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*
Unité 429 and
Department dAnatomie Pathologique, Hôpital Necker, Paris, France;
Department of Genetics, Mother and Child Institute, Warsaw, Poland;
Department of Immunology-Histocompatibility, Aghia Sophia Childrens Hospital, Athens, Greece;
¶ Institut National de la Santé et de la Recherche Médicale Unité 396, Institut Biomedical des Cordeliers, Paris, France; and
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Hans-Spemann Laboratory, Max Planck Institut für Immunbiologie, Freiburg, Germany
| Abstract |
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| Introduction |
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-induced HLA
class II gene expression is characteristic of MHC class II
immunodeficiency, an autosomal recessive disorder. It results from
the defective transcription of all MHC class II genes
(1, 2). Since this disease was first described,
70
patients, in 50 families, have been reported. Four major
complementation groups (A, B, C, and D) have been described by
analyzing B cell lines from patients and experimental mutant
HLA-deficient cell lines (3, 4, 5). The genes responsible for
this deficiency encode the proteins that coordinately control MHC class
II locus expression; these are class II trans-activator
(CIITA),3 regulatory
factor binding to the X box (RFX) protein containing ankyrin repeats,
RFX5, and RFX-associated protein (6, 7, 8, 9). In a clinical survey of 30 patients, MHC class II deficiency resulted in combined T and B cell immunodeficiency, with an early onset and an average life expectancy of 4 years (10). Bone marrow transplantation was proposed as the only curative treatment (11) due to the very poor prognosis of most patients (despite appropriate medical care).
We report herein an unusual MHC class II deficiency phenotype in three affected siblings. Two siblings, now 21 and 22 years old, are mildly affected, and the third, who is 24 years old, is asymptomatic. However, apart from residual HLA-D staining in PBMC and rare HLA-DR-positive dermal macrophages, HLA class II expression was not detected in these siblings. Consistent with the biological manifestations, but not the clinical status of the patients, a mutation in CIITA gene was detected, which is responsible for the defect in bare lymphocyte syndrome (BLS) complementation group A. This homozygous L469P substitution in the coding region of the CIITA cDNA was shown to be responsible for defective expression of MHC-II.
| Materials and Methods |
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Isolation of PBMC, mitogen-, Ag-, and allogenic cell-induced
lymphocyte proliferation and MLR were conducted as previously described
(12). EBV B cell lines and SV40-transformed skin
fibroblasts were obtained and cultured as described previously
(4). Fibroblasts, or their heterokaryons, were treated by
IFN-
(Genex, 250 and 500 IU/ml) for 48 h before analyzing MHC
class II expression. DLD1 is a gut epithelial cell line, which was
donated by Dr. N. Cerf-Bensussan. RJ 2.5.5 is a CIITA-deficient variant
of the Raji cell line. ABL, SJO, and ZM are EBV-transformed cell lines
from MHC-II-deficient patients from the B, C, and D complementation
groups, respectively (5). The RC SV40-transformed
fibroblast cell line was established from another CIITA-deficient
patient (4).
Immunofluorescence
The anti-HLA Abs used were anti-class HLA II (-DR, -DQ,
-DP) clone IQU9 (BioDesign, Carmel, NY), and the anti-class
I Ab was W6/32 (Sera-Lab, Crowley, U.K.). The HLA-II
isotype-specific mAbs were: anti-DR L243 IgG2a (BD Biosciences, San
Jose, CA) or L112, anti-DP L227; anti-DQ Genox or L2. The
anti-CIITA Abs were IgG1 clone 7-1H (R&D Systems, Minneapolis, MN).
Ab binding was revealed by incubation with an anti-mouse Ig coupled
to FITC (Immunotech, Luminy, France). Anti-DR L243 mAb, directly
coupled to FITC (BD Biosciences) was also used. Anti-CD4, -CD8, -CD14,
-CD19, and -CD25 have been described elsewhere (12). PBMC,
B cells, untreated and IFN-
-induced fibroblasts, and different
stable transfectants were stained in suspension and analyzed with a BD
Biosciences cytofluorograph. Fibroblasts transfected with pEGFP vectors
were fixed after transfection with 0.1% glutaraldehyde for 48 h
and 2% formaldehyde in PBS for 5 min, permeabilized with cold
(-20°C) 100% methanol for 5 min, stained with
4',6'-diamidino-2-phenylindole and analyzed with a Leitz Ortoplan
microscope.
