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Variable Phenotype of Severe Immunodeficiencies Associated With RMRP Gene Mutations
Variable Phenotype of Severe Immunodeficiencies Associated With RMRP Gene Mutations
DOI 10.1007/s10875-015-0135-7
ORIGINAL RESEARCH
Received: 8 September 2014 / Accepted: 23 January 2015 / Published online: 8 February 2015
# Springer Science+Business Media New York 2015
Abstract
Purpose Mutations in RMRP primarily give rise to Cartilage
Hair Hypoplasia (CHH), a highly diverse skeletal disorder
which can be associated with severe immunodeficiency. Increased availability of RMRP mutation screening has uncovered a number of infants with significant immunodeficiency
W. Ip : H. B. Gaspar : E. G. Davies : W. Qasim
Molecular and Cellular Immunology Section, Institute of Child
Health, University College of London, London, UK
W. Ip : H. B. Gaspar : E. G. Davies : W. Qasim
Department of Clinical Immunology, Great Ormond Street Hospital,
London, UK
R. Kleta
Centre for Nephrology University College London, Royal Free
Hospital, London, UK
E. Chanudet : C. Bacchelli
Centre for Translational Omics-GOSgene, Institute of Child Health,
University College, London, UK
A. Pitts : Z. Nademi : M. A. Slatter : A. R. Gennery
Institute of Cellular Medicine, Newcastle University, Newcastle upon
Tyne, UK
Z. Nademi : M. A. Slatter : A. R. Gennery
Bone Marrow Transplant Unit, Royal Victoria Infirmary, Great North
Childrens Hospital, Newcastle upon Tyne, UK
P. Amrolia : K. Rao : P. Veys
Bone Marrow Transplantation Department, Great Ormond Street
Hospital, London, UK
W. Ip (*)
Molecular and Cellular Immunology Section, UCL Institute of Child
Health, 30 Guilford Street, London WC1N 1EH, UK
e-mail: w.ip@ucl.ac.uk
Abbreviations
CHH
Cartilage hair hypoplasia
RMRP Ribonuclease mitochondrial RNA processing
SCT
Stem cell transplantation
SCID
Severe combined immunodeficiency
148
Introduction
Cartilage Hair Hypoplasia (CHH) was first described in
Amish populations as an autosomal recessive form of
metaphyseal chondrodysplasia with short-limbed dwarfism
and light-coloured hypoplastic hair [1] and affects 1.5/1000
births in this North American community compared to an
incidence of 1 in 20,000 Finnish births, the most affected
European population [2]. It has also been reported in patients
from other parts of Europe, South America, and Asia [35].
Characteristic radiological findings include short tubular
bones with widened, scalloped and sclerotic metaphyses most
notable in knees and ankles [6]. Other findings include coneshaped epiphyses, short metacarpals and phalanges, lumbar
lordosis, and femoral bowing [7, 8]. A variety of extraskeletal features have been recognised ranging from
Hirschsprungs disease to variable degrees of immunodeficiency, bone marrow dysplasia, granulomatous inflammation
and predisposition to malignancies [912]. The genetic basis
of CHH maps to chromosome 9p, a region encoding an untranslated RNA component of the mitochondrial RNAprocessing (RMRP) complex [13]. Mutations in RMRP cause
disruption of ribosomal processing and disruption of cell cycle
progression in rapidly dividing cells such as lymphocytes and
chondrocytes [14]. Over 70 different mutations have been
described [15] with a common mutation (70 A>G) accounting
for 92 % of Finnish CHH patients and 48 % of non-Finnish
patients [3]. Clinical heterogeneity and variable degree of immunodeficiency have been previously reported [9, 16, 17]. In
subjects with the most severe immunodeficiency, marrow insufficiency or haematological malignancy, allogeneic
haematopoietic stem cell transplant (SCT) offers the possibility of life saving therapy. Transplant outcomes have previously been published in a European collaborative study [18] with
overall survival of 63 % in cohort of 16 children treated between the years 19912006. Here we survey the UK experience of allo-SCT infants with RMRP mutations and uncover a
highly variable clinical phenotype, including children presenting with SCID but without skeletal manifestation of CHH.
up with a median follow-up period of 50 months from transplantation (range 21.6 to 168 months).
