Biallelic mutations in calcium release activated channel regulator 2A (CRACR2A) cause a primary immunodeficiency disorder

  1. Beibei Wu
  2. Laura Rice
  3. Jennifer Shrimpton
  4. Dylan Lawless
  5. Kieran Walker
  6. Clive Carter
  7. Lynn McKeown
  8. Rashida Anwar
  9. Gina M Doody
  10. Sonal Srikanth
  11. Yousang Gwack  Is a corresponding author
  12. Sinisa Savic  Is a corresponding author
  1. Department of Physiology, David Geffen School of Medicine, UCLA, United States
  2. Leeds Institute of Medical Research, University of Leeds, United Kingdom
  3. Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, United Kingdom
  4. Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
  5. Department of Clinical Immunology and Allergy, St James's University Hospital, United Kingdom
  6. Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, United Kingdom
  7. National Institute for Health Research-Leeds Biomedical Research Centre and Leeds Institute of Rheumatic and Musculoskeletal Medicine, Wellcome Trust Brenner Building, St James's University Hospital, United Kingdom
8 figures, 2 tables and 3 additional files

Figures

Figure 1 with 1 supplement
Clinical and immunological features of index patient.

(A) A computerized tomography scan of the chest showing area of cylindrical bronchiectasis at the basal segment of the left lower lobe. (B) TCR repertoire as assessed by T receptor spectraphenotyping. Data are representative of one independent assay. (C) Phytohaemagglutinin (PHA) and (D) anti-CD3 T cell proliferation. CPM (counts per minute). Data are representative of three independent assays.

Figure 1—figure supplement 1
T helper (TH) TH1, TH2, and TH17 peripheral blood phenotyping.

(A) T-helper (Th) 1, Th2 and Th17 cell distribution among CD4+ T cells in the peripheral blood. Grey bars healthy controls (N = 6), blue bars patient (two separate evaluations). (B) Representative dot plot shows the gating strategy. Whole EDTA blood was stained with a combination of CD3-V500, CD4-BV421, CCR6-Pe, and CXCR3-Alexa-Fluoro 647.

A rare biallelic mutation in CRACR2A segregates with the disease.

(A) Pedigree showing the index case and p.[R144G/E300*] and p.E278D CRACR2A variant carriers. The circles and squares represent female and male members, respectively. Black shading shows affected individuals, either heterozygous (partial black) or homozygous (completely black). (B) Sanger sequencing data of the proband showing the indicated mutations. (C) Schematic of human CRACR2A showing the location of compound heterozygous mutations from the patient’s alleles. The maternal allele comprised of an p.R144G variant that was located in the EF-hand motif and an p.E300* truncation variant within the leucine-rich region (LR). The paternal allele contained the p.E278D variant that was located in the coiled-coil domain 2 (CC1 and CC2). CRACR2A also contains a proline-rich domain (PRD) and a C-terminal Rab GTPase domain. (D) Detection of CRACR2A in human PBMCs harvested from healthy control and patient by immunoblotting (left) and real-time quantitative RT-PCR (right). For qRT-PCR, cells were left unstimulated or re-stimulated with PMA plus ionomycin for 5 hr. β-actin was used as a loading control for immunoblotting. Immunoblot is representative of two independent experiments and mRNA analysis shows representative triplicate from two independent experiments. * p < 0.05.

Patient B cell responses to T cell-dependent (TD) stimulation.

(A) Schematic representation of the culture conditions used to assess plasma cell differentiation in vitro. PBs – Plasmablasts, PCs – Plasma cells (B) Representative flow plots showing CD38 and CD138 expression profile following TD stimulation with F(ab’)two anti-IgG/M and CD40L. Percentages are indicated within individual quadrants. Data are representative of 2 independent assays. (C) Secreted levels of IgM (left) and IgG (right) from the cells in (B) at indicated time points. HC1-5 (Healthy control) represents data from five independent healthy donor cells.

Figure 4 with 1 supplement
Patient T cell responses to T cell receptor stimulation.

