Applying the discovery of the Philadelphia chromosome

Genotypic and phenotypic classification of cancer: How should the impact of the two diagnostic approaches best be balanced?

Neoplastic tumors are traditionally named based on their differentiation (i.e., which normal cells and tissues they resemble) and bodily site. In recent years, knowledge about the genetic basis of tumorigenesis has grown rapidly, and the new information has in several instances been incorporated into the very definition of cancerous entities. The proper contribution of the diseases' phenotype and genotype to what they are called and how they are delineated from one another has rarely been subjected to explicit reasoning, however, nor is it often made clear whether existing naming practices are founded on ontological or utilitarian grounds. We look at several examples of how the new cytogenetic and molecular genetic understanding of tumorigenesis has impacted oncological nomenclature in a significant manner, but also at counterexamples where no similar change has taken place. In all likelihood, more and more neoplastic diseases will in the future be defined and named based on their pathogenesis rather than their phenotype, not least because effective and specific drug therapies directed against the molecular change at the very heart of oncogenesis will increasingly become available. The fact that this shift in emphasis is primarily guided by utilitarian considerations rather than any perception of acquired genetic changes as somehow being more ontologically "profound" or "important" in tumorigenesis, is as it should be; both the phenotype and the genotype of tumors are key parameters across most of oncology and are likely to be retained as the basis of coexisting disease classifications for as long as we can foresee.

Critical roles for mTORC2- and rapamycin-insensitive mTORC1-complexes in growth and survival of BCR-ABL-expressing leukemic cells

mTOR-generated signals play critical roles in growth of leukemic cells by controlling mRNA translation of genes that promote mitogenic responses. Despite extensive work on the functional relevance of rapamycin-sensitive mTORC1 complexes, much less is known on the roles of rapamycin-insensitive (RI) complexes, including mTORC2 and RI-mTORC1, in BCR-ABL-leukemogenesis. We provide evidence for the presence of mTORC2 complexes in BCR-ABL-transformed cells and identify phosphorylation of 4E-BP1 on Thr37/46 and Ser65 as RI-mTORC1 signals in primary chronic myelogenous leukemia (CML) cells. Our studies establish that a unique dual mTORC2/mTORC1 inhibitor, OSI-027, induces potent suppressive effects on primitive leukemic progenitors from CML patients and generates antileukemic responses in cells expressing the T315I-BCR-ABL mutation, which is refractory to all BCR-ABL kinase inhibitors currently in clinical use. Induction of apoptosis by OSI-027 appears to negatively correlate with induction of autophagy in some types of BCR-ABL transformed cells, as shown by the induction of autophagy during OSI-027-treatment and the potentiation of apoptosis by concomitant inhibition of such autophagy. Altogether, our studies establish critical roles for mTORC2 and RI-mTORC1 complexes in survival and growth of BCR-ABL cells and suggest that dual therapeutic targeting of such complexes may provide an approach to overcome leukemic cell resistance in CML and Ph+ ALL.

Imatinib therapy reduces radiation-induced pulmonary mast cell influx and delays lung disease in the mouse

PURPOSE

Radiotherapy can induce the inflammatory response of alveolitis and the excessive repair response of fibrosis through incompletely defined mechanisms. In previous murine studies we showed the alveolitis response to thoracic irradiation to correlate with pulmonary mast cell numbers and fibrosis severity to partially depend on the extent of alveolitis. Herein we investigate whether the mast cell blocker imatinib reduces the alveolitis and/or fibrosis response to irradiation.

MATERIAL AND METHODS

Mice of three strains received 18 Gy whole thorax irradiation and a subset of these were treated with imatinib (100 mg/kg) daily from the day of irradiation until euthanasia due to the presentation of distress symptoms.

RESULTS

Imatinib treatment increased the post irradiation survival time of the mice by an average of 23% and significantly reduced the pulmonary mast cell influx. The alveolitis and fibrosis phenotypes, evident histologically, were not altered by imatinib treatment in mice euthanised upon presentation of respiratory distress. The imatinib treated mice did, however, have less disease than did mice receiving radiation alone, when both groups were assessed at a common time point.

