Publisher Correction: Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1-3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.

Commercial Immunoglobulin Products Contain Neutralizing Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein.

BACKGROUND: Patients with antibody deficiency respond poorly to coronavirus disease 2019 (COVID-19) vaccination and are at risk of severe or prolonged infection. They are given long-term immunoglobulin replacement therapy (IRT) prepared from healthy donor plasma to confer passive immunity against infection. Following widespread COVID-19 vaccination alongside natural exposure, we hypothesized that immunoglobulin preparations will now contain neutralizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike antibodies, which confer protection against COVID-19 disease and may help to treat chronic infection. METHODS: We evaluated anti-SARS-CoV-2 spike antibody in a cohort of patients before and after immunoglobulin infusion. Neutralizing capacity of patient samples and immunoglobulin products was assessed using in vitro pseudovirus and live-virus neutralization assays, the latter investigating multiple batches against current circulating Omicron variants. We describe the clinical course of 9 patients started on IRT during treatment of COVID-19. RESULTS: In 35 individuals with antibody deficiency established on IRT, median anti-spike antibody titer increased from 2123 to 10 600 U/mL postinfusion, with corresponding increase in pseudovirus neutralization titers to levels comparable to healthy donors. Testing immunoglobulin products directly in the live-virus assay confirmed neutralization, including of BQ1.1 and XBB variants, but with variation between immunoglobulin products and batches.Initiation of IRT alongside remdesivir in patients with antibody deficiency and prolonged COVID-19 infection (median 189 days, maximum >900 days with an ancestral viral strain) resulted in clearance of SARS-CoV-2 at a median of 20 days. CONCLUSIONS: Immunoglobulin preparations now contain neutralizing anti-SARS-CoV-2 antibodies that are transmitted to patients and help to treat COVID-19 in individuals with failure of humoral immunity.

Novel NFKB2 mutation in early-onset CVID.

Common variable immunodeficiency (CVID) is heterogeneous, clinically, immunologically and genetically. The majority of genetic mechanisms leading to CVID remain elusive. We studied a Greek Cypriot family of non-consanguineous parents. Two children were diagnosed with CVID at an early age. Whole exome sequencing revealed 8bp deletion in the C-terminal part of NFKB2 gene associated with disease. The mutation leads to a frameshift (p.Asp865Valfs*17) altering 17 C-terminal amino acids from residue 865, and creating a premature stop-codon resulting in a truncated protein, 19 amino acids shorter than wild type (p100Δ19). We validated the results with Dye-termination sequencing and Western blot, and confirmed that the conserved residue at 866 is mutated from serine to arginine in p100Δ19, leaving the mutant protein unphosphorylated at this critical regulatory position. Consequently, NFKB2/p100 processing and nuclear translocation were abrogated. Using flow cytometry, we further demonstrated that there was a reduction in B cells (CD19+), switched memory B cells (CD27+IgD-) and T follicular helper (Tfh) cells (both CD4+CXCR5+ and CD4+CXCR5Hi) in a CVID patient with NFKB2/p100Δ19, compared to healthy controls. These data support the notion that the non-canonical NFκB pathway plays an important role in B cell differentiation and the development of Tfh cells, and may pave the way for better understanding of the pathology of CVID.

Evaluation of interference from hemoglobin C, D, E and S traits on measurements of hemoglobin A1c by fifteen methods.