(A) Representative flow plots showing expression of IFN-γ in human PBMCs from a healthy donor and the patient. PBMCs were stimulated with anti-CD3 and anti-CD28 antibodies for 48 hr and cultured for further 4 days in the presence of IL-2 before re-stimulation with PMA plus ionomycin for 5 hr for cytokine analysis. Cells were gated for CD4+ T cells. (B) Quantitative mRNA expression analysis (± s.d.m.) of indicated cytokines from human PBMCs (cultured as mentioned above) with or without stimulation with PMA plus ionomycin for 5 hr. (C) Levels of IL-2 and TNF in human PBMCs from culture supernatants of cells stimulated as described above (B) were determined by ELISA. (D) Representative traces showing averaged (± SEM) SOCE responses from healthy control and patient PBMCs (cultured as indicated in A), after transient stimulation with anti-CD3 antibody cross-linking, or ionomycin (0.5 µM) in the presence of external solution containing 2 mM Ca2+ (left) as indicated. Bar graphs show baseline subtracted ratio values for anti-CD3 antibody cross-linking or ionomycin (average± SEM) from six independent experiments (right). (E) Representative traces showing averaged (± SEM) SOCE responses from healthy control and patient PBMCs (cultured as indicated in A), after store-depletion with thapsigargin (1 µM) stimulation in Ca2+-free Ringer’s solution. SOCE was measured by addition of 2 mM Ca2+-containing Ringer’s solution as indicated (left). Bar graph shows baseline subtracted ratio values at the peak of SOCE (average± SEM) from four independent experiments (right). (F) Phosphorylated JNK levels in CD4+ T cells from healthy control and patient PBMCs (cultured as indicated in A), stimulated with anti-CD3 antibody for indicated times. Bar graphs show average± SEM from three independent experiments. ** p < 0.005, *** p < 0.0001.

Figure 4—figure supplement 1
Expression of ORAI1 and STIM1 in PBMCs from healthy control and patient.

(A) Representative immunoblot showing expression of indicated proteins in PBMC lysates from control and patient. (B) Relative transcript expression of indicated genes from PBMCs of healthy control and patient using real-time quantitative RT-PCR measurements.

Figure 5 with 1 supplement
Cytokine expression profiles in T cells expressing individual allelic mutations in CRACR2A.

(A) Representative flow plots showing expression of IL-2 in control or CRACR2A KO Jurkat T cells stably expressing FLAG-tagged WT CRACR2A, CRACR2AE278D (E278D), or CRACR2AR144G/E300* (DM) after stimulation with PMA plus ionomycin for 16 hr (left). Bar graph shows means ± s.e.m. of pooled technical replicates from two independent experiments (right). (B) Representative flow plots showing expression of IFN-γ in primary human CD4+ T cells transduced with lentiviruses encoding CRACR2A-targeting sgRNA and those encoding cDNAs of WT or indicated mutants of CRACR2A after stimulation with anti-CD3 and anti-CD28 antibodies for 5 hr (left). Bar graph (right) shows means ± s.e.m. of pooled technical replicates from three independent experiments. (C) Representative flow plots showing expression of IFN-γ in primary human CD4+ T cells purified from healthy donors and transduced with lentiviruses encoding cDNAs for WT or indicated mutant of CRACR2A after stimulation with anti-CD3 and anti-CD28 antibodies for 5 hr (left). Bar graph (right) shows means ± s.e.m. of pooled technical replicates from three independent experiments. * p < 0.05, *** p < 0.0001.

Figure 5—figure supplement 1
Expression profile of individual allelic mutants of CRACR2A in different cell types.

(A) Lysates of HEK293 cells stably expressing N-terminally FLAG-tagged WT or indicated mutants of CRACR2A were immunoblotted with anti-FLAG antibody. (B) Representative immunoblot showing endogenous CRACR2A expression in lysates of Jurkat T cells expressing control sgRNA or three different CRACR2A-targeting sgRNAs (# 1, #2, and #3). (C) Lysates of CRACR2A KO Jurkat T cells (sgRNA#2) stably expressing N-terminally FLAG-tagged WT or mutant CRACR2A were immunoblotted for detection of indicated proteins. β-actin – loading control.

SOCE and JNK phosphorylation in T cells expressing individual allelic mutations in CRACR2A.

