Issue 4 : April, 2011

Professor of Systems Biology
Chief, Division of Biomedical Informatics
Director, Columbia Initiative in Systems Biology
Director, Center for the Multiscale Analysis of Genetic Networks (MAGNet)
Associate Director for Bioinformatics, Irving Cancer Research Center (ICRC)

Dr. Andrea Califano serves as Principal Investigator of the Cancer Target Discovery and Development (CTD²) Center at Columbia University. Below he describes how his lab works to identify models of cancer regulation through the application of systems biology, a field of interdisciplinary study that examines complex interactions between components of biological systems. Researching cancer from this vantage point affords Dr. Califano and colleagues the opportunity to study physiological processes in a comprehensive and highly integrated manner that incorporates in vivo (in living organisms), in vitro (in the test tube), and in silico (in the computer) methods.

Throughout my career, my research interests have been focused on understanding dynamic systems. At the start of my career, I was a physicist working on deterministic chaos. More recently, over the last 20 years, I have been a systems biologist using a variety of physics and knowledge-based methodologies to elucidate molecular mechanisms that are dysregulated in disease.

My lab at Columbia University combines advanced in silico reverse engineering methods and high-throughput experimental biology to reconstruct and interrogate cell-context specific gene regulatory networks underlying pathophysiological processes. On the computational side, we have developed a repertoire of algorithms for the dissection of transcriptional, post-transcriptional, and post-translational regulatory interaction networks (or interactomes) in mammalian cells. We have also developed tools for interrogating interactomes to identify genes that are master regulators of specific cancer subtypes or to elucidate the mechanisms of action of small-molecules. We have shown that master regulator genes can constitute both oncogene and non-oncogene addiction points of the cancer cell and that compounds targeting these addictions can be effectively identified using computational approaches.

Our key strength, however, is in the ability to follow-up these computational inferences with rigorous experimental validation using biochemical or functional assays. For example, in collaboration with Dr. Antonio Iavarone, also at Columbia, we computationally predicted and experimentally validated that synergistic activation of two transcription factors, C/EBP and Stat3, is necessary and sufficient to reprogram neural stem cells along an aberrant mesenchymal lineage. The synergistic activation contributes to the worst prognosis of Glioblastoma (GBM) and establishes a synergistic addiction point in these tumors. In fact, their silencing led to collapse of the mesenchymal signature and reduction of tumor aggressiveness in vivo. Recently, we have been able to use the high-grade glioma regulatory network to further identify and experimentally validate both genetic alterations that contribute to the activation of C/EBP and Stat3 in more than 70% of mesenchymal GBMs. We have also been able to identify druggable targets and associated drugs (either FDA approved or in clinical studies) that can inhibit the activity of these transcription factors in vitro.

Thanks to the CTD² Network initiative, we set up a Translational Cancer Systems Biology Center that combines the strength of several Columbia investigators with expertise in cancer biology, reverse engineering, pooled siRNA screening, and high-throughput screening. These investigators systematically identify and prioritize biomarkers, therapeutic targets, and small compounds for several tumor subtypes, including the mesenchymal phenotype of GBM, glucocorticoid resistance in T-cell Acute Lymphoblastic Leukemia, and the non-oncogene addiction of the ABC subtype of Diffuse Large B-Cell Lymphoma to NF-κB. Our pipeline can be applied to a variety of cancer subtypes, as long as appropriate molecular profile data and cell lines are available. The CTD² Network initiative has allowed us to leverage the highly complementary expertise of the other Network Centers, thus dramatically accelerating progress towards our goals.

The CTD² Network initiative comes at a propitious moment in the progression of cancer research. The availability of large and comprehensive public datasets and functional models is allowing researchers the unprecedented opportunity to create and interrogate highly accurate models of cancer regulation, both in silico and in vivo. The CTD² Network provides the framework to optimally exploit these models to discover safe and effective compounds, in a patient-centered fashion, and to facilitate their clinical development by providing associated targets, biomarkers, and mechanisms of action.

