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2011 Innovative Research Grant 36-Month Progress Reports

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Targeting MLL in Acute Myeloid Leukemia

Yali Dou, Ph.D., University of Michigan

In the past three years, Dr. Dou has made significant progress toward the goal of developing therapeutics that specifically target Mixed Lineage Leukemia 1 (MLL1), which functions as an enzyme called histone methyltransferase. Her results show that blocking a specific interaction between MLL1 and a protein called WDR5 hinders MLL leukemia but not normal blood formation (hematopoiesis). In addition, while working on these proteins, she identified the molecular mechanism for the role of MLL1 activity in disease progression and has used this information to better understand other therapeutic agents for MLL leukemia. The work supported by SU2C was instrumental in translating basic knowledge of histone methyltransferase into potential clinical application. In the future, Dr. Dou will keep working in this area to examine the potential for cooperative or synergistic actions with other therapies used to treat leukemia. She will also try to identify and confirm new compounds that target MLL methyltransferase activity that are more suitable for clinical development.

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Targeting Genetic and Metabolic Networks in T-ALL

Adolfo A. Ferrando, M.D., Ph.D., Columbia University

For the past three years, Dr. Ferrando has worked towards identifying new drugs for the treatment of acute lymphoblastic leukemia (ALL). Towards this goal, he has analyzed a highly representative panel of human T-cell leukemia samples to catalog their genetic alterations, genetic programs, and metabolic signatures. He focused on cellular pathways that were specific to leukemia to identify new drugs. His work has resulted in the identification of two molecularly distinct groups of T-cell leukemia. He has identified numerous new genes mutated in T-ALL which have resulted in new biomarkers to help identify high-risk patients in the clinic.

His studies also looked at drug resistance in leukemia patients who have relapsed. These studies have identified new recurrent mutations that activate NT5C2, which is a metabolic gene responsible for the inactivation of mercaptopurine, an essential drug in the treatment of T-ALL. This result highlights the importance of drug metabolism in the response to therapy. In addition, he has uncovered the mechanistic role of two major genes driving T-cell leukemia (TLX1 and TLX3) and identified the PI3K-AKT1 cell signaling pathway as a new therapeutic target in this disease. He has also uncovered new mechanisms of resistance to therapies directed against a target called NOTCH1. Finally, Dr. Ferrando has profiled T-cell leukemias at the cellular level to better understand their metabolism and showed that targeted therapies result in dramatic changes in cell metabolism.

Overall, Dr. Ferrando’s SU2C-work has pointed to new drugs and drug combinations for the treatment of T-ALL and shown that perturbed cell metabolism represents an important Achilles heel in leukemia cells. This work demonstrate the role of high throughput technologies and network analyses to identify key regulators of leukemic cell growth and survival, and to identify novel and highly effective targeted therapies in high risk human leukemias.

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Targeting Protein Quality Control for Cancer Therapy

Estela Jacinto, Ph.D., University of Medicine & Dentistry of New Jersey - Robert Wood Johnson Medical School

Dr. Jacinto has continued her work on the mTORC2 signaling pathway that plays an important role in protein production and quality control in the cell. Dr. Jacinto focused on two enzymes related to mTORC2; one a cellular receptor called CD147 and the other,called GFAT1, which she identified as a target of mTORC2. During this reporting period, she analyzed how mTORC2 can directly or indirectly regulate GFAT1. Since GFAT1 responds directly to cellular nutrients such as glucose and glutamine, she examined how these nutrients can regulate mTORC2. She also studied CD147 processing and found that this cellular receptor needs mTORC2 to function. During the 6 month no cost extension of the grant, Dr. Jacinto will continue to analyze how mTORC2 regulates GFAT1 and how blocking mTORC2 and GFAT1 activity can prevent mammary tumorigenesis in mice.

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Targeting PP2A and the Glutamine-Sensing Pathway as Cancer Treatment

Mei Kong, Ph.D., City of Hope

Previously, Dr. Kong demonstrated that among 16 different PP2A regulatory proteins, only one, called the B55α subunit, was specifically upregulated upon glutamine deprivation. She also identified the molecular pathway that is critical for mediating B55α’s pro-survival effect on cancer cells. In this reporting period, Dr. Kong again showed that B55α is important for tumor growth in mice and decreased levels of B55α sensitizes tumor to a drug that inhibits glutamine metabolism. In addition, she identified a mechanism, mediated by a protein named IKK, that leads to B55α induction. During her 6 month no cost extension of the grant, she will continue to examine the effect of targeting glutamine metabolism in tumors.