(A) Representative traces showing averaged SOCE from control (48 cells) or CRACR2A-KO Jurkat T cells (KO) transduced with an empty vector (55 cells) or those encoding FLAG-tagged WT CRACR2A (45 cells), CRACR2AE278D (E278D, 40 cells), or CRACR2AR144G/E300* (DM, 50 cells) mutants (left). Cells were stimulated with anti-CD3 antibodies, followed by ionomycin treatment in the presence of external solution containing 2 mM Ca2+. Bar graphs show averaged baseline subtracted peak SOCE (± s.e.m.) from anti-CD3 antibody and ionomycin treatments, from three independent experiments (right). (B) Representative traces showing averaged SOCE induced by thapsigargin (TG) treatment from control (52 cells) or CRACR2A-KO Jurkat T cells (KO) transduced with empty vector (46 cells) or those encoding FLAG-tagged WT CRACR2A (49 cells), CRACR2AE278D (E278D, 51 cells), or CRACR2AR144G/E300* (DM, 50 cells) mutants (top). Cells were stimulated with thapsigargin in Ca2+-free solution to deplete the intracellular stores and exposed to external solution containing 2.0 mM Ca2+. Bar graphs below show averaged baseline subtracted SOCE levels (± s.e.m.) at the peak (center) or later time point (sustained – 900 s, bottom) from three independent experiments. (C) Phosphorylated JNK levels in control or CRACR2A KO Jurkat T cells stably expressing WT and indicated mutants of CRACR2A, stimulated with anti-CD3 antibody for indicated times. Graphs show average± SDM from three independent experiments. * p < 0.05, ** p < 0.005, *** p < 0.0001.

Biochemical interactions and localization profiles of individual allelic mutations in CRACR2A.

(A) Immunoprecipitation for detection of binding between WT and indicated mutants of CRACR2A (E278D, or DM) with ORAI1/STIM1. Lysates of HEK293T cells expressing FLAG-tagged CRACR2A in the presence of 6 X His-tagged ORAI1 and STIM1, were subjected to immunoprecipitation with anti-FLAG antibodies and analyzed by immunoblotting for detection of the indicated proteins. Bar graphs below show densitometry analysis of binding of CRACR2A to ORAI1 (left) and STIM1 (right), normalized to that of WT CRACR2A, from three independent experiments. (B) Immunoprecipitation for detection of binding between CRACR2A and VAV1. Lysates of HEK293T cells expressing FLAG-tagged WT or indicated mutants of CRACR2A in the presence of GFP-tagged VAV1, were subjected to immunoprecipitation with anti-FLAG antibodies and analyzed by immunoblotting for detection of indicated proteins. Bar graph below shows densitometry analysis of binding of CRACR2A to VAV1, normalized to that of WT CRACR2A, from three independent experiments. (C) Representative confocal images of CRACR2A KO Jurkat cells stably expressing N-terminally FLAG-tagged WT or indicated mutants of CRACR2A under resting conditions (top panels) or 20 min after dropping on stimulatory anti-CD3 antibody-coated coverslips (middle and bottom panels). The top panels showed images from the center of the cell. The middle panels show images from the bottom of the cell, which was in contact with the coverslip and the bottom panels showed images from the center of the anti-CD3 antibody-stimulated cell. F-Actin staining – green, anti-FLAG antibody staining – red. Images are representative of at least 10 cells in each condition. * p < 0.05, ** p < 0.005.

Author response image 1
Levels of intracellular Ca2+ are measured in primary T cells by exchanging Ca2+-free solution with that containing 2 mM CaCl2.

Copied from PMID: 22586105.

