Improved targeting of leukemia stem cells using advanced genomic strategies.

Illumina HiSeq 2000 Genome Sequencers

Acute myeloid leukemia (AML)Abbreviated "AML", this leukemia is an abnormal accumulation of immature myeloid cells, which comprises all white blood cells that are not lymphocytes. The accumulation of abnormal cells prevents the formation of healthy blood cells. Thus, symptoms can include fatigue and abnormal bruising and bleeding.

Relapse of this leukemia is frequent and survival is poor. Most patients will relapse and die of their disease. However, the specific prognosis for any one patient depends on the particular characteristics of their disease, including cytogenetic features and subtype. The capacity for AML to relapse is thought to be driven by leukemia stem cells.

 is a fatal disease marked by extremely high relapse rates and, consequently, low rates of survival. The standard of careThe "standard of care" equates to the treatment guidelines for a particular disease. for this disease consists largely of inductionInduction therapy is administered to reduce the overall leukemic burden in a patient. The regimen in AML is "7+3", named for 7 consecutive days of cytarabine followed by 3 consecutive days of anthracycline. This regimen is excessively toxic and may not be offered to the very elderly. and consolidationConsolidation therapy is offered after leukemia cells are not detectable but is necessary since most patients will relapse in the absence of a consolidation therapy. The specific form of therapy varies with prognosis and can consist of further chemotherapy or stem cell transplantation depending on specific situation of the patient. therapies using toxic chemotherapeutics. Despite the lack of efficacy, the treatment regimen has remained mostly unchanged for the last several decades.

The standard therapeutic regimen involves treatment with chemotherapeutics that target actively cycling cells by interfering with DNA metabolism, specifically cytarabine (Ara-C) and anthracyclines. While these drugs can eliminate most of the AML cells in a patient, AML is maintained by a rare subpopulation of leukemia stem cells (LSCs)Leukemia stem cells are cancer stem cells in leukemia. As with other cancer stem cells, these cells are capable of regrowing the entire tumor and have been shown to resist chemotherapy.. Standard therapy fails to target leukemia stem cells (LSCs) because these cells remain in a quiescent non-dividing state with reduced DNA synthesis. By surviving chemotherapy, months later the LSCs can regrow the AML, resulting in a relapseThe re-emergence of cancer following treatment. With acute myeloid leukemia, relapse often occurs within 8 months!. This hypothesis is supported by clinical evidence showing that patients who have a higher percentage of LSCs demonstrate worse outcome.

There is a clear need for the development of new therapies to overcome this deadly disease by eliminating LSCs. We therefore use genomic strategies including gene expression profilingGene expression profiling involves measuring the level of all genes expressed in a population of cells. These data are then useful for looking at what genes are turned on and off in a particular disease or in response to a drug perturbation. and genome sequencing to understand LSCs and how they respond when challenged with various drugs. Using these data, we are developing essential blueprints for defining the genes and pathways crucial for ablating LSCs so that we can tailor better drugs and drug combinations. Moreover, we hope to define subsets of patients who are more likely to respond to a particular therapy. As not all complex patterns in genome-scale datasets with thousands or millions of variables are likely to be appreciable to humans, we have successfully used and continue to "train" machine learningThe use of artificial intelligence to learn from examples of data, discover hidden and complex patterns in that data, and search for these patterns in new data. algorithms to recognize important patterns that may lead to a new drug for targeting LSCs. Ultimately, we envision these trained artificial intelligences scouring through public and private datasets, improving hit-to-lead times in drug discovery so that patients can benefit from biomedical research more quickly.

Detailed molecular profiling of leukemia.

We are currently working in collaboration with other investigators in the Leukemia Program at Weill Cornell Medical College to develop a more detailed molecular understanding of LSCs. The ultimate goal is to develop therapeutic targets and state-of-the-art tests that are likely to positively impact patient care in the near term. First, we aim to understand what drives the molecular evolution of AML, eventually leading to relapse and therapy refractory disease. Second, we are developing a molecular map of the pathways that are dysregulated in AML stem, progenitor, and bulk cells toward defining therapeutic targets with greater precision. Third, we are employing next generation sequencing to map the mutations and gene expression changes that give rise to drug resistance and leukemia relapse.

Understanding the emergence of secondary malignancies.

Sometimes, patients who receive treatment for cancers such as breast cancer and multiple myeloma develop secondary malignanciesA cancer or "pre-cancer" such as leukemia or myelodysplastic syndrome arising as a result of the treatment another type of cancer. such as acute myeloid leukemiaAbbreviated "AML", this leukemia is an abnormal accumulation of immature myeloid cells, which comprises all white blood cells that are not lymphocytes. The accumulation of abnormal cells prevents the formation of healthy blood cells. Thus, symptoms can include fatigue and abnormal bruising and bleeding.