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Chimeric RNAs Generated by Trans-Splicing and Their Implications in Cancer

Hui Li, Ph.D, University of Virginia

To better understand gene fusions and their chimeric fusion products, Dr. Li focused on a known fusion: PAX3-FOXO1. This gene fusion is common in the pediatric cancer alveolar rhabdomyosarcoma (aRMS) and detection of PAX3-FOXO1 fusion RNA by RT-PCR is a standard diagnostic procedure. Dr. Li found the PAX3-FOXO1 fusion in normal cells, which raises concern for tests coming back positive for aRMS when in fact they are negative. Furthermore, therapies targeting this fusion protein may have side effects due to the disruption of functions performed by PAX3-FOXO1 in normal developing muscle.

Another gene fusion Dr. Li studied was SLC45A3-ELK4, which is expressed at much higher level in malignant prostate cancer. His preliminary studies suggest that expression of SLC45A3-ELK4 correlate with prostate cancer progression. He plans to continue to study the SLC45A3-ELK4 fusion, specifically, how it occurs (the mechanisms) in order to enhance the understanding of disease and develop better strategies to fight cancer.

Dr. Li’s work during the 3-year grant term has not only enhanced the understanding of specific RNA and protein fusions, but has also provided valuable insight to understand the mechanism for generating chimeric RNAs in the absence of DNA rearrangement. His work has also resulted in the identification of other RNA fusions that are not the result of DNA rearrangement and plans to continue to study their importance in the development of cancer.

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Exome sequencing of melanomas with acquired resistance to BRAF inhibitors

Roger Lo, M.D., Ph.D., Santa Monica-UCLA Medical Center and Orthopaedic Hospital

Previously, Dr. Lo made the unexpected observation that certain mutations, proposed previously as a mechanism of drug resistance, cannot account for acquired resistance since these mutations are found prior to therapy. He has identified genetic alterations in key resistance pathways for further study.

He has identified a pathway (PI3K-AKT) that contributes to BRAF inhibitor resistance and has proposed Phase I/II clinical trial using combined AKT inhibitor and BRAF inhibitor drugs, which have been approved. In his final progress report, he states that he exceeded his goals in both the number of patient-matched tumor samples analyzed and the types of analysis performed as a result of additional funding for this work. He also reported that several publications and manuscripts have resulted from the work sponsored by this grant.

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Identification and Targeting of Novel Rearrangements in High-Risk ALL

Charles G. Mullighan, MBBS(Hons), MSc, MD., St. Jude Children’s Research Hospital

Dr. Mullighan has sequenced leukemic cells from 156 individuals with Ph-like ALL and identified the genetic basis of 91% of cases, which includes 31 different fusions. He has also developed experimental models to examine how these fusions affect the cells. Furthermore, he has tested drugs in animal models, which showed profound inhibition of leukemia growth. Dr. Mullighan has exceeded the stated aims of the project in terms of the size of the sample cohorts, the extent of genomic characterization, and the range of experimental models established. Importantly, the studies funded by this grant have provided preliminary data justifying clinical trials of a therapy (tyrosine-kinase inhibitor) in ALL.

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A Systems Approach to Understanding Tumor Specific Drug Response

Dana Pe’er, Ph.D., Columbia University Medical Center

During the past 3 years, Dr. Pe’er’s computational work resulted in the identification of a novel synergy between two FDA approved drugs to treat melanoma. This observation supported the use of a combination approach to treatment that is currently being tested in clinical trials. Furthermore, a sub-type of melanoma, which currently does not have a personalized care approach (NRAS melanoma), may benefit from this combination approach. In addition, the Pe’er group have found a genetic marker that may help predict which patients will respond to a certain drugs. Her work on this grant has resulted in new technology to better investigate differences in the tumor.