Tables

Table 1
Immunological characteristics of patient with variants in EFCAB4B.
Date/year20052011201720192021 (Feb)2021 (Nov)Ref
Total lymphocyte count2,8809901,2011,5721,4721,2681000–2800 cells/µl
CD3+ T cells2,505733891990952846700–1200 cells/µl
CD4+ T cellTotal216235148165122112300–1400 cells/µl
CD27+ CD45RA+ (naïve)%20.9212.6525.514–65%
CD27+ CD45RA- (memory)%42.3447.0442.915–52%
CD27-CD45RA- (memory effector) %36.0137.6720.58–35%
CD27+ CD45RA-2.6411.10–22%
CD25+ CD127- (Treg)%0.731.62.93.53–10%
CD8+ T cellsTotal2080475738840772689200–900 cells/µl
CD27+ CD45RA+ (naïve)17.6931.31.5–65.5%
CD27+ CD45RA- (memory)25.1619.13.5–28.6%
CD27- CD45RA- (memory effector)16.0911.10.7–72.6%
CD27- CD45RA+ (effector)41.0738.61.6–53%
CD19+ (B cells)Total24510273778771100–500 cells/µl
CD27- IgM+ IgD + (naïve) %63.189.1867.77844–84%
CD24hi CD38hi (Transitional) %6.710.38.2112–14%
CD27+ IgM + IgD+ (non-switched) %15.43.6922.5115–32%
CD27+ IgM- IgD- (switched memory) %14.77.155.755–33%
Plasmablasts %0.20.41.110.2–5%
CD56+ CD16+ (NK cells)14413929048642934090–600 cells/µl
Immunoglobulin profile
IgG1.48.410.38.39.96–16 g/l
IgA< 0.06< 0.06< 0.06< 0.06< 0.060.8–4 g/l
IgM< 0.05< 0.05< 0.05< 0.05< 0.050.5–2 g/l
IgE< 0.21–120 ku/l
Key resources table
Reagent type (species) or
resource
DesignationSource or referenceIdentifiersAdditional information
Gene
(Homo sapiens)
CRACR2ANCBIGene ID: 84,766
Strain, strain background (Escherichia coli)DH5αThermo fisher ScientificCat# 18265017
Cell line (Homo sapiens)Jurkat E6-1 T cellsATCCNot tested for mycoplasmaCat# TIB-152
Cell line (Homo sapiens)HEK293TATCCNot tested for mycoplasmaCat# CRL-3216
Cell line (Mus musculus)CD40L-expressing L cell fibroblastsDiehl et al., 2008Irradiated at 50 Gy
for 50 minutes prior
to use
Cell line (Mus musculus)M2-10B4 bone marrow stromal cellsLemoine et al., 1988Irradiated at 57 Gy
for 57 minutes prior
to use
Transfected construct (Homo sapiens)Primers for plasmid constructionThis paperSupplementary file 1
Biological sample (Homo-sapiens)Primary human peripheral blood mononuclear cellsThis paperIsolated from the
patient and healthy
controls
AntibodyAnti-human
Phospho JNK
(mouse monoclonal)
Cell Signaling TechnologiesCat# 9,255Flow cytometry (1:100)
AntibodyAnti-Human STIM1(rabbit)Cell Signaling TechnologiesCat# 5,668 SWB (1:5000)
AntibodyAnti-His-tag(rabbit)Cell Signaling TechnologiesCat# 12,698 SWB (1:5000)
AntibodyAnti-FLAG tag(mouse
monoclonal)
Millipore SigmaCat# F3040WB (1:5000)
AntibodyAnti-human
ORAI1(rabbit
polyclonal)
Millipore SigmaCat# AB9868WB (1:5000)
AntibodyAnti-Vav1(rabbit)Cell Signaling TechnologiesCat# 2,502WB (1:2000)
AntibodyAnti-β-actin(mouse
monoclonal)
Santa Cruz BiotechnologyCat# sc-47778WB (1:2500)
Antibodyanti-human CD3 antibody (mouse monoclonal)Bio X CellClone OKT-31 μg/ml
AntibodyAnti-human CD28 antibody (mouse monoclonal)Bio X CellCat. #: BE0921Clone CD28.21 μg/ml
AntibodyAnti-CD4-FITC(mouse
monoclonal)
eBioscienceClone OKT-4FACS5 μl/test
AntibodyAnti-IFN-
gama-PE-Cy7
eBioscienceClone 45.B3FACS5 μl/test
AntibodyAnt-IL2-PEeBioscienceCat# MQ1-17H12FACS5 μl/test