CONCLUSIONS

We conclude that imatinib treatment reduces radiation-induced mast cell influx into the lungs and delays the alveolitis or fibrosis response of mice.

Imatinib and docetaxel in combination can effectively inhibit glioma invasion in an in vitro 3D invasion assay

The main problem in the treatment of malignant astrocytomas is their invasive behaviour. Successful resection of the main tumour mass cannot prevent recurrence due to single cells invading the surrounding brain parenchyma at the time of diagnosis. The classical combination therapy, PCV (Procarbazine, CCNU and Vincristine) used for over 30 years; has shown its clinical effectiveness in the treatment of malignant astrocytomas and glioblastomas is still doubtful. Using an in vitro three dimensional invasion model, we tested the effect of the tyrosine kinase inhibitor imatinib and the microtubule inhibitor docetaxel on the invasion activity of a panel of astrocytic tumour cell lines, including two established glioma cell lines, IPSB-18 and SNB-19, and two primary cell lines, originating from glioblastomas, CLOM002 and UPHHJA, and in normal astrocytes. A dose response curve for each drug alone and in combination was determined. The half maximal inhibitory concentration (IC(50)) concentration of imatinib was between 15.7 and 18.7 μM, which did not affect invasion activity of the cell lines. The IC(50) concentration of docetaxel was between 0.7 and 19.8 nM, and at 14.9 nM docetaxel had a slight transient inhibitory effect on invasion activity of all tested cells. The combination of imatinib at 13.5 μM and docetaxel at 14.9 nM, however, synergistically inhibited cell growth and invasion activity and could not be reversed by drug removal. A combination treatment with tyrosine kinase inhibitors and cytotoxic drugs shows promise in tackling both glioma proliferation and invasion, and could present a new treatment regimen for malignant astrocytomas.

Imatinib resistance associated with BCR-ABL upregulation is dependent on HIF-1alpha-induced metabolic reprograming

As chronic myeloid leukemia (CML) progresses from the chronic phase to blast crisis, the levels of BCR-ABL increase. In addition, blast transformed leukemic cells display enhanced resistance to imatinib in the absence of BCR-ABL resistance mutations. Here we show that when BCR-ABL transformed cell lines were selected for imatinib resistance in vitro, the cells that grew out displayed higher BCR-ABL expression comparable to increase seen in accelerated forms of the disease. This enhanced expression of BCR-ABL was associated with an increased rate of glycolysis but a decreased rate of proliferation. The higher level of BCR-ABL expression in the selected cells correlated with a non-hypoxic induction of HIF-1α that was required for cells to tolerate enhanced BCR-ABL signaling. HIF-1α induction resulted in an enhanced rate of glycolysis but reduced glucose flux through both the TCA cycle and the oxidative arm of the pentose phosphate pathway (PPP). The reduction in oxidative PPP mediated ribose synthesis was compensated by the HIF-1α-dependent activation of the non-oxidative PPP enzyme, transketolase, in imatinib-resistant CML cells. In both primary cultures of cells from patients exhibiting blast transformation and in vivo xenograft tumors, use of oxythiamine which can inhibit both the pyruvate dehydrogenase complex and transketolase resulted in enhanced imatinib sensitivity of tumor cells. Together, these results suggest that oxythiamine can enhance imatinib efficacy in patients that present in the accelerated form of the disease.

Molecular mechanisms of cardiovascular toxicity of targeted cancer therapeutics

In 2002, Hoshijima and Chien drew largely theoretical parallels between the dysregulation of the signaling pathways driving cancer and those driving cardiac hypertrophy (Hoshijima M, Chien KR. J Clin Invest. 2002;109:849-855). On the surface, this statement appeared to stretch the limits of reason, given the fact that cancer cells are known for their proliferative capacity, and adult cardiomyocytes are, except under unusual circumstances, terminally differentiated and incapable of re-entering the cell cycle. However, on closer examination, there are numerous parallels between signaling pathways that drive tumorigenesis and signaling pathways that regulate hypertrophic responses and survival in cardiomyocytes. Indeed, this issue appears to be at the core of the cardiotoxicity (often manifest as a dilated cardiomyopathy) that can result from treatment with agents typically referred to as "targeted therapeutics," which target specific protein kinases that are dysregulated in cancer. Herein, we examine the cardiotoxicity of targeted therapeutics, focusing on the underlying molecular mechanisms, thereby allowing an understanding of the problem but also allowing the identification of novel, and sometimes surprising, roles played by protein kinases in the heart.