RMRP Gene Mutation Analysis
P1, P6 P13 underwent sequence analysis of the RMRP gene
by Regional Molecular Genetics Lab (Great Ormond Street
NHS Trust, London). RMRP gene mutation screening for P2
was performed at Centre for Pediatrics and Adolescent Medicine Freiburg University Hospital. P3-5 had gene mutation
analyses (linkage analyses, custom DNA capture and Next
Generation Sequencing) performed by UCL Genomics and
GOSgene (Centre for Translational Omics, UCL Institute of
Child Health).
Immunological Evaluation
Lymphocyte populations were enumerated using flow cytometry. Whole blood was labelled with combinations of monoclonal antibodies conjugated with fluorescein isothiocyanate
(FITC), phycoerythrin (PE), allophycocyanin (APC),
peridinin chlorophyll protein (PerCP), or fluorochrome combinations with cyanines (PerCP-Cy5.5, APC-Cy7, and PECy7) (BD Biosciences). Lymphocyte subsets were detected
with reagent containing CD3 FITC, CD16+56 PE, CD45
PerCP-Cy5.5, CD19 APC, CD4 PE-Cy7, and CD8-APCCy7. Nave, effector, and memory T cell populations were
detected with CD45RA FITC, CD27 PE, CD45 PerCP, and
CD4 or CD8 APC.
T-cell repertoire was evaluated either by flow analysis of
TCRV expression as percentage of total CD3+ T population;
or by CDR3 TCR molecular spectratyping. For the latter, template cDNA corresponding to rearranged transcripts with different CDR3 lengths from specific TCR variable region genes
was amplified by PCR and the products run on AB3130 Genetic Analyzer (Applied Biosystems) and analyzed with SpA
Web-based software [19]. T-cell functionality was assessed by
measuring T-cell proliferation in response to mitogen (PHA)
as described previously [20].
Thymopoiesis was quantified by nave T-cell numbers (as
above) and levels of T-cell receptor rearrangement excision
circles (TRECs) measured by real-time qPCR as described
previously [21].
B-cell immunity was evaluated by immunoglobulin levels
(IgG, A, M) measured with a Dade Behring (Milton Keynes)
nephelometer (BN II), according to the manufacturers instructions; and by measuring vaccine responses against childhood immunisations.
Analysis of Chimerism
Engraftment studies were performed by short tandem repeat
variability on peripheral blood samples using PowerPlex 16
Results
Clinical Features (Table 1)
149
patients had abnormal T cell repertoire. P2 (Omenns syndrome) had abnormal spectratype with oligoclonal expansions. P6 and P7 had reduced percentage of T cells expressing
a V marker without oligoclonal expansions. TRECs were
measured in 9 out of 12 patients and they were low or absent
in all.
Thirteen different mutations in the RMRP gene were identified (Table 3) including 3 new mutations that have not been
reported previously. Five patients (P1, P2, P6, P10, P12) were
compound heterozygotes for either duplication or insertion in
the promoter region and a single nucleotide substitution in the
transcribed region. P1 had a 17-nucleotide insertion at position 20 located between the TATA box and the transcription
initiation site on one allele and a 748C>T point mutation in the
5 region of the other allele. P2 had on one allele a 15-bp
duplication at position 25 in the promoter region followed
by a 4C>T point mutation in the second allele. P6 (of mixed
race African and Caucasian) was compound heterozygote for
the common 70A>G mutation, and a 7-nucleotide insertion at
position 20 in the promoter region on another allele. P10 had
monoalleic 13 bp duplication in the promoter (not previously
described) along with previously reported 4C>T point mutation on the other allele (described in McCann LJ et al. 2014).
P12 inherited from one parent a 28-nucleotide duplication at
position 28 (not previously described), and a 154 G>C point
mutation from another parent. P7 and P8 were compound
heterozygous for single base pair substitutions only. P7 had
a 151 G>A point mutation in one allele which is newly identified but position 151 is known to be highly conserved between species. This patient carried the common 70 A>G mutation in the other allele. P8 was compound heterozygous for
two previously reported mutations.
Homozygous mutations were identified in six patients, two
of whom carried the common 70 A>G mutation (P9 and P13).