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Targeting Sleeping Cancer Cells

Sridhar Ramaswamy, M.D., Harvard Medical School

During the term of this grant, Dr. Ramaswamy has outlined a complete signaling pathway that governs sleeping cancer cells using cell lines grown in the laboratory. He has also generated preliminary evidence that suggests slowly dividing cells may actually promote tumor growth in certain contexts – a surprising and exciting possibility that may change the way people think about cancer progression, dormancy, and treatment resistance. He is currently finishing analysis of other important cellular regulatory mechanisms (the epigenetic state) of these slow proliferators, which is providing novel insight into potential ways to therapeutically target these cells.

Taken together, his work raises the possibility that new drugs to specifically target the pathway associated with slow proliferators (AKT1low) may also prove clinically useful. The molecular details, framework, and rationale that he provided through the SU2C-IRG grant mechanism may aid in developing such drugs. Dr. Ramaswamy believes that these findings will be of broad interest to those interested in cancer biology and therapeutics.

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Inhibiting Innate Resistance to Chemotherapy in Lung Cancer Stem Cells

E. Alejandro Sweet-Cordero, M.D., Stanford University School of Medicine

Previously, Dr. Sweet-Cordero established a 3D culture method and analyzed the genes expressed in 3D cell culture in response to the cancer therapy drug cisplatin. In this reporting period, Dr. Sweet-Cordero identified 3 cell surface markers that are associated with tumor re-initiation, and identified a population of cells associated with drug resistance. During the no-cost-extension period of this grant, Dr. Sweet-Cordero will work on further validation of these results.

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Developing New Therapeutic Strategies for Soft-Tissue Sarcoma

Amy Wagers, Ph.D., Harvard Medical School and Joslin Diabetes Center

During the past 6 months, Dr. Wagers has made important progress towards identify new candidate drug targets for sarcoma-induced genes. She has performed additional studies to assess the anti-sarcoma activity of 8 chemical compounds she previously identified. One drug in particular, Asparaginase (an FDA-approved drug to treat blood cell cancers), works exceedingly well in humanized mouse models of alveolar rhabdomyosarcoma. Given that Asparaginase is a drug that already is used routinely in the treatment of blood cell cancers, Dr. Wager’s is hopeful that this data may translate rapidly into clinical trials to test the efficacy of this FDA-approved drug in patients with sarcoma.

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Framing Therapeutic Opportunities in Tumor-Activated Gametogenic Programs

Angelique Whitehurst, Ph.D., University of North Carolina, School of Medicine

Previously, Dr. Whitehurst used a panel of tumor derived cell lines representing six different tumor types to assess the specific contribution of certain proteins to the hallmarks of cancer cell biology. She identified a number of individual cancer-germline proteins that make essential contributions to cellular survival. In the current reporting period, Dr. Whitehurst made progress in understanding how each of these proteins contributes to tumor cell survival. In particular, her studies have identified proteins referred to as Cancer Testes Antigens (CTAs) that can directly activate normal cell suicide programs in response to stress. She has uncovered a CTA (ZNF165) that promotes the expression of pro-tumor oncogenes and oncogenic signaling pathways and a CTA (FATE1) that induces the activation of genes required for cell growth.

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Coupled Genetic and Functional Dissection of Chronic Lymphocytic Leukemia

Catherine J. Wu, M.D., Dana-Farber Cancer Institute

In this reporting period, Dr. Wu has continued to focus on understanding the impact of mutations in the gene for an RNA splicing factor called SF3B1 on CLL, and is optimizing methods to better understand the impact of these mutations. She has continued to investigate the hypothesis that epigenetic (methylation) variability also shapes CLL clonal evolution through interrelation with genetic variability. She identified random methylation as the primary cause of methylation changes in CLL, and cancer in general, and determined that this phenomenon influences gene transcription, genetic evolution, and clinical outcome. She has also analyzed how resistance to the drug ibrutinib arises, which is generally thought to result from mutations in a gene called Burton tyrosine kinase (BTK) or related genes. Dr. Wu has found, however, that that ibrutinib resistance does not uniformly involve mutations in BTK or related genes, but involves possible cancer-driving mutations that can bypass the need for BTK-dependent survival signaling. She has 8 publications further detailing this work.

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