Relapse of this leukemia is frequent and survival is poor. Most patients will relapse and die of their disease. However, the specific prognosis for any one patient depends on the particular characteristics of their disease, including cytogenetic features and subtype. The capacity for AML to relapse is thought to be driven by leukemia stem cells.

 or myelodysplastic syndrome (MDS)MDS is group of hematopoietic stem cell disorders in which the the formation of mature myeloid cells is impaired. It is considered a form of pre-leukemia as approximately 30% of patients progress to AML. The mechanisms driving the development and progression of secondary malignanciesA cancer or "pre-cancer" such as leukemia or myelodysplastic syndrome arising as a result of the treatment another type of cancer. are poorly understood. Recent advances in genomics allow unprecendented insight into the cellular changes occuring as these processes unfold. We are currently using advanced genomic strategies to develop novel approaches for preventing the emergence of secondary malignanciesA cancer or "pre-cancer" such as leukemia or myelodysplastic syndrome arising as a result of the treatment another type of cancer. and understanding the mechanisms driving this progression.

Publications

These publications and commentaries on our work highlight some of our efforts:

  • Ashton JM, Balys M, Neering SJ, Hassane DC, Cowley G, Root DE, Miller PG, Ebert BL, McMurray HR, Land H, Jordan CT. Gene Sets Identified with Oncogene Cooperativity Analysis Regulate In Vivo Growth and Survival of Leukemia Stem Cells. Cell Stem Cell. 2012 Aug 1. [Epub ahead of print] PubMed PMID: 22863534.

  • Felipe Rico J, Hassane DC, Guzman ML. Acute myelogenous leukemia stem cells: From Bench to Bedside. Cancer Lett. 2012 Jun 17. [Epub ahead of print] PubMed PMID: 22713929.

  • Hassane DC, Sen S, Minhajuddin M, Rossi RM, Corbett CA, Balys M, Wei L, Crooks PA, Guzman ML, Jordan CT. Chemical genomic screening reveals synergism between parthenolide and inhibitors of the PI-3 kinase and mTOR pathways. Blood. 2010 Dec 23;116(26):5983-90. Epub 2010 Oct 1. PubMed PMID: 20889920.
    [ Highlighted in Inside Blood commentary by Dr. Kimberly Stegmaier ]

  • Hassane DC, Guzman ML, Corbett C, Li X, Abboud R, Young F, Liesveld JL, Carroll M, Jordan CT. Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. Blood. 2008 Jun 15;111(12):5654-62. Epub 2008 Feb 27. PubMed PMID: 18305216; PubMed Central PMCID: PMC2424160.
    [ Highlighted in Inside Blood commentary by Dr. Mickie Bhatia ]
  • [ Highlighted in The Hematologist by Dr. Steven Grant ]

  • Guzman ML, Rossi RM, Neelakantan S, Li X, Corbett CA, Hassane DC, Becker MW, Bennett JM, Sullivan E, Lachowicz JL, Vaughan A, Sweeney CJ, Matthews W, Carroll M, Liesveld JL, Crooks PA, Jordan CT. An orally bioavailable parthenolide analog selectively eradicates acute myelogenous leukemia stem and progenitor cells. Blood. 2007 Dec 15;110(13):4427-35. Epub 2007 Sep 5. PubMed PMID: 17804695; PubMed Central PMCID: PMC2234793.
    [ Highlighted in Inside Blood commentary by Drs. Tessa Holyoake and Mhairi Copland ]

  • Sengoku T, Bondada V, Hassane D, Dubal S, Geddes JW. Tat-calpastatin fusion proteins transduce primary rat cortical neurons but do not inhibit cellular calpain activity. Exp Neurol. 2004 Jul;188(1):161-70. PubMed PMID: 15191812.

  • Lee RB, Hassane DC, Cottle DL, Pickett CL. Interactions of Campylobacter jejuni cytolethal distending toxin subunits CdtA and CdtC with HeLa cells. Infect Immun. 2003 Sep;71(9):4883-90. PubMed PMID: 12933829; PubMed Central PMCID: PMC187314.

  • Hassane DC, Lee RB, Pickett CL. Campylobacter jejuni cytolethal distending toxin promotes DNA repair responses in normal human cells. Infect Immun. 2003 Jan;71(1):541-5. PubMed PMID: 12496208; PubMed Central PMCID: PMC143155.

  • Hassane DC, Lee RB, Mendenhall MD, Pickett CL. Cytolethal distending toxin demonstrates genotoxic activity in a yeast model. Infect Immun. 2001 Sep;69(9):5752-9. PubMed PMID: 11500452; PubMed Central PMCID: PMC98692.