Regulation of cell proliferation and survival: convergence of protein kinases and caspases

Intricate networks of protein kinases are intimately involved in the regulation of cellular events related to cell proliferation and survival. In addition to protein kinases, cells also contain networks of proteases including aspartic-acid directed caspases organized in cascades that play a major role in the regulation of cell survival through their involvement in the initiation and execution phases of apoptosis. Perturbations in regulatory protein kinase and caspase networks induce alterations in cell survival and frequently accompany transformation and tumorigenesis. Furthermore, recent studies have documented that caspases or their substrates are subject to phosphorylation in cells illustrating a potential convergence of protein kinase and caspase signaling pathways. Interestingly, a number of caspase substrates are protected from cleavage when they are phosphorylated at sites that are adjacent to caspase cleavage sites. While it is theoretically possible that many distinct protein kinases could protect proteins from caspase-mediated cleavage, protein kinase CK2 is of particular interest because acidic amino acids, including aspartic acid residues that are recognized by caspases, are its dominant specificity determinants.

Dasatinib treatment of chronic-phase chronic myeloid leukemia: analysis of responses according to preexisting BCR-ABL mutations

Dasatinib is a BCR-ABL inhibitor with 325-fold higher potency than imatinib against unmutated BCR-ABL in vitro. Imatinib failure is commonly caused by BCR-ABL mutations. Here, dasatinib efficacy was analyzed in patients recruited to phase 2/3 trials with chronic-phase chronic myeloid leukemia with or without BCR-ABL mutations after prior imatinib. Among 1043 patients, 39% had a preexisting BCR-ABL mutation, including 48% of 805 patients with imatinib resistance or suboptimal response. Sixty-threedifferent BCR-ABL mutations affecting 49 amino acids were detected at baseline, with G250, M351, M244, and F359 most frequently affected. After 2 years of follow-up, dasatinib treatment of imatinib-resistant patients with or without a mutation resulted in notable response rates (complete cytogenetic response: 43% vs 47%) and durable progression-free survival (70% vs 80%). High response rates were achieved with different mutations except T315I, including highly imatinib-resistant mutations in the P-loop region. Impaired responses were observed with some mutations with a dasatinib median inhibitory concentration (IC(50)) greater than 3nM; among patients with mutations with lower or unknown IC(50), efficacy was comparable with those with no mutation. Overall, dasatinib has durable efficacy in patients with or without BCR-ABL mutations. All trials were registered at http://www.clinicaltrials.gov as NCT00123474, NCT00101660, and NCT00103844.

Mitotic drivers--inhibitors of the Aurora B Kinase

In this article we review the basis for current anti-mitotic, anti-cancer, therapy and the potential for Aurora B kinase inhibitors as a new differentiated class of agents--"mitotic drivers". We review the current understanding of Aurora B inhibition from basic cell biology to inhibitors currently undergoing clinical trials.

Selective reduction of JAK2V617F-dependent cell growth by siRNA/shRNA and its reversal by cytokines