Three siblings (P3, P4 and P5) who had originally undergone
SCT for undefined SCID were homozygous for 35 C>A nucleotide substitutions. This molecular diagnosis was uncovered by linkage analyses performed on all members of the
family which had identified a 46 Mb region containing around
426 genes. Sanger sequencing confirmed the homozygous
mutations within the RMRP gene. Compound heterozygous
mutations have previously been reported at the same position
of 35 in CHH in association with a 70A>G mutation. The
affected P3 domain is critical for RMRP binding to protein
subunits and nucleolar localisation [22]. Interestingly homozygous 35 C>A mutations in our kindred have resulted in
different skeletal phenotypes, with only P3 and P5 having
radiological evidence of skeletal dysplasia. More recently, a
newborn member of the extended family was found to encode
the same mutations but has completely normal immunological
and growth parameters at 1 year of age. There are perhaps yet
unknown modifier genes at play that determine the manifestations of genetic mutations in the RMRP gene.
Siblings
17 m
120 m
108 m
ND c
+0.4
M
0m
P 5*
17 m
+
-
+
+ ADV gut
-c
+<<0.4
F
3m
P6
3m
Neutropenia
(auto immune)
ND
+ <0.4
M
8m
P7
276 m
Sclerosing
cholangitis
+
-
++
+<<<0.4
M
24 m
P8
12 m
+
+ EBV,
ADV,
HHV6
+f
+g
-
+ <0.4
F
0m
P 9^
+
+ EBV associated
B cell lymphoma
Neutropenia,
Granulomatous
skin lesions
1m
+
+ EBV
+ <0.4
F
32 m
P10#
6m
+
-
+d
+ <0.4
M
19 m
P 11
1m
+ EBV
LPD
+
+e
+ <0.4
F
29 m
P 12^
4m
+
+ EBV,
HHV6
++
+ <0.4
M
11 m
P 13^
these three siblings did not undergo skeletal surveys until after the diagnosis of CHH was made. P3 had typical features of CHH (degree of metaphyseal dysplasia ++) P4 had normal X-ray. P5 had mild
metaphyseal and epiphyseal changes without shortening of long bones
P9-P13 were treated at Great North Childrens Hospital, Newcastle upon Tyne
++ bowed, shortened long bones, marked metaphyseal cupping, cone-shaped metaphyses in phalanges
5m
24 m
Time to diagnosis
(from presentation)
+
Omenns
+
+
-
Other Features
GI symptoms
Anaemia
Malignancy
+
-
+ severe
varicella
+ EBV
ND c
ND c
+
+ RSV, Para flu,
CMV, Candida,
polio stool
+
-
+0.4
+0.4
+a<<<0.4
+<<<0.4
F
0m
P 4*
F
5m
P 3*
F
5m
P2
M
108 m
P1
General features
Sex
Age at Presentation
Clinical features
Short Statue
(height %ile) at
presentation
Radiological skeletal
changes b
Fine silky hair
Recurrent Infections
Table 1
150
J Clin Immunol (2015) 35:147157
P1
P2
P9
26 months
951 (14003700)
251 (7002200)
76 (4901300)
0a (3901400)
179 (130720)
ND
ND
ND
ND
1885 (14003700)
459 (7002200)
714 (4901300)
1064 (3901400)
615 (130720)
ND
Absent
Absent
IgG
+IgM
390 (25005500)
160 (16004000)
140 (5601700)
430 (3002000)
1060 (1701100)
ND
Absent
Absent
IgA
32 months
P 11
620 (25005500)
200 (16004000)
400 (5601700)
370 (3002000)
160 (1701100)
ND
ND
Impaired
IgA, IgM
1280 (25005600)
210 (18004000)
820 (5901600)
320 (4303000)
660 (170830)
ND
V low
Absent
Normal
0 months
P5
570 (14003700)
190 (7002200)
9 (4901300)
290 (3901400)
ND (130720)
ND
Absent
Absent
IgG, IgA, IgM
2 years
P 12
210 (25005600)
110 (18004000)
30 (5901600)
670 (4303000)
680 (170830)
36 % V expression
V low
Normal
IgG,A,M
3 months
P6
ND not done
* T-cell repertoire was evaluated either by analysis of TCRV expression as a percentage of the total CD3+ T population; or by CDR3 TCR spectratyping
24 months
12 months
Lymphocyte subsets (cells/L) (normal range of values for age)