BACKGROUND: Hemoglobin C, D Punjab, E or S trait can interfere with hemoglobin A1c (HbA1c) results. We assessed whether they affect results obtained with 15 current assay methods. METHODS: Hemoglobin AA (HbAA), HbAC, HbAD Punjab, HbAE and HbAS samples were analyzed on 2 enzymatic, 4 ion-exchange HPLC and 9 immunoassay methods. Trinity Premier Hb9210 boronate affinity HPLC was the comparative method. An overall test of coincidence of least-squared linear regression lines was performed to determine if HbA1c results were statistically significantly different from those of HbAA samples. Clinically significant interference was defined as >6% difference from HbAA at 6 or 9% HbA1c compared to Premier Hb9210 using Deming regression. RESULTS: All methods showed statistically significant effects for one or more variants. Clinically significant effects were observed for the Tosoh G11 variant mode (HbAD), Roche b 101 (HbAC and HbAE) and Siemens DCA Vantage (HbAE and HbAS). All other methods (Beckman Coulter B93009 and B00389 on DxC700AU, and Unicel DxC, Ortho Clinical Vitros 5.1, Roche cobas c 513, Siemens Dimension RxL and Vista, and Enzymatic on Advia and Atellica, Tosoh G8 5.24 and 5.28, and GX) showed no clinically significant differences. CONCLUSIONS: A few methods showed interference from one or more variants. Laboratories need to be aware of potential HbA1c assay interferences.

The effect of elevated fetal hemoglobin on hemoglobin A1c results: five common hemoglobin A1c methods compared with the IFCC reference method.

Hemoglobin A1c (HbA1c) is an important indicator of risk for complications in patients with diabetes mellitus. Elevated fetal hemoglobin (HbF) levels have been reported to interfere with results of some HbA1c methods, but it has generally been assumed that HbA1c results from boronate-affinity methods are not affected by elevated HbF levels. None of the previous studies used the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) reference method as the comparative HbA1c method. We, therefore, measured HbA1c in samples with normal and elevated HbF levels by several common assay methods and compared the results with those of the IFCC reference method.HbF levels of more than 20% artificially lowered HbA1c results from the Primus CLC 330/385 (Primus Diagnostics, Kansas City, MO), Siemens DCA2000 (Siemens Healthcare Diagnostics, Tarrytown, NY), and Tosoh 2.2+ (Tosoh Bioscience, South San Francisco, CA), but not the Bio-Rad Variant II (Bio-Rad Laboratories, Hercules, CA) and Tosoh G7. Physicians and laboratory professionals need to be aware of potential interference from elevated HbF levels that could affect HbA1c results, including those from boronate-affinity methods.

Stat3 is involved in control of MASP2 gene expression.

Little is known about determinants regulating expression of Mannan-binding lectin associated serine protease-2 (MASP-2), the effector component of the lectin pathway of complement activation. Comparative bioinformatic analysis of the MASP2 promoter regions in human, mouse, and rat, revealed conservation of two putative Stat binding sites, termed StatA and StatB. Site directed mutagenesis specific for these sites was performed. Transcription activity was decreased 5-fold when StatB site was mutated in the wildtype reporter gene construct. Gel retardation and competition assays demonstrated that proteins contained in the nuclear extract prepared from HepG2 specifically bound double-stranded StatB oligonucleotides. Supershift analysis revealed Stat3 to be the major specific binding protein. We conclude that Stat3 binding is important for MASP2 promoter activity.

Effects of hemoglobin C, D, E and S traits on measurements of hemoglobin A1c by twelve methods.

BACKGROUND: Hemoglobin C, D Punjab, E or S trait can interfere with hemoglobin A1c (HbA1c) results. We assessed whether they affect results obtained with 12 current assay methods. METHODS: Hemoglobin AA (HbAA), HbAC, HbAD Punjab, HbAE and HbAS samples were analyzed on one enzymatic, nine ion-exchange HPLC and two Capillary Electrophoresis methods. Trinity ultra(2) boronate affinity HPLC was the comparative method. An overall test of coincidence of least-squared linear regression lines was performed to determine if HbA1c results were statistically significantly different from those of HbAA samples. Clinically significant interference was defined as >7% difference from HbAA at 6 or 9% HbA1c compared to ultra(2) using Deming regression. RESULTS: All methods showed statistically significant effects for one or more variants. Clinically significant effects were observed for the Tosoh G8 variant mode and GX (all variants), GX V1.22 (all but HbAE) and G11 variant mode (HbAC). All other methods (Abbott Architect c Enzymatic, Bio-Rad D-100, Variant II NU and Variant II Turbo 2.0, Menarini HA-8180T thalassemia mode and HA-8180V variant mode, Sebia Capillarys 2 and Capillarys 3) showed no clinically significant differences. CONCLUSIONS: Several methods showed clinically significant interference with HbA1c results from one or more variants which could adversely affect patient care.