(adaptation from NCI Bypass BudgetOpens in a New Tab)

Comprehensive molecular characterization of cancers is revealing somatic changes that may be part of the root cause of malignant disease. Tumor cells acquire mutations in their genes that, in turn, lead to production of abnormal proteins. This allows the cancer to interrupt a normal physiological process and further manipulate it to promote proliferation and survival of the tumor. Large-scale genomics initiatives, such as those investigated in programs managed by the NCI Office of Cancer Genomics (OCG), are identifying and characterizing these mutations, thereby uncovering novel mechanisms for cancer initiation and progression, and new ways to treat cancer in the future. One recent finding has been the discovery of a mutation in a gene coding for an enzyme called isocitrate dehydrogenase (IDH). IDH plays an essential role in converting simple carbohydrates into a key molecule involved in producing energy in all normal cells.

There are two IDH genes, IDH1 which works in the cytoplasm and IDH2 that functions in mitochondria. A mutation in IDH1 was initially discovered in gliomas (a tumor affecting the brain or spinal cord), and subsequent research over the past two years has shown that both IDH1 and IDH 2 enzymes have heterozygous mutations (only 1 of the 2 alleles is affected) in >70% of grade II-III gliomas and secondary glioblastomas (highly lethal brain tumors which arise from low grade gliomas). In addition, it is now known that IDH1/2 are mutated in up to 15% of acute myeloid leukemias (AML) and possibly other cancers at low frequency. These mutations appear to reduce the normal activity of each enzyme (namely the conversion of isocitrate to alpha-ketoglutarate (a-KG)), and give rise to a new function (the conversion of a-KG to (R)-2-hydroxyglutarate (2-HG)). Indeed 2-HG levels are elevated >50-fold in tumor cells from patients with IDH1/2 mutations, motivating further study of 2-HG as a disease biomarker, as well as deeper investigation of the molecular mechanism by which this putative 'oncometabolite' may contribute to disease. Additionally, initial studies suggest that the mutant form of the 2-HG enzyme changes the epigenetic state (modification of gene expression by a mechanism independent of the underlying DNA sequence) of the cancer cells. One compelling implication of these novel findings is that mutations of IDH genes in multiple cancers could preliminarily provide some supportive evidence of Warburg's hypothesis that malignant growth is caused by tumor cells that mainly generate energy by non-oxidative breakdown of glucose (rather than normal oxidative breakdown of pyruvate), and cancer is actually a result of mitochondrial dysfunction.

While identification of altered enzyme activity was pivotal in understanding the cellular impact of IDH1/2 mutations, the dependency of IDH1/2-mutant cancers on the newly-acquired function for initiation of malignant transformation remains mostly uncharacterized. This is largely due to the lack of high-quality small-molecule probes for mutant IDH1/2 activity available to the cancer biology community. As part of the NCI's Cancer Target Discovery and Development (CTD²) Network, the Broad Institute is developing small molecules that inhibit the 2-HG-generating activity of IDH1/2 mutants in cells, providing much needed tools to study the role of IDH mutations in cancer cell biology and to validate mutant IDH1/2 as a possible target for drug development. This research dovetails well with efforts underway within the pharmaceutical industry, as well as within the NCI's Experimental Therapeutics (NExT) programOpens in a New Tab. In less than one year, the Broad-CTD² Center identified highly novel small molecules (derived from innovative synthetic organic chemistry methods) that inhibit the novel activity of one of the IDH1 mutant forms which has 50% inhibition concentration (IC50 of 2uM) and that has ~10-fold selectivity over the normal activity of the wild-type enzyme. The molecules screened have properties that facilitate modifications, so as to become either more specific for a given target (in this case the mutant form of IDH1/2) or confer activity at lower concentrations, which are two features not present in typical compound collections. The Broad-CTD² Center will continue to characterize and optimize the cell-based activity and selectivity of these preliminary leads to develop a high-quality probe that will be made available to other investigators and potentially may serve as a starting point for clinical studies. These compounds will enable thorough investigation by the research community into the role of mutant IDH1/2 in cancer biology, as well as further validate it as potential target for therapy.