Somatic complementation analysis
B and fibroblasts cell lines from the patients and the RJ 2.5.5,
ABL, SJO, and ZM B cell lines, previously classified into
complementation groups A, B, C, and D, respectively, and fibroblasts RC
(group A) and ZM (group D) were used to obtain transient heterokaryons,
as previously described (4). KER B cell lines (13, 14) from the patients were also used. Phenotypic complementation
was tested by immunofluorescence 4872 h after cell fusion.
Fibroblasts were treated with IFN-
for 48 h before
immunofluorescence analysis.
Nucleic acid analysis
RNA extraction and RT-PCR analysis were conducted as previously described (4, 5). The CIITA was sequenced according to standard methods. PCR products were purified with the Aquick Kit (Qiagen, Chatsworth, CA). The DNA sequence of both strands was determined by Taq polymerase cycle sequencing with fluorochrome-labeled dideoxy terminators and resolved by a laser detection system (310 ABI sequencer; Applied Biosystems, Foster City, CA).
Mutagenesis
Mutagenesis of pIRES- and pEGFP-WT-CIITA vectors was conducted by use of the Transformer Site-Directed Mutagenesis kit (Clontech Laboratories, Palo Alto, CA), according to the manufacturers instructions. The primers used were: F, 5'-CAG GAT CTG CCC TTC TCC CTG-3'; and R, 5'-CAG GGA GAA GGG CAG ATC CTG-3'. The pIRES- and pEGFP-CIITA-L469P clones were sequenced before the transfection experiments.
Transfections
Transfection experiments with wild-type (WT) and mutated CIITA vectors were conducted as previously described (5). The plasmids used were pIRES-WT-CIITA, pIRES-L469P-CIITA, pEGFP-WT-CIITA, pEGFP-L469P-CIITA, pEGFP-CIITA-MT1 (15) and the corresponding empty vectors, pIRES-neo and pEGFP (both from Clontech). EGFP-CIITA is an N-terminal fusion of EGFP to the second in-frame ATG of the gene encoding CIITA. Stable pIRES-WT-CIITA and -L469P-CIITA transfectants were analyzed 26 wk after transfection.
CIITA protein sequence homologies
Sequences homologous to CIITA were identified through BLASTp and tBLASTN (16) searches with aa 400600 of human CIITA in the nonredundant databases of the National Center for Biotechnology Information. Multiple sequence alignments were performed with CLUSTALW 1.8 (BCM Search launcher) and rendered with BOXSHADE (Swiss EMBnet). Accession numbers: HSCIITA, emb|X74301.1| (6); Mus musculus CIITA mRNA, gb|U60653.1| (17); Rattus norvegicus MHC class II trans-activator, gb|AF251307.1|AF251307 (18); Homo sapiens chromosome 19 clone CTD-3022G6, gb|AC008753.8|; H. sapiens NOD2 protein (NOD2), ref|NM_022162.1| (19); H. sapiens caspase recruitment domain 4 (NOD1/CARD4), gb|AF298548.1| (20, 21); H. sapiens caspase recruitment domain protein 7 mRNA, AF298548 (22).
| Results |
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MHC class II deficiency was detected in siblings SaE, SaM, and SaA
at 15, 12, and 11 years of age, respectively. The patients are of Greek
origin and were born to nonconsanguinous parents.
Immunodeficiency was diagnosed in SaM and
SaA (Tables I
and II
) and clinical
and biological findings were consistent throughout the 7-year follow-up
period. The immune status of SaE was tested because of her sisters
disease, but she never underwent treatment. In addition to the HLA-D
expression defect, the siblings had hypoglobulinemia and an absence of
Ag-induced in vivo and in vitro immune responses after immunization.
Serum Abs to common germs (Streptococcus pneumoniae and
Haemophilus influenzae) were detected in SaE. A minor CD4
lymphopenia was detected in SaA ,whereas her sisters had normal CD4 T
cell counts. Patients SaM and SaA were treated symptomatically, and a
prophylactic treatment with intravenous Ig was then started and has
been continued since for sibling SaM. SaM became asymptomatic and has
remained so for the last 3 years, as is the eldest sibling, SaE,
without treatment. Currently, both SaM and SaE refuse to be followed by
the immunology department. No information is available on the follow-up
of SaA.
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Defective expression of HLA-DR, -DQ, and -DP molecules was
observed by immunofluorescence analysis in all three patients (Fig. 1
and data not shown). In resting PBMC
(Fig. 1
a), B cells (CD19 panels) and monocytes (CD14 panels)
were faintly stained with anti-HLA-DR mAbs L243 and L112. HLA-DQ
was weakly expressed on B cells and monocytes, and HLA-DP was faintly
detected on monocytes (Fig. 1
a). PHA-induced T cell blasts
were HLA-DR, -DQ, and -DP negative (Fig. 1
b), as were CD4
and CD8 MLR-induced blasts (Fig. 1
c). In contrast, PHA and
MLR blasts expressed CD25 normally (shown for MLR blasts (Fig. 1
c)). EBV B cell lines from SaE and SaM did not express
HLA-DR, -DP, or -DQ (Fig. 1
d), although FACS staining
revealed low, but detectable, levels of HLA-DQ and -DP expression on
fresh B CD19 cells.
