The Role of Chromatin Remodeling and Epigenetics
in Hematopoiesis and Hematologic Malignancies
Overview: We are interested in molecular mechanisms that
direct gene expression during the development of normal
and malignant blood cells. We focus in particular on silencing
mechanisms used by transcription factors that play master
regulatory roles in these processes. The ordered repression
of certain genes is as important for cell differentiation
and proliferation as is the process of gene activation,
yet far less is known about these silencing mechanisms.
In general, mechanisms of transcriptional repression are
highly complex and involve multiple effects on chromatin.
Such effects include modifications of histone tails by methylation
and acetylation, remodeling of nucleosomes by helicases
and direct methylation of DNA. Furthermore, regulatory proteins
form chromatin-associated complexes that directly shut down
gene expression. All of these events are coordinated by
binding of sequence-specific transcriptional repressors
to their target DNA, in response to multiple signaling and
developmental pathways.
BTB transcription factors: A major class of transcriptional
repressor proteins involved in hematopoiesis is characterized
by the presence of an N-terminal BTB/POZ domain. We found
that the BTB domain was required for both dimerization and
transcriptional repression by these proteins. In a detailed
structure function analysis we observed that the repression,
dimerization and oligomerization could be mapped to different
regions of the BTB domain. We found that the repression
motif of the BTB domain directly recruits co-repressor proteins
that serve as a scaffold for histone deacetylases (HDACs).
In the absence of this motif, proteins that play important
roles in leukemias and lymphomas such as PLZF and Bcl-6
fail to repress their target genes and fail to mediate their
biological effects. On the basis of these results, and in
collaboration with structural biology colleagues, we are
using crystallographic analysis coupled with molecular biology
techniques, to develop a novel form of specific therapy
for cancers where BTB proteins play a prominent role.
Transcriptional repression and common pathways of aberrant
gene expression in hematologic malignancies: Hematologic
malignancies are characterized by an extensive number of
nonrandom mutations. Such mutations most often lead to de-regulation
of transcription factors that lead to aberrant patterns
of gene expression and malignancy transformation. The large
number of these mutations makes a concerted approach towards
these diseases difficult. We hypothesize however that many
of these targeted transcription factors might in fact be
part of common complexes. This is in fact the case since
we found that the ETO protein involved in the M2 form of
acute myeloid leukemia (AML) is part of repression complex
by the PLZF protein that is involved in the M3 form of AML.
In fact, ETO enhances the repression effects of PLZF through
recruitment of histone deacetylases. Interestingly, the
fusion protein of ETO with AML-1, which is characteristic
of AML with the 8;21 translocation, acts as a dominant anti-corepressor
that abrogates PLZF repression. In this way, leukemia cells
that express this fusion protein are able to escape the
growth suppressive effects of PLZF and grow indefinitely.
We are currently exploring the interactions of several other
leukemia and lymphoma oncoproteins. These studies are allowing
us to define networks of hematopoietic transcription factor
networks in blood development and differentiation, as well
as opportunities for molecular targeted therapeutics.
Chromatin, epigenetics and leukemia: Recent data indicate
that covalent modifications of nucleosomal histone tails
regulate the transcriptional status of gene expression.
These changes, along with alterations in the relationship
between DNA and core histones mediated by chromatin remodeling
machines, are coordinated by DNA binding transcription factors.
We are interested in how these different machineries and
their effects are choreographed by transcriptional factors
such as the BTB family of repressors mentioned above. To
this end we are establishing in vitro models of these regulatory
events using chromatinized templates and correlating these
findings in appropriate vivo systems. The combination of
the approaches outlined in these paragraphs are designed
to collectively facilitate a comprehensive analysis of gene
silencing and contribute to the understanding of normal
and malignant hematopoiesis.
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Selected References: 
Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas.
Polo JM, Juszczynski P, Monti S, Cerchietti L, Ye K, Greally JM, Shipp M, Melnick A.
2007 Proc Natl Acad Sci U S A. 104(9):3207-12.
Targeting APL fusion proteins by peptide interference. Melnick A. 2007 Curr Top Microbiol Immunol. 313:221-43.
Comparative isoschizomer profiling of cytosine methylation: the HELP assay..
Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. 2006 Genome Res. 16(8):1046-55.
Specific peptides for the therapeutic targeting of oncogenes. Prive GG, Melnick A. 2006 Curr Opin Genet Dev. 16(1):71-7.
Kaiso-deficient mice show resistance to intestinal cancer. Prokhortchouk A, Sansom O, Selfridge J, Caballero IM, Salozhin S, Aithozhina D, Cerchietti L, Meng FG, Augenlicht LH, Mariadason JM, Hendrich B, Melnick A, Prokhortchouk E, Clarke A, Bird A.
2006 Mol Cell Biol. 26(1):199-208
Predicting the effect of transcription therapy in hematologic malignancies. Melnick A. 2005 Leukemia 19(7):1109-17.
Reprogramming specific gene expression pathways in B-cell lymphomas. Melnick A. 2005 Cell Cycle. 4(2):239-41.
Specific peptide interference reveals BCL6 transcriptional and oncogenic mechanisms in B-cell lymphoma cells. Polo JM, Dell'Oso T, Ranuncolo SM, Cerchietti L, Beck D, Da Silva GF, Prive GG, Licht JD, Melnick A. 2004 Nat Med. 10(12):1329-35
Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain.
Ahmad KF, Melnick A, Lax S, Bouchard D, Liu J, Kiang CL, Mayer S, Takahashi S, Licht JD, Prive GG. 2003 Mol Cell. 12(6):1551-64.
ETO protein of t(8;21) AML is a corepressor for Bcl-6 B-cell lymphoma oncoprotein. Chevallier N, Corcoran CM, Lennon C, Hyjek E, Chadburn A, Bardwell VJ, Licht JD, Melnick A. 2004 Blood. 103(4):1454-63.
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