Cancer Gene Regulation

 Program Description:

The combined research interests of the Gene Regulation and Epigenetics faculty include: the study of oncogenes and tumor suppressor genes associated with leukemia and lymphoma; MLL protein and MLL fusion proteins that cause leukemia; understanding the multitude of critically important roles chromatin structure plays in normal development and disease; role for angiogenesis in leukemia and lymphoma.

Program Directors:

Basic Research:
Nancy Zeleznik-Le, PhD
Professor of Medicine

Clinical Research:
Patrick J. Stiff, MD
Professor of Medicine (Hematology/Oncology)

Programmatic Objectives:

  • To increase our understanding of the genetic and epigenetic events that determine the initiation and progression of leukemias and lymphomas.  
  • To develop these basic research efforts into translational research studies conducted jointly with our strong clinical research programs in these areas.  
  • To improve the survival of leukemia and lymphoma patients through innovative clinical research studies.  
  • To conduct meaningful studies of leukemia and lymphoma biology.

Scientific Goals

Both the basic research group and the clinical research group have been steadily developing and have recently come together to form the Gene Regulation and Epigenetics Program. The present basic research focus is on the genetic and epigenetic events that drive neoplastic initiation and progression, and that distinguish normal cells from malignant cells in leukemias and lymphomas.

The general objective of the Gene Regulation and Epigenetics Program is to understand the process of oncogenesis in leukemias and lymphomas, and utilize this knowledge to innovate and improve diagnostic and therapeutic strategies. The Gene Regulation and Epigenetics Program therefore combines the strong molecular oncology expertise of this basic research group with the recognized clinical investigative skills of this clinical research group. The primary areas of scientific interest for the Gene Regulation and Epigenetics Program are:

  • To identify mechanisms by which hematopoietic stem cells are immortalized during the oncogenic process.  
  • To identify mechanisms by which leukemia cell differentiation is interrupted or altered as part of the oncogenic process.  
  • To study epigenetic events that affect cell function through changes in chromatin structure or DNA methylation as part of the oncogenic process.  
  • To study the nature and role in oncogenesis of the nucleolytic process associated with apoptosis, and its role in the generation of secondary leukemia.  
  • To explore the role of VEGF and VEGF receptors in the proliferation and survival of leukemia cells.  
  • To evaluate new therapies in non-Hodgkin's lymphoma, chronic lymphocytic leukemia, multiple myeloma, myelodysplastic syndromes and acute leukemia.


Manuel Diaz, MD
Department of Medicine and Microbiology/Immunology

Diaz's research activities focus on the mechanisms that lead to leukemia development by mutant proteins that arise from mutations of the MLL gene. This is primarily through the function of the normal MLL protein, and how the mutant MLL-fusion proteins differ from the normal MLL in their function. Since these proteins regulate the expression of a subset of genes that are master regulators of cell proliferation and differentiation during development, studies are directed toward the effect of MLL mutations on the development of blood cells, and especially on the transition from blood stem cells to the different lineages of differentiated blood cells. This transition is altered in all leukemias, and understanding how MLL mutants affect it may allow understanding of a crucial initial step for leukemogenesis in general. This may be important not only to find appropriate targets for new and more specific therapies, but also to conceive new ways to reduce the incidence of leukemia by preventive measures.

MLL is very similar to a protein called trithorax, found in the fruit fly. As there is a well-developed understanding of how trithorax functions in controlling development in the fruit fly, fruit fly cells are used to understand how trithorax regulate genes involved in development, and these results are extrapolated to the human MLL function.

Mouse blood stem cells infected with viruses that can express mutant forms of MLL are used to study the role of different parts of the MLL molecule, and of other proteins or RNA molecules that interact with MLL, in leukemogenesis. The infected cells can be grown in vitro to observe how they differentiate into blood cell colonies, or can be injected in live mice to observe if they give rise to leukemia.


Andrew Dingwall, PhD
Department of Pathology

In most living cells, chromosomes are formed from highly condensed DNA and basic proteins that  function to compact the chromosomes into a structure called chromatin. Dr. Dingwall's research is  focused on understanding the multitude of critically important roles chromatin structure plays in normal development and disease. In particular, his lab studies a highly conserved group of proteins that form a complex whose main function is to regulate gene expression through direct effects on chromatin structure. As this complex is quite large and composed of at least eight different proteins, research efforts are targeted at understanding how each subunit contributes to the various intricate functions of the complex in regulating tissue-specific gene expression during organismal development, as well as tumor cells. For example, when individual components of this complex are missing or mutated, certain cells lose the ability to properly control their fates and growth, leading to a variety of diseases including aggressive cancers. As part of the Gene Regulation and Epigenetics within the Oncology Institute, the Dingwall lab is focused on understanding the molecular, genetic and epigenetic mechanisms involving chromatin remodeling that govern normal animal development, as well as several types of leukemia, lymphoma and aggressive soft-tissue cancers. Investigative approaches utilize a systems biology perspective, incorporating model organism (Drosophila melanogaster) genetics and biochemistry, cell biology, fly and mammalian cell culture, as well as microarray-based gene expression profiling technologies.