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Classification of HLA class II deficiency in complementation group A in the Sa family
B cell somatic fusions induced the expression of HLA-class II in heterokaryons between ABL, SJO, and ZM cells, belonging to the complementation groups B, C, and D, respectively, in SaE. Heterokaryons between SaE and RC fibroblasts from group A were HLA class II negative. Somatic complementation was also obtained between B cells from SaE and patient KER (14), who did not belong to the AD complementation groups. Correction of the HLA-II expression was obtained by transfection of SaE and RC fibroblasts with the CIITA cDNA (see below).
CIITA mutation
The CIITA mRNA from EBV cell lines from Sa patients was amplified
by RT-PCR and analyzed by sequencing. A single homozygous T1524C
mutation, causing a leucine to proline substitution at position 469
(L469P), was found in all three patients. This mutation was confirmed
in the genomic level (Fig. 3
). A
heterozygous mutation was found in the mother. No cells were available
from the father. No other mutations were found in the entire 4.5-kb
CIITA cDNA.
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The CIITA-negative epithelial cell lines DLD1 and HeLa, the
CIITA-deficient Burkitt lymphoma cell line RJ2.2.5, and the
fibroblast cell line RC were stably transfected with the expression
vector pIRES containing WT-CIITA or L469P-CIITA and tested for HLA-DR
expression. Sixty percent of the DLD1 and HeLa cells transfected with
WT-CIITA expressed HLA-DR (Fig. 4
b and e), whereas only 0.5% of cells transfected
with the empty vector were DR+ (Fig. 4
, a and d). From 1 to 4% of the DLD1 and HeLa
L469P-CIITA transfectants were DR+ cells (Fig. 4
, c and f). Of the RJ2.2.5 cells transfected with
the same vectors, 80% of the WT transfectants became
HLA-DR+ (Fig. 4
h), whereas 14% of the
L468P transfectants expressed HLA-DR (Fig. 4
i). Ninety-six
percent of the RC cells transfected with WT-CIITA expressed HLA-DR at a
mean fluorescence intensity of 1 x 10-4
(Fig. 4
k). Thirty-one percent of cells transfected with
L469P-CIITA displayed HLA-DR staining, although at a mean fluorescence
intensity of between 10- and 1000-fold lower (Fig. 4
l).
Western blots of total cell lysates from transfected fibroblasts were
used to assess the level of transgene expression and showed that it was
even higher for the L469P CIITA protein than for the WT-CIITA (not
shown).
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L469 is part of a so-called leucine-charged domain (LCD);
465LQDLL469) conforming to the consensus LxxLL. Replacement of all
theree leucines by alanine severely impaired CIITA function
(23). Recently, several sequences were discovered that
contained homologies to both the nucleotide-binding domain and the
C-terminal leucine-rich repeats (LRRs) of CIITA (19, 20, 21, 22).
To test whether the region containing L469 is conserved among these
proteins, we identified CIITA-homologous sequences through Blast
searches and performed multiple sequence alignments of the
corresponding region with the three known CIITA sequences (human,
mouse, rat) and four homologous sequences (NOD1/CARD4, NOD2, CARD7, and
sequence AC008753). Fig. 6
shows the part
of CIITA containing both the P loop region (positions 420427), the
Mg2+ coordination region (461DAYG464), and the
LCD motif (23, 24). Whereas the P loop region is very
highly conserved among all sequences, the DxxG motif in human CIITA is
only partly conserved in mice and rats and not at all in the other
CIITA-homologous sequences. The LxxLL motif is also highly conserved
among the different sequences with an acidic amino acid at position 3
(D/E). The most highly conserved amino acid is L468, which is invariant
among all sequences. Residue L469 is also highly conserved with only
two conservative exchanges of the leucine to isoleucine (Fig. 6
).