Evaluation of hemoglobin A1c measurement by Capillarys 2 electrophoresis for detection of abnormal glucose tolerance in African immigrants to the United States.

BACKGROUND: Hemoglobin A1c (HbA1c) is used to monitor long-term glycemic control in individuals with diabetes, guide therapy, predict the risk of microvascular complications, and more recently to diagnose diabetes. An automated liquid-flow capillary electrophoresis method was recently developed to measure HbA1c using the Capillarys 2 Flex Piercing instrument. METHODS: Analytical evaluation was performed at 2 clinical centers. A clinical analysis was conducted in 109 African-born individuals, 24% of whom have variant hemoglobin (HbAS or HbAC). Abnormal glucose tolerance (which includes both diabetes and prediabetes) was defined as 2h glucose of ≥ 140 mg/dl (7.8 mmol/l) during an oral glucose tolerance test. RESULTS: Interlaboratory CVs were ≤ 2.1%. The method showed satisfactory correlation with 2 other analyzers that measure HbA1c by high-performance liquid chromatography. Neither labile HbA1c, carbamylated hemoglobin, uremia, bilirubin nor common hemoglobin variants (HbC/HbS/HbE) interfered. Forty-five individuals (41%) had abnormal glucose tolerance. The sensitivity of HbA1c for diagnosing abnormal glucose tolerance was 38%, 36% and 42% for total, normal and variant hemoglobin groups, respectively. CONCLUSIONS: The analytical performance of HbA1c on the Capillarys 2 is suitable for clinical application. Variant hemoglobin in Africans did not interfere with the detection of abnormal glucose tolerance by HbA1c measured on the Capillarys 2.

Effects of 49 Different Rare Hb Variants on HbA1c Measurement in Eight Methods.

BACKGROUND: Previous studies have shown interference with HbA1c measurement from the 4 most common heterozygous Hb variants (HbAS, HbAE, HbAC, and HbAD) with some assay methods. Here we examine analytical interference from 49 different less common variants with 7 different HbA1c methods using various method principles. METHODS: Hb variants were screened using the Bio-Rad Variant or Variant II beta thal short program, confirmed by alkaline and acid electrophoresis, and identified by sequence analysis. The Trinity ultra2 boronate affinity high-performance liquid chromatography (HPLC) method and Roche Tinaquant immunoassay were used as primary and secondary comparative methods, respectively, since these methods are least likely to show interference from Hb variants. Other methods included were the Tosoh G7 and G8, Bio-Rad D-10 and Variant II Turbo, Diazyme Enzymatic, and Sebia Capillarys 2 Flex Piercing. To eliminate any inherent calibration bias, results for each method were adjusted using regression verses the ultra2 with nonvariant samples. Each method's calibration-adjusted results were compared and judged to be acceptable if within the 99% prediction interval of the regression line for nonvariant samples. RESULTS: Almost all variant samples were recognized as such by the ion-exchange HPLC methods by the presence of abnormal peaks or results outside the reportable range. For most variants, interference was seen with 1 or more of the ion-exchange methods. Following manufacturer instructions for interpretation of chromatograms usually, but not always, prevented reporting of inaccurate results. RESULTS: Laboratories must be cautious about reporting results when the presence of a variant is suspected.

Pseudomonas infection in antibody deficient patients.

