a susceptibility to infections and an array of comorbidities. CVID symptoms can include; lung damage owing to recurrent infections, joint inflammation, bowel disorders and stomach disorders. In addition, these patients are also at a greater risk of developing cancer.
Jordan Orange, co-lead author of the study published in The Journal of Allergy and Clinical Immunology commented on the need to develop a diagnostic test for CVID: “Currently, there may be a delay of up to 9 years from the first time a child becomes sick from this very complex disease until he or she is diagnosed. During this delay, a child may suffer repeated infections and life-shortening organ damage. Identifying CVID at an early stage may allow physicians to intervene earlier with appropriate treatment”.
During the study, the researchers searched for both SNPs and copy number variations that could potentially allow for the identification of genetic patterns in individuals with CVID using automated genotyping technology. A total of 363 CVID patients and 3013 controls were included in the investigation. A strong association was detected in the genes of the MHC region, an area already known to be associated with other immune-related conditions.
Excitingly, these findings allowed the researchers to develop a predictive algorithm, which when tested on CVID cases and controls allowed researchers to distinguish CVID from healthy controls with 99% accuracy.
Prior to the execution of the recent genetic study, little was known about the development of CVID. Orange commented on the implications of the study: “This is very exciting. It suggests that we may be able to use a patient‘s genetic profile at an early stage to predict whether he or she will develop CVID. Since earlier treatment may greatly improve a child‘s ability to live with CVID, this research may represent an important advance in managing a complex, puzzling disease”.
Sources: The Children‘s Hospital of Philadelphia news release: www.chop.edu/news/gene-research-opens-door-to-first-diagnostic-test-for-immune-disorder.html; Orange JS, Glessner JT, Resnick et al. Genome-wide association identifies diverse causes of common variable immunodeficiency. J. Allergy Clin. Immunol. 127(6), 1360–1367 (2011).
Meta-Analysis Reveals Asian Lung Cancer Patients have Better Survival than Caucasians
Researchers from Singapore have demonstrated that Asian lung cancer patients survive longer and exhibit a better response to chemotherapy than Caucasians do. The meta-analysis study, published in the Journal of Thoracic Oncology, examined results from 191 randomized controlled studies carried out over the last 35 years and identified a significantly better response for all chemotherapy regimens in Asian patients than in Caucasian patients. This study marks the first analysis of survival outcomes based on ethnicity and suggests that ethnic differences should be considered in clinical trial designs especially in the global context.
The research, headed by Dr Ross Soo from the Department of Haematology–Oncology at the National University Hospital, Singapore, compared Caucasian and Asian studies of treatment regimens for advanced stage non-small-cell lung cancer from 1975–2010 trial data. The researchers found that better survival in Asian patients was consistent, both pre- and post-introduction of EGF receptor tyrosine kinase inhibitors.
“It is recognized that Asian patients with a common type of lung cancer, the non-small-cell type, have a better survival than Caucasian patients when treated with chemotherapy”, commented Dr Soo, “What wasn‘t known previously was whether this effect was seen in patients given just one or a combination of drugs”.
The researchers looked at data for median overall survival, time to progression, progression-free survival and overall response rate, as indicators of patient survival and response to treatment, for patients undergoing chemotherapy. The researchers believe that their study is unique in its scale for examining ethnicity in cancer therapy, with their analysis encompassing a total of 48,369 patients.
The senior consultant commented, “We found Asian patients indeed had a longer survival and also a higher chance of tumor shrinkage regardless of the number of chemotherapy drugs given in the first-line setting”.
Across the study, Asian patients were found to have a median overall survival of 10.1 months and overall response rate of 32.2% to all chemotherapy, compared with 8.0 months and 25.9%, respectively, for Caucasians. Furthermore, it was found that, for monotherapy, median overall survival in Asian patients was 9.9 months, while it stood at just 6.8 months for Caucasians. Treatment with platinum doublets demonstrated a similar result (10.4 vs 8.6 months).
The researchers went on to demonstrate that the introduction of targeted therapy (EGF receptor tyrosine kinase inhibitors such as gefitinib and erlotinib) did not alter the observed trends. A statistically significant difference in patient survival was present between Asian and Caucasian patients both before and after 2002.
The researchers claim that their results provide strong implications for future clinical trial design. The link between ethnicity and patient survival clearly emphasizes the importance of ethnicity in the efficacy of chemotherapy.
Sources: Soo RA, Loh M, Mok TS et al. Ethnic differences in survival outcome in patients with advanced stage non-small cell lung cancer. J. Thorac. Oncol. 6(6), 1030–1038 (2011).