300 (14003700)
723 (21006200)
170 (7002200)
389 (13003400)
420 (4901300)
194 (6202000)
470 (3901400)
311 (7202600)
660 (100480)
914 (160950)
ND
ND
ND
ND
Impaired
Low
Normal IgG, IgA, IgM
Normal IgG, IgM IgA
P8
0 months
P4
5 months
P3
P 10
Age at Evaluation
9 years
5 months
Lymphocyte subsets (cells/L) (normal range of values for age)
CD3
270 (12002600)
1290 (25005600)
CD4
130 (6501500)
1250 (18004000)
CD8
70 (3701100)
20 (5901600)
CD19
50 (270860)
210 (4303000)
CD56
230 (100480)
300 (170830)
T cell repertoire*
Normal
Oligoclonal expansion
TRECs
Absent
Absent
Proliferative response to PHA
Absent
Impaired
IgG, IgA, IgM
IgG
IgG, IgA
Table 2
915 (21006200)
417 (13003400)
221 (6202000)
334 (7202600)
212 (180920)
ND
V low
ND
Normal
23 months
P 13
510 (19005900)
440 (14004300)
20 (5001700)
510 (6102600)
820 (160950)
48 % V expression
Low
Impaired
IgG,A,M
10 months
P7
152
Table 3
Patient
Ethnicity
Allele 1
Allele 2
Immunological
phenotype
Skeletal phenotypeb
Mutation references
(allele 1; allele 2)
Caucasian
20_-4 dup
4 C>T
CID
Caucasian
25_-11 dup
4 C>T
CID+OS
3
4
5
6
South Asian
South Asian
South Asian
African
35 C>A a
35 C>A a
35 C>A a
20_-14 dup
35 C>A a
35 C>A a
35 C>A a
70 A>G
CID
SCID
SCID
SCID
Caucasian
151 G>Aa
70 A>G
CID
Caucasian
146 G>A
242 A>G
CID
Caucasian
70 A>G
70 A>G
CID
CHH
10
11
Caucasian
South Asian
26_-14 dup
30 A>G
4 C>T
30 A>G
CID
CID
Atypical
Atypical
12
13
South Asian
Caucasian
28_-1dup
70 A>G
154 G>C
70 A>G
CID
CID
Atypical
CHH
Mutations not previously reported but nucleotides 35 and 151 are highly conserved between species
CSA/MTX
BM
100 %
A&W
30 m
P9
48 m 72 m (top-up)
7/10 MMUD
B/Cy
CSA
BM
100 %
A&W
168 m
GvHD prophylaxis
Stem cell source
Chimerism
Outcome
Last follow-up from tx
P8
125 m
10/10 MUD
F/M/A
CSA/MP
BM
53 %WB
A&W
71 m
A&W
142 m
CSA/MMF
BM
100 %
F/M/C
5m
10/10 MFD
P3
A&W
90 m
Unconditioned (1st)
F/M (2nd)
CSA/MMF(2nd)
Cord (1st) BM (2nd)
27 % WB 70 % CD3
18 % CD15 25 %
CD19
A&W
21.6 m
P5
A&W
48 m
P 11
CSA/MMF
PBSC
100 %
F/M/C
36 m
9/10 MMUD
P4
Died 1 m post
42 m
9/10 MMUD
T/Cy/C
CSA/MMF
BM
100 %
P 12
A&W
24 m
CSA/MMF
Cord (1st) PBSC (2nd)
100 %
8 m (1st) 23 m (2nd)
8/10 MMUD (1st) 9/10
MMUD (2nd)
T/F (1st) F/M/C (2nd)
P6
32.4 m
MSD
B/Cy/C
CSA
BM
100 % CD3 91 %
CD15 100 % CD19
A&W
108 m
P 13
Died 9 m post
CSA/MMF
PBSC
100 % WB 100 %
CD3 100 % CD15
F/M/C
16.8 m
10/10 MUD
P7
ATG 15 mg/kg
Campath 1 mg/kg
Treosulfan 42 g/m2
Busulfan 16 mg/kg
MUD Matched unrelated donor, MSD Matched sibling donor, MMUD Mismatched unrelated donor, MFD Matched family donor, A Anti-thymocyte globulin, F Fludarabine, M Melphalan, C Campath, B
Busulfan, T Treosulfan, Cy Cyclophosphamide, CSA Cyclosporin, MTX Methotrexate, MMF Mycophenolate Mofetil, MP Methylprednisolone, BM Bone marrow, PBSC Peripheral blood stem cell, WB
whole blood, A&W alive and well
36 m
10/10 MUD
T/F/C
CSA/MMF
PBSC
99 % CD3 87 %
CD15 95 % CD19
A&W
24 m
P 10
CSA/MMF
BM
22 % WB 79 %
CD3 0 % CD15
40 % CD19
A&W
50 m
T/F/C
B/F
Conditioning
8m
9/10 MMUD
P2
133 m
MSD
P1
Haematopoietic stem cell transplant characteristics in 13 patients with Cartilage Hair Hypoplasia
Age at transplant
Donor
Table 4
ND not done
50 m
2190
1280
730
520
150
Normal
Low at 7 m post tx
Normal
Normal
Normal
+ ND
1250
740
440
330
370
Normal
Normal
Normal
Normal
Borderline low IgG, A, M
+ ND
P2
30 m
P1
Table 5
+
+
3200
1390
1430
340
550
Near Normal
Low 2y9m post tx
Normal
Normal