The JAK(V617F) mutation is responsible for the majority of breakpoint cluster region (BCR)/Abelson (ABL)-negative myeloproliferative disorders. Ongoing clinical trials of Janus kinase 2 (JAK2) inhibitors in myeloproliferative disorder patients use small molecules targeting both wild-type and mutated JAK2. To selectively target malignant cells, we developed JAK2(V617F)-specific small interfering RNAs or short hairpin RNAs. Expression of these RNAs in cell lines or CD34(+) cells from patients reduced JAK2(V617F)-driven autonomous cell proliferation. Mechanisms of inhibition involved selective JAK2(V617F) protein down-regulation, and consequently, decrease in signal transducer and activator of transcription 5 phosphorylation, cell-cycle progression, and cell survival. However, the addition of high concentrations of cytokines to cell lines or erythropoietin to patient cells greatly reduced growth inhibition. Similarly, the efficacy of a JAK2 small molecule inhibitor on cell line and patient cell proliferation dose dependently decreased with the addition of cytokines. Our results demonstrate that it is possible to specifically target JAK2(V617F) by RNA interference (RNAi) strategies. In addition, cytokines partially reverse the inhibition induced by both RNAi and small molecule approaches. This strongly suggests that patient cytokine levels in current JAK2 inhibitor clinical trials modulate the outcome of these therapies.

A new era for small molecule screening: from new targets, such as JAK2 V617F, to complex cellular screens

Traditionally reserved to research and development in pharmaceutical companies, screening of small molecule libraries is rapidly becoming an approach undertaken by academic laboratories. Novel cellular assays, sensitive systems to probe function, emerging new molecular targets are just some of the reasons explaining this shift. Targets of small molecules identified in cellular screens begin to be amenable to identification by elegant genetic approaches, such as probing toxicity of candidate small molecules on libraries of genetically modified yeast strains. Several new targets, such as JAK2 V617F, an activated JAK2 (Janus Kinase 2) mutant genetically associated with the majority of human myeloproliferative neoplasms, are being actively pursued. In this Review Series, we will learn how libraries of small molecules are harnessed to identify novel molecules, that alone or in combination, have the ability to alter cell fate, cell signalling, gene expression or response to extracellular cues.

Cardiovascular effects of tyrosine kinase inhibitors used for gastrointestinal stromal tumors

Small-molecule tyrosine kinase inhibitors (TKIs) have revolutionized the targeted treatment of various cancers, including gastrointestinal stromal tumors (GISTs). Recent evidence suggests the possibility of cardiotoxicity secondary to TKI treatment of GISTs. Preclinical studies indicate that imatinib and sunitinib may be directly toxic to cardiac myocytes. Clinically, cardiotoxicity attributable to imatinib seems to be infrequent and manageable, whereas that attributable to sunitinib is more common and more severe. Further prospective studies with objective cardiac monitoring and long-term follow up are needed to define more accurately the incidence, natural history, and risk factors for developing cardiotoxicity associated with TKIs used in the treatment of patients who have GISTs. In this review, the authors discuss what is known regarding the cardiovascular effects of TKIs used in the treatment of GISTs.

Utilizing the molecular gateway: the path to personalized cancer management

BACKGROUND

Personalized medicine is the provision of focused prevention, detection, prognostic, and therapeutic efforts according to an individual's genetic composition. The actualization of personalized medicine will require combining a patient's conventional clinical data with bioinformatics-based molecular-assessment profiles. This synergistic approach offers tangible benefits, such as heightened specificity in the molecular classification of cancer subtypes, improved prognostic accuracy, targeted development of new therapies, novel applications for old therapies, and tailored selection and delivery of chemotherapeutics.

CONTENT

Our ability to personalize cancer management is rapidly expanding through biotechnological advances in the postgenomic era. The platforms of genomics, proteomics, single-nucleotide polymorphism profiling and haplotype mapping, high-throughput genomic sequencing, and pharmacogenomics constitute the mechanisms for the molecular assessment of a patient's tumor. The complementary data derived during these assessments is processed through bioinformatics analysis to offer unique insights for linking expression profiles to disease detection, tumor response to chemotherapy, and patient survival. Together, these approaches permit improved physician capacity to assess risk, target therapies, and tailor a chemotherapeutic treatment course.

SUMMARY

Personalized medicine is poised for rapid growth as the insights provided by new bioinformatics models are integrated with current procedures for assessing and treating cancer patients. Integration of these biological platforms will require refinement of tissue-processing and analysis techniques, particularly in clinical pathology, to overcome obstacles in customizing our ability to treat cancer.

