Download Gene Section PRDM1 (PR domain containing 1, with ZNF domain)

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Gene Section
Review
PRDM1 (PR domain containing 1, with ZNF
domain)
Wayne Tam
Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
(WT)
Published in Atlas Database: September 2011
Online updated version : http://AtlasGeneticsOncology.org/Genes/PRDM1ID41831ch6q21.html
DOI: 10.4267/2042/46945
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence.
© 2012 Atlas of Genetics and Cytogenetics in Oncology and Haematology
Transcription
Identity
The mRNAs encoded by PRDM1 have two transcript
isoforms, PRDM1alpha and PRDM1beta, which are
5164 and 4675 bp long, respectively. The shorter
isoform is generated by usage of the alternative
promoter located in intron 3 and contains a different 5'
untranslated region. It lacks the 5' inframe portion of
the coding region present in PRDM1alpha. A deletion
exon 6 (exon 7 in mice) variant has also been described
(Schmidt et al., 2008).
Other names: BLIMP-1, BLIMP1, PRDI-BF1
HGNC (Hugo): PRDM1
Location: 6q21
DNA/RNA
Description
The gene encompasses 23,6 kb DNA in humans, from
106534195 to 106557814 (hg19-Feb, 2009) in the long
arm of chromosome 6. It encodes 7 exons. The open
reading frame spans all 7 exons.
Pseudogene
None.
Figure 1.
Atlas Genet Cytogenet Oncol Haematol. 2012; 16(2)
135
PRDM1 (PR domain containing 1, with ZNF domain)
Tam W
Figure 2.
Protein
Description
PRDM1alpha is the larger isoform and contains 825
amino acids, with a predicted molecular weight of 92
kD. It has a PR domain at the N-terminal portion (86207 aa) of the protein, which is related to the SET
domain (SM00317, SMART) found in many histone
methyltransferases. In contrast to bona fide SETdomain proteins, the PR domain in PRDM1 does not
possess intrinsic histone methyltransferase activity.
Five C2H2-type zinc fingers (SM00355, SMART),
which represent the DNA binding domain, are present
at the C-terminal portion of the protein (575-707 aa).
The middle part of PRDM1 (about 300-400 aa) is rich
in proline and serine. PRDM1beta lacks the N-terminal
101 amino acids of the PRDM1alpha, and has a
truncated PR domain. PRDM1beta has been shown to
be functionally impaired in its transcriptional
repression activity (Gyory et al., 2003). The proximal 3
zinc fingers in PRDM1/Blimp-1 delta exon 6 variant
are disrupted (Schmidt et al., 2008). This protein
variant has auto-regulatory potential through negative
regulation of PRDM1/Blimp-1 expression and
functions.
Expression
PRDM1/Blimp-1 is expressed in several tissues and
organs, including hematopoietic tissues, skin, central
nervous system, testis and gut. Within the
hematopoietic system, PRDM1/Blimp-1 is expressed in
plasma cells, B cells, T cells, natural killer cells,
monocytes, granulocytes and dendritic cells. In the B
cell population, PRDM1/Blimp-1 starts to be expressed
when they are committed to undergo terminal
differentiation (Cattoretti et al., 2005). Consistent with
its expression in normal lymphoid cells, PRDM1 is also
expressed in 100% of multiple myeloma, and in various
frequency in B and T lymphomas (Garcia et al., 2006;
D'Costa et al., 2009). PRDM1/Blimp-1 expression is
regulated by a number of transcription activators and
repressors (Martins and Calame, 2008). MicroRNAs
have also been implicated in the down-regulation of
PRDM1 in both normal germinal center B cells
(Malumbres et al., 2009; Zhang et al., 2009; Gururajan
et al., 2010) and in neoplastic lymphoid cells (Nie et
Atlas Genet Cytogenet Oncol Haematol. 2012; 16(2)
136
al., 2008; Nie et al., 2010). Among PRDM1 isoforms,
PRDM1alpha is the most abundantly expressed,
although relative abundance between PRDM1alpha and
PRDM1beta may vary between cell types (Garcia et al.,
2006). PRDM1/Blimp-1 delta 6 isoform is
preferentially expressed in resting B cells (Schmidt et
al., 2008).
Localisation
Nuclear.
Function
Mechanisms of action
PRDM1/Blimp-1 is a transcription repressor that binds
to specific DNA sequences through its zinc fingers, and
functions as a scaffold for recruiting co-repressors that
catalyze histone modifications. It has no known
intrinsic
histone
methyltransferase
activity.
PRDM1/blimp-1 has been shown to mediate
transcriptional silencing via interactions with H3 lysine
methyltransferase G9a (Gyory et al., 2004), histone
deacetylases HDAC1 and HDAC2 (Yu et al., 2000),
and H3 lysine demethylase LSD1 (Su et al., 2009).