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| Discussion |
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The HLA-II molecule expression defect in the Sa siblings was found in B
lymphocytes, monocytes, IFN-
-induced fibroblasts, dendritic cells,
and T and B cell blasts. However, faint but detectable HLA-DR, -DQ and
-DP staining was observed on B cells and monocytes. Similarly, there
was faint but detectable HLA-D staining on PBMC from KhM, another
MHC-II-deficient patient from complementation group B suffering from a
milder form of immunodeficiency (Fig. 1
f). In contrast, B
cells from HeJ, a CIITA-deficient patient with a severe
immunodeficiency, were HLA-DR- (Fig. 1
e). Therefore, it appears that a residual HLA-D staining of
PBMC correlates with less severe clinical symptoms. We have no
explanation why there was no residual HLA-D expression on any blast
types. Although mitogen and MLR stimulation led to blastogenesis and
the expression of CD25 on both CD4 and CD8 T cell blasts (shown for
SaA, Fig. 1
c), in both patients Sa and HeJ T and B cell
blasts were HLA-II negative (Fig. 1
, b, c, and
e). However, in patients Sa, in addition to PBMC, some
dermal macrophages were HLA-DR+, although dermal
dendritic cells were not.
MHC II-deficient patients with mild clinical presentation have previously been reported, e.g., the 7-year-old KER twins. Their T cells were able to respond in vivo to antigenic challenge (13, 14). Although the molecular basis of the MHC II defect was not elucidated in these twins, the Sa patients do not share the same defects, because their cells complemented the KER cell line for MHC-II expression.
Complementation experiments by somatic cell fusion assigned the Sa family defect to complementation group A, indicating that the CIITA gene was affected in cis. CIITA encodes a 1130-aa protein, the N-terminal region of which acts as a transcriptional activator and the C-terminal region of which provides MHC-II promoter specificity (6, 25, 26). CIITA controls both constitutive and inducible MHC-class II expression (27) and is considered to be a master gene in MHC class II regulation. In all tissues tested, CIITA expression correlates with MHC class II expression (28, 29), and CIITA knockout mice reproduce the phenotype of CIITA-deficient patients with only minor differences (30).
Analysis of the CIITA gene in family Sa revealed a homozygous T1524C substitution which is responsible for a leucine to proline missense mutation at aa 469 (L469P) in the CIITA coding region.
All group A patients studied thus far have T and B immunodeficiency, with severe clinical consequences (10). In one case, patient BCH, a stop codon was found at position 1256 in one CIITA allele. However, all other patients with a severe phenotype carry mutations in the 3' end of the CIITA gene (6, 31, 32, 33, 34). This is consistent with mutation analysis, which showed that MHC class II specific transcription depends on the 830 C-terminal residues of CIITA (25, 26).
The L469P mutation is the first CIITA mutation to be identified in the
N-terminal part of this 830-aa region which contains a LCD (LCD motif)
essential for CIITA activity (23). This motif is very
close to the second tripartite GTP-binding region motif, described by
Harton et al. (24). A mutant, in which the conserved LCD1
motif leucine residues (positions 465, 468, and 469) were replaced with
alanines, was unable to drive transcription from the DR-X1-X2-Y or
-W-X-Y promoters (23). Recently, several sequences showing
homology to the nucleotide binding and LRR regions of CIITA have been
published (19, 20, 21, 22). A search for protein sequence
homologies revealed that the LCD motif containing L469 is very highly
conserved in these sequences. Position 468 is the most conserved, but
L469 is also highly conserved, indicating a functional relevance of
this motif in this group of GTP-binding proteins (Fig. 6
). It also
shows that other human proteins share this motif. In the CIITA gene of
the Sa family, only leucine 469 was replaced (by proline), indicating
the importance of this motif in vivo.
Functional analysis revealed that the L469P allele of CIITA is not
completely inactive. Stable transfection of DLD1 or HeLa cells with the
L469P-CIITA cDNA did not lead to the trans activation of
MHC-II genes, but we observed a residual trans activation
potential of L469P-CIITA in RC and in RJ2.2.5 cells (Fig. 4
, i and l). In the patient-derived, CIITA-deficient
RC fibroblasts transfected with L469P-CIITA, DR expression was restored
in 30% of cells, albeit at a much lower level than that observed in
WT-CIITA transfectants. In the RJ2.5.5 B cell line, which has genomic
deletions of the CIITA gene (6), transfection with L469P
CIITA led to an abnormally low but clearly detectable HLA class II
expression in 14% of the cells. The mutated CIITA alleles from
patients BLS-2 (
940963) and BCH (BCH-1
10791106; BCH-2
E381Stop) had been tested functionally in RJ2.2.5 earlier. None of
these alleles, which were derived from patients with severe
immunodeficiency, led to residual HLA class II expression in RJ2.2.5
(6, 32). Thus, partial HLA-DR expression in the RJ2.5.5
and RC transfectants shows that the expression of the L469P-CIITA cDNA
allows partial trans activation of MHC II genes. This
probably corresponds to the residual MHC class II expression detected
on fresh PBMC from the patients.