Normal
142 m
P3
+
+
3630
1590
1820
500
270
Normal
Normal
Normal
Normal
Normal
90 m
P4
3660
2000
1120
780
390
Normal
Normal
Normal
Normal
Normal
21.6 m
P5
ND
ND
2350
1840
430
110
230
ND
Low at 6 m post tx
Normal
ND
Normal
24 m
P6
+
+
860
430
300
120
200
ND
Normal
ND
Normal
Normal
71 m
P8
+
+
848
475
354
226
57
ND
Low
ND
Normal
Low IgA
168 m
P9
ND
ND
1861
1296
459
411
920
ND
Low
Normal
Normal
Normal
24 m
P 10
+
+
3898
1974
1791
543
187
ND
Normal
Normal
Normal
Normal
48 m
P 11
+
+
1540
768
680
212
146
ND
Low
Normal
Normal
Normal
108 m
P 13
154
J Clin Immunol (2015) 35:147157
Discussion
This cohort of patients with RMRP mutations demonstrates
that although CHH may typically present with distinctive phenotypic features of skeletal dysplasia, disproportionate short
stature, hypoplastic hair and associated immunological deficiency, in the immunology clinic the phenotype can be highly
variable and may include severe immune deficiency with or
without associated short stature. [9, 16, 2224]. Importantly,
characteristic metaphyseal changes seen in CHH may not be
present at birth and often manifest after 2 years of age [8,
2527]. In this cohort, 5 subjects were transplanted in infancy
before the onset of radiological changes and only 7 out of 13
patients had evidence of characteristic radiological features
such as metaphyseal dysplasia and bowing of femora. Remarkable clinical heterogeneity may even occur within
sibships [9, 16], and we found that of three siblings in our
cohort with identical homozygous mutations in the RMRP
gene, only two had clinical and radiological skeletal manifestations of CHH. Interestingly newborn screening of a cousin
from this consanguineous kindred uncovered a further subject
with identical homozygous mutations but no evidence of either immune deficiency or skeletal dysplasia.
155
156
A number of subjects have mixed myeloid or B cell chimerism, and here it may be that donor derived T cell immune
surveillance is sufficient to control transformation events. Experience from other disorders, including Fanconi anaemia [33]
suggests that the risk of malignancy in other organ systems,
including the skin, may persist.
In summary we report the UK transplant experience for
CHH and include a group of subjects who presented with
short stature and immunodeficiency as predominant features
rather than typical CHH skeletal changes. We advocate that
RMRP mutation screening is considered in any child with
undefined combined immunodeficiency even in the absence
of skeletal features.
Acknowledgments The authors would like to thank Kerra Pearce and
Mike Hubank (UCL Genomics) for their assistance with microarrays and
NGS work.
Funding Source This work was undertaken at GOSH/UCL Institute of
Child Health which received funding from the Department of Healths
NIHR Biomedical Research Centres funding scheme and GOSH charity
special trustees. The UK service for primary immunodeficiency received
support from the Department of Health via the national commissioning
group (NCG).
Financial Disclosure Winnie Ip has no financial relationships relevant
to this article. All the other authors also have no financial disclosures
relevant to this article.
Conflict of Interest Winnie Ip has no conflict of interest to disclose. All
the other authors also have no conflicts of interest relevant to this article to
disclose.
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