Pseudomonas aeruginosa (PA) is commonly isolated from the respiratory secretions of antibody deficiency patients, but the significance of this has not been well studied. We have reviewed our adult antibody deficiency cohort of 179 patients and assessed the prevalence and characteristics of PA infection and the effects of early antibiotic eradication treatments. Of the 34 patients with PA, 55.9% (19) underwent successful eradication and were infection-free, 38.2% (13) had intermittent infection, and 5.9% (2) had chronic PA. PA infection was significantly associated with bronchiectasis (p < 0.0001), with 36.1% (22 out of 61) of patients with bronchiectasis developing a PA infection. Infection status was also significantly associated with chronic sinusitis (p < 0.0001). Most treated PA exacerbations were symptomatic and with colony counts of ≥1000 cfu/ml. Current eradication protocols used at our center involve early treatment at first positive isolate with ciprofloxacin for 3 weeks and nebulized colomycin for 3 months, and if eradication fails, intravenous ceftazidime and gentamycin or colomycin is administered for 2 weeks. Continued sputum surveillance and early eradication treatments upon positive PA culture may help to limit chronic PA infection in antibody deficiency patients.

Measurement of Hba(1C) in patients with chronic renal failure.

BACKGROUND: Carbamylated hemoglobin (carbHb) is reported to interfere with measurement and interpretation of HbA(1c) in diabetic patients with chronic renal failure (CRF). There is also concern that HbA1c may give low results in these patients due to shortened erythrocyte survival. METHODS: We evaluated the effect of carbHb on HbA(1c) measurements and compared HbA(1c) with glycated albumin (GA) in patients with and without renal disease to test if CRF causes clinically significant bias in HbA(1c) results by using 11 assay methods. Subjects included those with and without renal failure and diabetes. Each subject's estimated glomerular filtration rate (eGFR) was used to determine the presence and degree of the renal disease. A multiple regression model was used to determine if the relationship between HbA(1c) results obtained from each test method and the comparative method was significantly (p<0.05) affected by eGFR. These methods were further evaluated for clinical significance by using the difference between the eGRF quartiles of >7% at 6 or 9% HbA(1c). The relationship between HbA(1c) and glycated albumin (GA) in patients with and without renal failure was also compared. RESULTS: Some methods showed small but statistically significant effects of eGFR; none of these differences were clinically significant. If GA is assumed to better reflect glycemic control, then HbA(1c) was approximately 1.5% HbA(1c) lower in patients with renal failure. CONCLUSIONS: Although most methods can measure HbA(1c) accurately in patients with renal failure, healthcare providers must interpret these test results cautiously in these patients due to the propensity for shortened erythrocyte survival in renal failure.

Effects of whole blood storage on hemoglobin a1c measurements with five current assay methods.

BACKGROUND: Hemoglobin A1c (HbA1c) is an important index of average glycemia in patients with diabetes mellitus that is widely used in clinical trials and large-scale epidemiological studies. Previous studies have shown that adverse sample storage conditions can cause erroneous HbA1c results. We examined the effect of storage at different temperatures with five current HbA1c methods: Tosoh G7 and G8 (Tosoh Bioscience, Inc., South San Francisco, CA) and Bio-Rad Variant™ II (Bio-Rad Laboratories, Hercules, CA) (all ion-exchange high-performance liquid chromatography); Siemens DCA 2000+ (Siemens Healthcare Diagnostics, Deerfield, IL) (immunoassay); and Trinity Biotech (Kansas City, MO) ultra(2) (boronate-affinity high-performance liquid chromatography). METHODS: Five whole blood specimens with different HbA1c levels were analyzed by each assay method on Day 0 and then divided into aliquots that were stored at six different temperatures (-70°C, -20°C, 4°C, room temperature, 30°C, and 37°C) for analyses on subsequent days out to Day 84. Acceptance limits were defined as within ±3 SD of all -70°C results or ±0.2% HbA1c, whichever was wider, for each sample. Stability was considered acceptable for a given temperature only if results for all five specimens were acceptable on that day. RESULTS: The DCA 2000+ demonstrated the best stability at -20°C and room temperature, whereas the ultra(2) showed the best stability with specimens stored at 4°C. No methods demonstrated stability at 30°C or 37°C for more than 3 days. CONCLUSIONS: Exposure of specimens to high temperatures should be avoided regardless of assay methodology. For the ion-exchange methods tested 4°C storage is preferable to -20°C (stability 14-21 days vs. 4-10 days). For studies where long-term stability is required, samples should be stored at -70°C or colder.