Dingwall Lab -



Charles Hemenway, MD, PhD
Department of Pediatrics

Among the more commonly recurring chromosomal translocations in acute lymphoblastic leukemia (ALL) is t(4;11)(q21;q23). As a consequence of this translocation, the MLL gene at 11q23 is fused to AF4 at 4q21 and a chimeric MLL-AF4 protein is expressed in leukemia cells. The t(4;11) translocation is present in 5-10% of older children and adults with ALL, and, remarkably, this abnormality is detected in more than 50% of infants with ALL. Unfortunately, in both children and adults, t(4;11) ALL has a particularly poor prognosis. However, it may be possible to exploit the t(4;11) translocation to therapeutic advantage. We have found that another MLL fusion protein, AF9, interacts with AF4 through a protein-binding domain that is retained in MLL-AF4 chimeras. Moreover, we have generated a small synthetic peptide that disrupts AF4-AF9 protein complexes. This peptide, PFWT, is a potent inducer of cell death in t(4;11) leukemia cell lines, but the peptide does not inhibit the colony forming potential of hematopoietic progenitor cells. PFWT, or other small molecules that block AF4-AF9 protein interactions, represent a new and potentially effective venue for the treatment of t(4;11) leukemia.

Using PFWT as a drug prototype, we have developed a method to rapidly analyze a large number of different compounds for their ability to block AF4-AF9 interactions and have produced a collection of synthetic peptide derivatives with potential activity. We have screened nearly 1500 molecules and have found 30 compounds with activity. These compounds are now being analyzed for their anti-leukemic properties as well as for biochemical characteristics associated with potentially useful drugs. Finally, we are actively studying the mechanism of PFWT-induced leukemia cell death. Unlike most conventional chemotherapeutic compounds, PFWT does not kill cells through a classical apoptotic pathway. Understanding this non-apoptotic death pathway may reveal other molecules that could be manipulated to realize more effective treatment for this disease.


Ameet Kini, MD, PhD
Department of Pathology

Dr. Kini's laboratory examines the role of angiogenesis in hematologic malignancies.  The notion that angiogenesis is important in cancer was first popularized by Dr. Judah Folkman in 1971. Since then numerous studies have shown that growth of tumors beyond a diameter of about 2mm requires angiogenesis.  Anti-angiogenic strategies have been successfully used in mouse models to eliminate tumors.  A large number of clinical trials are now taking place to assess different anti-angiogenic drugs in humans.

Meanwhile, the role of angiogenesis in leukemias was ignored because there did not appear to be any obvious need for angiogenesis in these "blood cancers".  However, numerous recent studies have demonstrated increased bone marrow angiogenesis in leukemias, and this bone marrow angiogenesis may be required for the proliferation of the leukemic cells.  In addition, it appears that the "angiogenic" factors play an important role in cell survival and apoptosis, through paracrine or autocrine loops.

Dr. Kini's lab focuses on the role of vascular endothelial growth factor (VEGF) and other angiogenic factors in acute promyelocytic leukemia, a subtype of acute myeloid leukemia.  This research may lead to novel, relatively non-toxic, anti-angiogenic therapies for hematologic malignancies.


Nancy Zeleznik-Le, PhD
Department of Medicine and Microbiology/Immunology

Dr. Zeleznik-Le's research interest is focused on the MLL protein, and on MLL fusion proteins that cause leukemia.  MLL is involved in the proper maintenance of expression of downstream target genes, including genes of the HOX cluster.  How MLL functions to help maintain proper expression of target genes is not well understood, but it is thought to involve epigenetic mechanisms acting at the level of chromatin.  One focus of her work is to identify chromatin changes that are mediated by MLL and MLL fusion proteins. This also includes studies to understand how proteins that interact with MLL compete and /or synergize to mediate these effects, and the role of post-translational modifications of MLL on its function.  Another main focus of her research utilizes in vitro and in vivo murine models of MLL leukemia to dissect critical functions required for immortalization and leukemogenesis.  Questions addressed concern hematopoietic cell lineage commitment, and specificity of MLL and partner gene functional domains for immortalization capability.

Dr. Zeleznik-Le has been involved in the cloning of several MLL fusion genes from patient leukemia samples, including the MLL-CBP fusion.  She has developed murine models of MLL leukemia that recapitulate the human disease.  Her laboratory has identified proteins that interact with MLL, including those with chromatin modifying capability.