A health services research agenda for cellular, molecular and genomic technologies in cancer care

BACKGROUND

In recent decades, extensive resources have been invested to develop cellular, molecular and genomic technologies with clinical applications that span the continuum of cancer care.

METHODS

In December 2006, the National Cancer Institute sponsored the first workshop to uniquely examine the state of health services research on cancer-related cellular, molecular and genomic technologies and identify challenges and priorities for expanding the evidence base on their effectiveness in routine care.

RESULTS

This article summarizes the workshop outcomes, which included development of a comprehensive research agenda that incorporates health and safety endpoints, utilization patterns, patient and provider preferences, quality of care and access, disparities, economics and decision modeling, trends in cancer outcomes, and health-related quality of life among target populations.

CONCLUSIONS

Ultimately, the successful adoption of useful technologies will depend on understanding and influencing the patient, provider, health care system and societal factors that contribute to their uptake and effectiveness in 'real-world' settings.

Multiplex reverse transcription-PCR screening for EML4-ALK fusion transcripts

PURPOSE

EML4-ALK is a fusion-type protein tyrosine kinase that is generated by inv(2)(p21p23) in the genome of non-small cell lung cancer (NSCLC). To allow sensitive detection of EML4-ALK fusion transcripts, we have now developed a multiplex reverse transcription-PCR (RT-PCR) system that captures all in-frame fusions between the two genes.

EXPERIMENTAL DESIGN

Primers were designed to detect all possible in-frame fusions of EML4 to exon 20 of ALK, and a single-tube multiplex RT-PCR assay was done with total RNA from 656 solid tumors of the lung (n = 364) and 10 other organs.

RESULTS

From consecutive lung adenocarcinoma cases (n = 253), we identified 11 specimens (4.35%) positive for fusion transcripts, 9 of which were positive for the previously identified variants 1, 2, and 3. The remaining two specimens harbored novel transcript isoforms in which exon 14 (variant 4) or exon 2 (variant 5) of EML4 was connected to exon 20 of ALK. No fusion transcripts were detected for other types of lung cancer (n = 111) or for tumors from 10 other organs (n = 292). Genomic rearrangements responsible for the fusion events in NSCLC cells were confirmed by genomic PCR analysis and fluorescence in situ hybridization. The novel isoforms of EML4-ALK manifested marked oncogenic activity, and they yielded a pattern of cytoplasmic staining with fine granular foci in immunohistochemical analysis of NSCLC specimens.

CONCLUSIONS

These data reinforce the importance of accurate diagnosis of EML4-ALK-positive tumors for the optimization of treatment strategies.

Peroxiredoxin I, platelet-derived growth factor A, and platelet-derived growth factor receptor alpha are overexpressed in carcinoma ex pleomorphic adenoma: association with malignant transformation

Carcinoma ex pleomorphic adenoma is a rare salivary gland malignancy. It constitutes an important model for the study of carcinogenesis, as it can display the tumor in different stages of progression, from benign pleomorphic adenoma to frankly invasive carcinoma. Growth signaling pathways undergo continuous activation in human tumors, commonly as a consequence of the overexpression of ligands and receptors such as platelet-derived growth factor and platelet-derived growth factor receptor. Hydrogen peroxide is produced after platelet-derived growth factor receptor activation, and it is essential for the sequential phosphorylation cascade that drives cell proliferation and migration. By their ability to degrade hydrogen peroxide, peroxiredoxins are involved in growth factor signaling regulation and in the oxidative stress response. To verify the potential association of peroxiredoxin I, platelet-derived growth factor-A, and platelet-derived growth factor receptor-alpha with carcinoma ex pleomorphic adenoma progression, we investigated the expression of these molecules in carcinoma ex pleomorphic adenoma showing different degrees of invasion. The peroxiredoxin I, platelet-derived growth factor-A, and platelet-derived growth factor receptor-alpha proteins were present in remnant pleomorphic adenoma to only a small extent, but, collectively, they were highly expressed as soon as the malignant phenotype was achieved and remained at elevated concentrations during progression to the advanced stages of carcinoma ex pleomorphic adenoma. In addition, their locations overlapped significantly, strengthening their connection to this growth-signaling pathway. Our results indicate that carcinoma ex pleomorphic adenoma cells acquire at least 2 significant advantages relative to their normal counterparts: resistance to oxidative stress-induced apoptosis, conferred by high peroxiredoxin I concentrations, and sustained growth, reflecting platelet-derived growth factor-A and platelet-derived growth factor receptor-alpha overexpression.