AntibodyAnti-human,CD19-BV421(mouse
monoclonal)
BDCat. #: 562,440Clone HIB19FACS5 μl/test
AntibodyAnti-human,
CD27-PE (mouse
monoclonal)
BDCat. #: No:555,441Clone: M-T271FACS20 μl/test
AntibodyAnti-human,IgD-FITC(mouse
monoclonal)
BDCat. #: 561,490Clone IA6-2FACS5 μl/test
AntibodyAnti-human,IgM-Perc-cy5.5(mouse
monoclonal)
BDCat. #: 561,285Clone G20-R7FACS5 μl/test
AntibodyAnti-human, CD24-FITC (mouse monoclonal)BDCat. #: 555,427Clone ML-5FACS20 μl/test
AntibodyAnti-human,CD38-Pecy7(mouse
monoclonal)
BDCat. #: 335,825CloneHB-7FACS5 μl/test
AntibodyAnti-human,CD3-V500(mouse
monoclonal)
BDCat. #: 561,416Clone UCHT-1FACS5 μl/test
AntibodyAnti-human,
CD4-BV421(mouse
monoclonal)
BDCat. #: 562,424Clone RPA-T4FACS5 μl/test
AntibodyAnti-human,
CD25-Pecy7monoclonal
BDCat. #: 335,824Clone 2A3FACS5 μl/test
AntibodyAnti-human,
CD127-PrcP
Cy5.5(mouse
monoclonal)
BDCat. #: 560,551Clone HIL-7R-M21FACS5 μl/test
AntibodyAnti-human,
FoxP3-
Alexa 488(mouse
monoclonal)
BDCat. #: 566,526Clone 2632/E7FACS5 μl/test
AntibodyAnti-human,
CD196-PE(mouse
monoclonal)
BDCat. #: 559 562Clone 11A9FACS10 μl/test
AntibodyAnti-human,CD-183-APC(mouse
monoclonal)
BDCat. #: 550,967FACS20 μl/test
AntibodyPolyclonal
F(ab′)two goat
anti-human IgM/IgG/IgA
Jackson ImmunoResearchCat. #: 109-006-12910 μg/ml
AntibodyAnti-human
CD138-APC(mouse
monoclonal)
Miltenyi BiotechCat. #: 130-117-395FACS2 μl/test
Recombinant
DNA reagent
FGllFThis paperN/A
Recombinant
DNA reagent
pmCherry-N1ClontechClontech plasmid#632,523
Recombinant
DNA reagent
pMD2.GAddgeneAddgene plasmid #12,259
Recombinant
DNA reagent
psPAX2AddgeneAddgene plasmid #12,260
Recombinant
DNA reagent
pLentiCas9-
blasticidin
AddgeneAddgene plasmid #52,962
Recombinant
DNA reagent
pLentiguide-puro_
hCRACR2Asg#1
This paperDetails in
Supplementary file 1
Recombinant
DNA reagent
pLentiguide-puro_
hCRACR2Asg#2
This paperDetails in
Supplementary file 1
Recombinant
DNA reagent
pLentiguide-puro_
hCRACR2Asg#3
This paperDetails in
Supplementary file 1
Recombinant
DNA reagent
pLentiguide-puro_
hORAI1sg
This paperDetails in
Supplementary file 1
Recombinant
DNA reagent
FG11F
CRACR2A WT
This paperDetails in
Supplementary file 1
Recombinant
DNA reagent
FG11F CRACR2AE278DThis paperDetails in
Supplementary file 1
Recombinant
DNA reagent
FG11F CRACR2AR144GThis paperDetails in
Supplementary file 1
Recombinant
DNA reagent
FG11F CRAC
R2AR144G,E300*
This paperDetails in
Supplementary file 1
Sequence-
based reagent
SureSelect XT Human
All Exon V5
Agilent
Sequence-
based reagent
CRACR2AExon 6_FThis paperATGATTCCT
GGCAGGTGAGA
Sequence-
based reagent
CRACR2AExon 6_RThis paperATTCCAGTG
CAGGGACCAG
Sequence-
based reagent
CRACR2AExon 9_FThis paperGGCCCTGATG
TTGAGTAGGT
Sequence-
based reagent
CRACR2AExon 9_RThis paperGTGAATGGC
AGGGAAAGTGG
Sequence-
based reagent
CRACR2AExon 10_FThis paperAAACAAGGT
GAGGCCAGGG
Sequence-
based reagent
CRACR2AExon 10_RThis paperAGCCCAAAT
CCTCTT
TTCACAG
Peptide,
recombinant
protein
IL-2RocheCat. #: HIL2-RO
Peptide,
recombinant
protein
IL-21PeprotechCat. #: 200–2150 ng/ml
Peptide,
recombinant
protein
IL-2PeprotechCat# 200–0220 units/ml
Commercial
assay or kit