The immunofluorescence data suggest that the recombinant L469P-CIITA
protein can translocate into the nucleus (Fig. 5
). This result is
confirmed by Western blotting, which revealed the presence of full
length L469P-CIITA protein in nuclear extracts (G. Barbieri, T.
Prodhomme, J. Vedrenne, B. Lisowska-Grospierre, D. Charron, and C.
Alcaide-Loridan, manuscript in preparation). Therefore, the
L469P mutant is the first loss-of-function mutant that retains the
ability to translocate into the nucleus. Interestingly, a mutation in
the 461DAYG465 motif that correlates with the conversion of
CIITA to the GDP-bound state leads to its exclusion from the
nucleus (24). The mutation (proline 469) is very close to
the 461DAYG465 motif and it may therefore be informative to test the
GTP binding of mutated CIITA, even if nuclear exclusion is not observed
in transfectants. The LCD1 motif mutated in Sa CIITA conforms to the
short LxxLL consensus of a putative nuclear export sequence, but
the fact that the L469P mutant protein is found in the nucleus argues
against such a function for this sequence. The role of neither the LCD
nor the GTP-binding motif (24) or of a recently shown
(35) interaction between the GTP-binding region (residues
336702) and the C-terminal leucine-rich region, LRR
(15), are well understood. Thus, further studies on the
L469P CIITA displaying these unusual features will contribute to our
understanding of the mechanisms that govern nuclear translocation and
transcriptional activation of CIITA.
Although it cannot be formally proved, it is tempting to speculate that
the residual HLA class II expression in cells from the Sa siblings and
indeed the residual trans activation potential of the L469P
allele of CIITA are responsible for the lesser severity of the
immunodeficiency than that affecting other patients. Residual HLA class
II expression was not observed on fresh B cells from two other
CIITA-deficient patients, patient HeJ (Fig. 1
e) and patient
BCH (31). However, a milder immunodeficiency associated
with a residual HLA class II expression has been described for the
Ker/Ken twins (14) and is shown here for a patient KhM
from BLS group B (Fig. 1
f). An unrelated patient with MHC II
deficiency caused by a CIITA defect presenting similarities with the Sa
patients has been described (33). This patient was not
diagnosed until the age of 27 years, well beyond the life expectancy of
most BLS patients. Clinical and immunological data for the patient have
not been reported. Interestingly, a single amino acid substitution,
F962S, was found in the coding region of CIITA (33). The
patients we describe are the first in which a mild phenotype of the
disease can be correlated with a residual trans activation
potential of the mutated regulatory factor (Fig. 4
). It can be assumed
that the ensuing residual HLA class II expression in the patients is
responsible for a substantial T cell differentiation and the capacity
to mount CD4 T cell-dependent immune responses in vivo. The fact the
patients did not develop the protracted diarrhea that affects most
patients with MHC II deficiency may be a consequence of residual MHC II
expression in intestinal epithelium, like that in PBMC.
These observations on MHC II deficiency in the Sa family have important medical implications. They show that an asymptomatic clinical course or an attenuated clinical phenotype can be observed in patients with a profound defect in the expression of HLA class II genes. Therefore, in patients with mild symptoms of immunodeficiency, an inherited MHC II expression defect should be considered. In CIITA-deficient patients, residual HLA-DR expression in peripheral blood leukocytes might be of prognostic value. When such residual HLA-DR expression is detected and coincides with an absence of severe infections, bone marrow transplantation should not be recommended. However, even those MHC II-deficient patients whose clinical status is good should be kept under close medical surveillance because late onset immunodeficiency can be fatal.
| Acknowledgments |
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| Footnotes |
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2 Address correspondence and reprint requests to Dr. Barbara Lisowska-Grospierre, Institut National de la Santé et de la Recherche Médicale Unité 429, Hôpital Necker Enfants-Malades, 149 rue de Sèvres, 75743 Paris Cedex 15, France. E-mail address: grospier{at}necker.fr ![]()
3 Abbreviations used in this paper: CIITA, class II trans-activator; RFX, regulatory factor binding to the X box; LCD, leucine-charged domain; LRR, leucine-rich repeat; GFP, green-fluorescent protein; BLS, bare lymphocyte syndrome; WT, wild type. ![]()
Received for publication January 22, 2001. Accepted for publication May 23, 2001.
| References |
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B. J. Biol. Chem. 276:4812.
B. J. Biol. Chem. 274:12955.
B. J. Biol. Chem. 274:14560.
mediated by the transactivator CIITA. Science 265:106.
induced class II expression in mouse tissue. Transplantation 62:1901.[Medline]
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