Factor H facilitates the clearance of GBM bound iC3b by controlling C3 activation in fluid phase.

Dense deposit disease (DDD) is strongly associated with the uncontrolled activation of the complement alternative pathway. Factor H (CFH)-deficient (Cfh(-/-)) mice spontaneously develop C3 deposition along the glomerular basement membrane (GBM) with subsequent development of glomerulonephritis with features of DDD, a lesion dependent on C3 activation. In order to understand the role of CFH in preventing renal damage associated with the dysregulation of the alternative pathway we administered purified mouse CFH (mCFH) to Cfh(-/-) mice. 24h following the administration of mCFH we observed an increase in plasma C3 levels with presence of intact C3 in circulation showing that mCFH restored control of C3 activation in fluid phase. mCFH resulted in the reduction of iC3b deposition along the GBM. The exogenous mCFH was readily detectable in plasma but critically not in association with C3 along the GBM. Thus, the reduction in GBM C3 was dependent on the ability of mCFH to regulate C3 activation in plasma. Western blot analysis of glomeruli from Cfh(-/-) mice demonstrated the presence of iC3b. Our data show that the C3 along the GBM in Cfh(-/-) mice is the C3 fragment iC3b and that this is derived from plasma C3 activation. The implication is that successful therapy of DDD is likely to be achieved by therapies that inhibit C3 turnover in plasma.

Radiographic evaluation of the Zurich cementless total hip acetabular component.

OBJECTIVE: To radiographically evaluate the Zurich cementless total hip (ZCTH) cup and correlate lucency with clinical signs of implant instability, time since surgery, and implant generation, using zonal analysis. STUDY DESIGN: Retrospective study. ANIMALS: Client-owned dogs (n = 53). METHODS: Radiographs of dogs that had ZCTH arthroplasty (>1 year) were evaluated using zonal analysis, for lucency surrounding the cup-bone interface (number of zones, length, area). Dogs were examined for clinical signs of implant instability (lameness, hip pain). Lucency was correlated with lameness, time after surgery, and implant generation. RESULTS: Radiographs of 68 implants (18 generation I, 50 generation II) were evaluated. Eight dogs were lame (11.8%). Dogs with lameness were more likely to have lucency in > or =2 zones of analysis (per view), have >2 times the average curvilinear length of lucency, and have >4 times the average area of lucency surrounding the implant compared with non-lame dogs. A weak relationship was observed between time after surgery and implant generation; however, there was no relationship between time after surgery and lucency. CONCLUSIONS: Dogs with lameness after ZCTH arthroplasty were more likely to have lucency at the cup-bone interface. Lucency was better evaluated by radiographic projection than zonal analysis. Temporal progression of lucency was weakly correlated with implant generation. CLINICAL RELEVANCE: Dogs with lucency in > or =2 zones of analysis should be evaluated more frequently for clinical signs of implant loosening. Further investigation of serial radiographs after ZCTH arthroplasty is warranted.

Organization of the MASP2 locus and its expression profile in mouse and rat.

The mouse, rat, and human MASP2 loci are situated on syntenic chromosome regions and are highly conserved. They comprise the genes for MASP-2/ MAp19, TAR DNA binding protein of 43 kDa, FRAP kinase, CDT6, Polymyositis-Scleroderma 100-kDa autoantigen, spermidine synthase, and TERE which were analyzed by annotation of available gene transcript data and cross-species comparison of available genomic sequences. The human and rat genes for spermidine synthase have an additional intron compared to the mouse gene. The mouse and rat genes for Polymyositis-Scleroderma 100-kDa autoantigen have an additional exon compared to the human gene. We find support for the hypothesis that the MAp19-specific exon within the MASP2 gene may have originated in a transposable element. Blocks of highly conserved intronic sequences were found in the MASP2 gene and the TARDBP gene. The expression of all genes within the MASP2 locus was analyzed in mouse and rat. The restricted expression of MASP-2 and MAp19 mRNA in liver contrasts with the ubiquitous expression of all neighboring genes studied.