Chronic myeloid leukaemia: the evolution of gene-targeted therapy

Chronic myeloid leukaemia (CML) was the first human cancer linked to an acquired chromosomal abnormality, subsequently shown to be a reciprocal translocation between chromosomes 9 and 22. The resulting fusion gene product, BCR-ABL, was shown to be the causative agent of the disease. CML has an incidence of around 1-2 cases per 100,000; in Australia, there are probably more than 200 new cases per year and more than 1300 prevalent cases. Treatment of CML with imatinib has been a powerful vindication of the concept of rational, gene-targeted drug design. Five-year published experience with imatinib at 400 mg orally daily demonstrates 89% overall survival and an estimated 93% freedom from disease progression. Adverse effects are mostly mild and transient. Higher doses of imatinib may be more efficacious and will be studied in upcoming clinical trials in Australia; however, imatinib is almost certainly not curative. Up to 28% of patients may have to stop imatinib because of intolerance or disease resistance, mostly due to point mutations of BCR-ABL. In this situation, many patients will respond to second- and third-generation tyrosine kinase inhibitors. Management of CML patients should involve close monitoring, especially in the first 2 years, with regular cytogenetics and quantitative polymerase chain reaction to optimise response and identify suboptimal responders as early as possible. Bone marrow transplantation remains the only known cure, but is reserved for patients whose kinase inhibitor therapy has failed, or who have advanced disease (accelerated phase or blastic transformation).

Molecular basis of drug resistance in aurora kinases

Aurora kinases have emerged as potential targets in cancer therapy, and several drugs are currently undergoing preclinical and clinical validation. Whether clinical resistance to these drugs can arise is unclear. We exploited a hypermutagenic cancer cell line to select mutations conferring resistance to a well-studied Aurora inhibitor, ZM447439. All resistant clones contained dominant point mutations in Aurora B. Three mutations map to residues in the ATP-binding pocket that are distinct from the "gatekeeper" residue. The mutants retain wild-type catalytic activity and were resistant to all of the Aurora inhibitors tested. Our studies predict that drug-resistant Aurora B mutants are likely to arise during clinical treatment. Furthermore, because the plasticity of the ATP-binding pocket renders Aurora B insensitive to multiple inhibitors, our observations indicate that the drug-resistant Aurora B mutants should be exploited as novel drug targets.

Utilization of genomic signatures to direct use of primary chemotherapy

The success of treatment of cancer patients depends on matching the most effective therapeutic regimen with the characteristics of the individual patient, balancing benefit against risk of adverse events. The primary challenge in achieving this goal is the heterogeneity of the disease, recognizing that breast, lung, colon and other cancers are not single diseases but rather an array of disorders with distinct molecular mechanisms. Genomic analyses, and in particular gene expression profiling, has been shown to have the capacity to dissect this heterogeneity and afford opportunities to match therapies with the characteristics of the individual patient's tumor. Here we review the success in developing gene expression signatures that have the capability of predicting response to various commonly used and newly developing cancer therapeutics. We further discuss the challenges and the opportunities in utilizing these tools in present-day clinical practice.

The legacy of the Philadelphia chromosome

The discovery of the Philadelphia chromosome as a hallmark of chronic myelogenous leukemia in 1960 by Peter Nowell provided evidence for a genetic link to cancer. As with most seminal scientific observations, the description of the Philadelphia chromosome posed many more questions than were answered. This Review series includes contributions from individuals who performed critical experiments addressing some of the most important of these questions, reflecting the nearly 50 years of work inspired by Nowell's initial finding. The legacy of the Philadelphia chromosome now serves as a paradigm for how basic science discoveries can lead to effective new approaches for the treatment of human disease.