aCD3 platesCorningCat. #:354,72510 ng/ml
Commercial
assay or kit
B cell isolation kitMiltenyi Biotech,Cat. #:130-091-151100 U/ml
Commercial
assay or kit
QIAamp
DNA Blood kit
QiagenCat. #:61,104
Commercial
assay or kit
Human IgG ELISA Quantitation SetBethyl Laboratories Inc,Cat. #: E80-104
Commercial
assay or kit
Human IgM ELISA Quantitation SetBethyl Laboratories Inc,Cat. #: E80-100
Commercial
assay or kit
MagniSort human naïve CD4+ T cell enrichment kitThermofisher ScientificCat. #: 8804-6814-74
Commercial
assay or kit
FOXP3/
Transcription Factor staining Buffer set
Thermofisher ScientificCat. #: 2229155
Chemical
compound,
drug
PHA-LSigmaCat. #:L-4144
Chemical
compound,
drug
3HThymidinePerkin ElmerCat. #: 027001
Chemical
compound,
drug
LymphoPrepAxis ShieldCat. #:1114547
Chemical
compound,
drug
7-AAD-PerCP-Cy5BDCat. #: 559,925FACS5 μl/test
Chemical
compound,
drug
Fura 2-AMThermofisher ScientificCat# F1221
Chemical
compound,
drug
Brefeldin AThermofisher ScientificCat# 00-4506-51
Chemical
compound,
drug
ThapsigarginEMD MilliporeCat# 80055–474
Chemical
compound,
drug
Phorbol 12-
myristate 13-
acetate (PMA)
EMD MilliporeCat# 5.00582.0001
Chemical
compound,
drug
IonomycinEMD MilliporeCat# 407,951
Chemical
compound,
drug
PolybreneMillipore SigmaCat# TR-1003
Chemical
compound,
drug
PuromycinInvivogenCat# ant-pr-1
Chemical
compound,
drug
BlasticidinInvivogenCat# ant-bl-05
Chemical
compound,
drug
Poly-D-LysineThermo Fisher ScientificCat# A003E
Chemical
compound,
drug
Fixable Viability
Dye eFluor 780
eBioscienceCat# 65-0865-141 μl/ml of cells
Software,
algorithm
FlowJo v10TreeStar
Software,
algorithm
Slidebook
software
Intelligent Imaging Innovations, Inc
Software,
algorithm
OriginProOriginlab
Software,
algorithm
Image JNIH
Software,
algorithm
Fluoview FV10i Confocal MicroscopeOlympus
Software,
algorithm
Fluoview softwareFlowJo, LLC
Software,
algorithm
Exome sequence analysis (various)Please see methods section
OtherLAS-3000 LCD cameraFujiFilm
OtherECM 830 electroporatorBTX
OtherBD Fortessa flow cytometerBD Biosciences
OtherCytoflex LX flow cytometerBeckman Coulter
OtherHiSeq 3,000Illumina

Additional files

Supplementary file 1

List of all the sgRNAs, and primers used for cDNA sub cloning and qRT-PCR in this study.

https://cdn.elifesciences.org/articles/72559/elife-72559-supp1-v1.docx
Transparent reporting form
https://cdn.elifesciences.org/articles/72559/elife-72559-transrepform1-v1.docx
Source data 1

Source data for all figures.

Zip folder containing raw and uncropped images for Western blots and Excel spreadsheets of quantitation.

https://cdn.elifesciences.org/articles/72559/elife-72559-supp2-v1.zip

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  1. Beibei Wu
  2. Laura Rice
  3. Jennifer Shrimpton
  4. Dylan Lawless
  5. Kieran Walker
  6. Clive Carter
  7. Lynn McKeown
  8. Rashida Anwar
  9. Gina M Doody
  10. Sonal Srikanth
  11. Yousang Gwack
  12. Sinisa Savic
(2021)
Biallelic mutations in calcium release activated channel regulator 2A (CRACR2A) cause a primary immunodeficiency disorder
eLife 10:e72559.
https://doi.org/10.7554/eLife.72559