PRDM1 can also tether Groucho family of transcription
factors to mediate repression of gene transcription (Ren
et al., 1999). Interaction of PRDM1/Blimp-1 with these
co-repressors is mediated through the proline/serine
rich domain and/or the zinc fingers. PRDM1 exerts its
biological functions by repressing expressions of
various target genes, which can be cell-type specific.
For example, PRDM1/Blimp-1 mediates cell-cycle
arrest in B cells by repressing c-myc, and in CD4
positive helper T cells by inhibiting expressions of IL-2
and Fos, an IL-2 activator (Martins and Calame, 2008).
Biologic functions
PRDM1 was originally identified as a novel repressor
of human beta-interferon gene expression called PRDIBF1 (positive regulatory domain I binding factor 1)
(Keller and Maniatis, 1991). Later Blimp-1 (B
lymphocyte-induced maturation protein), which
represents the murine homolog of PRDI-BF1(Huang,
1994), was discovered as a protein the enforced
expression of which was sufficient to drive plasma cell
differentiation of a mouse lymphoma cell line with an
activated B cell phenotype (Turner et al., 1994).
Studies since then have revealed a role of
PRDM1/Blimp-1 in multiple cell types.
PRDM1 (PR domain containing 1, with ZNF domain)
Tam W
PRDM1/Blimp-1 is the master regulator of plasma cell
differentiation, critical for the generation of
immunoglobulin-secreting
plasma
cells
and
maintenance of long-lived plasma cells (Shapiro-Shelef
et al., 2003; Shapiro-Shelef et al., 2005; Martins and
Calame, 2008). It mediates terminal B cell
differentiation by extinguishing gene programs related
to B cell signaling and proliferation (Shaffer et al.,
2002), and allowing induction of XBP1 which
coordinates phenotypic changes, including expansion
of endoplasmic reticulum and increased protein
synthesis, that define the plasma cell phenotype
(Shaffer et al., 2004).
PRDM1/Blimp-1 is also required for T cell
homeostasis (Kallies et al., 2006; Martins et al., 2006;
Calame, 2010). It attenuates proliferation and survival
of CD4 positive helper T cells by repressing IL-2dependent activation; inhibits Th1 differentiation by
down-regulating IFNgamma, Tbx21 and BCL6; and
antagonizes BCL6-dependent follicular T cell
differentiation. PRDM1/Blimp-1 also plays critical role
in the differentiation of CD8-positive T cells.
Besides its critical functions in B and T cells,
PRDM1/Blimp-1
promotes
differentiation
of
macrophages (Chang et al., 2000). It is also important
for homeostatic development of dendritic cells as well
as dendritic cell maturation (Chan et al., 2009).
PRDM1/Blimp-1 negatively regulates NK cell
activation by suppressing effector cytokine production
(Smith et al., 2010).
In the non-hematopoietic cell types, PRDM1/Blimp-1
plays an important role in the terminal differentiation of
keratinocytes (Magnusdottir et al., 2007) and sebaceous
cells (Sellheyer and Krahl, 2010). It also regulates
postnatal reprogramming of intestinal enterocytes
(Harper et al., 2011).
Furthermore, PRDM1/Blimp-1 is required in
embryonic developmental cell fate specification and
organ morphogenesis, as demonstrated by mouse and
zebrafish model systems (Bikoff et al., 2009). Blimp-1
specifies cell fate of primordial germ cells (Vincent et
al., 2005), neural crests and neuron progenitors (Roy
and Ng, 2004), and also muscle fiber identity
(Baxendale et al., 2004; Hofsten et al., 2008). Blimp-1
is also critical for the normal development of the
cardiovascular system, forelimbs and vibrissae
(Robertson et al., 2007).
Homology
PRDM1 is conserved in chimpanzee, dog, cow, mouse,
rat, chicken and zebrafish.
Mutations
Somatic
Somatic mutations have been identified in diffuse large
B cell lymphomas (DLBCL) at a frequency of about 8
to 23% (Tam et al., 2006; Pasqualucci et al., 2006;
Mandelbaum et al., 2010). One group did not detect
Atlas Genet Cytogenet Oncol Haematol. 2012; 16(2)
137
mutations in 82 cases of DLBCLs in the Chinese
population, suggesting geographic differences in
PRDM1 mutations in DLBCL (Liu et al., 2007).
PRDM1 mutations are exclusively detected in about 24
to 35% of the activated B cell(ABC)/non-germinal
center B cell (non-GCB) subtype of DLBCL, and have
not been identified in GCB-like DLBCL. In addition,
about 20% of primary DLBCL of the central nervous
system, a subtype of DLBCL, harbor PRDM1
mutations (Courts et al., 2008). PRDM1 mutation was
also found in one case of primary effusion lymphoma
out of 2 cases analyzed (Tate et al., 2007). The types of
somatic mutations seen in PRDM1 include splice site
mutations, frameshift insertion/deletion and less
frequently, nonsense and missense mutations. The vast
majority of these mutations result in inactivating
truncations lacking one or more of the critical domains
including PR, proline rich region, and the zinc fingers.
Missense mutations have been demonstrated to affect
PRDM1 functions (Mandelbaum et al., 2010). Most of
the somatic mutations (about 90%) are associated with
inactivation of the other allele by deletion, consistent
with biallelic inactivation characteristic of a tumor
suppressor gene. Mutations in acute leukemias and
solid tumors have been not identified (Hangaishi and
Kurokawa, 2010).
Implicated in
Diffuse large B cell lymphomas
Prognosis
Diffuse large B cell lymphoma (DLBCL) with partial
plasmablastic differentiation, as indicated by PRDM1
expression, has a worse overall and failure free survival
compared to conventional DLBLC without PRDM1
expression, suggesting that PRDM1 may be useful as a
prognostic marker in DLBCL (Montes-Moreno et al.,
2010).
Expression of PRDM1beta has been implicated as a
poor prognostic marker in DBLCL treated with CHOP
(but not R-CHOP) and in T cell lymphomas. Resistance
to chemotherapeutic agents mediated by PRDM1beta
has been proposed as a potential mechanism (Liu et al.,
2007; Zhao et al., 2008).
Oncogenesis
Inactivation or down-regulation of PRDM1 appears to
be an important event in the pathogenesis of DLBCLs
of the ABC/non-GCB subtype. In about 50% of
DLBCLs of this subtype, PRDM1 is inactivated by
truncating or missense mutations, biallele gene
deletions or transcription repression by a constitutively
active, translocated BCL6 (Mandelbaum et al., 2010).
In non-GCB/ABC-like DLBCL without these genetic
lesions, asynchronous PRDM1 mRNA and protein
expressions have been observed, suggesting a posttranscriptional down-regulation (Mandelbaum et al.,
2010; Nie et al., 2010). MicroRNAs have been
postulated as a potential mechanism of down-regulation
PRDM1 (PR domain containing 1, with ZNF domain)
Tam W
(Nie et al., 2010). All these findings are consistent with
a tumor suppressor role of PRDM1 in DLBCL. In
addition, PRDM1/Blimp-1 has been directly
demonstrated in mouse models to function as a tumor
suppressor gene (Calado et al., 2010; Mandelbaum et
al., 2010). Mice lacking PRDM1/Blimp-1 are
predisposed to develop lymphoproliferative disorders
resembling human ABC-like DLBCL. One of these
mouse models also demonstrated a cooperative
pathogenic effect between PRDM1 inactivation and
constitutive NF-kB activation. These findings suggest
that PRDM1 inactivation contributes to the
pathogenesis of ABC-like DLBCL by inhibiting
terminal B cell differentiation induced by constitutive
canonical NF-kB activation characteristically present in
this lymphoma type.
Natural killer cell neoplasms
Oncogenesis
PRDM1 is frequently (about 40%) deleted as part of a
minimal deleted region in aggressive natural killer
(NK) cell neoplasms such as extranodal NK/T cell
lymphomas, nasal type, and aggressive NK cell
leukemias (Iqbal et al., 2009; Karube et al., 2011). This
deletion is generally associated with a down-regulation
of PRDM1 expression, associated with focal
hypermethylation of the 5' region of the other PRDM1
allele. Enforced expression of PRDM1 in NK
lymphoma cell lines results in cell cycle arrest and
apoptosis (Karube et al., 2011). Inactivating nonsense
mutations have also been found in two NK cell lines
and one clinical NK neoplasm (Iqbal et al., 2009;
Karube et al., 2011). These findings indicate a tumor
suppressor role of PRDM1 in NK cell neoplasms.
Radiation-therapy induced second
malignant neoplasms
Prognosis
Pediatric Hodgkin lymphoma patients treated by
radiation are at risk of developing second malignancies
later in life. Two SNP variants were identified at 6q21
(intergenic between ATG5 and PRDM1) in a genome
wide association study that are associated with
increased risk of second neoplasms for pediatric
patients with Hodgkin lymphoma who received
radiation therapy. These variants correlate with
decreased basal PRDM1 expression and reduced
PRDM1 induction after radiation therapy, implicating
PRDM1 in the etiology of radiation-therapy induced
second malignancies (Best et al., 2011).
Plasma cell myeloma
Oncogenesis
PRDM1 is consistently expressed in plasma cell
myeloma. A plasmacytoma transgenic mouse model
demonstrates that PRDM1/Blimp-1 is not a tumor
suppressor gene in myeloma. Instead, it appears to be a
limiting factor in plasma cell transformation (D'Costa
et al., 2009). Reducing PRDM1/Blimp-1 dosage
Atlas Genet Cytogenet Oncol Haematol. 2012; 16(2)
138
decreases incidence of plasmacytoma in mice but does
not cause reduction of normal plasma cells in
nontransgenic mice. Loss of PRDM1/Blimp-1
eliminates plasmacytoma development.
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