Loss of B Cells in Patients with Heterozygous Mutations in IKAROS.

BACKGROUND: Common variable immunodeficiency (CVID) is characterized by late-onset hypogammaglobulinemia in the absence of predisposing factors. The genetic cause is unknown in the majority of cases, and less than 10% of patients have a family history of the disease. Most patients have normal numbers of B cells but lack plasma cells. METHODS: We used whole-exome sequencing and array-based comparative genomic hybridization to evaluate a subset of patients with CVID and low B-cell numbers. Mutant proteins were analyzed for DNA binding with the use of an electrophoretic mobility-shift assay (EMSA) and confocal microscopy. Flow cytometry was used to analyze peripheral-blood lymphocytes and bone marrow aspirates. RESULTS: Six different heterozygous mutations in IKZF1, the gene encoding the transcription factor IKAROS, were identified in 29 persons from six families. In two families, the mutation was a de novo event in the proband. All the mutations, four amino acid substitutions, an intragenic deletion, and a 4.7-Mb multigene deletion involved the DNA-binding domain of IKAROS. The proteins bearing missense mutations failed to bind target DNA sequences on EMSA and confocal microscopy; however, they did not inhibit the binding of wild-type IKAROS. Studies in family members showed progressive loss of B cells and serum immunoglobulins. Bone marrow aspirates in two patients had markedly decreased early B-cell precursors, but plasma cells were present. Acute lymphoblastic leukemia developed in 2 of the 29 patients. CONCLUSIONS: Heterozygous mutations in the transcription factor IKAROS caused an autosomal dominant form of CVID that is associated with a striking decrease in B-cell numbers. (Funded by the National Institutes of Health and others.).

Determination of RET Sequence Variation in an MEN2 Unaffected Cohort Using Multiple-Sample Pooling and Next-Generation Sequencing.

Multisample, nonindexed pooling combined with next-generation sequencing (NGS) was used to discover RET proto-oncogene sequence variation within a cohort known to be unaffected by multiple endocrine neoplasia type 2 (MEN2). DNA samples (113 Caucasians, 23 persons of other ethnicities) were amplified for RET intron 9 to intron 16 and then divided into 5 pools of <30 samples each before library prep and NGS. Two controls were included in this study, a single sample and a pool of 50 samples that had been previously sequenced by the same NGS methods. All 59 variants previously detected in the 50-pool control were present. Of the 61 variants detected in the unaffected cohort, 20 variants were novel changes. Several variants were validated by high-resolution melting analysis and Sanger sequencing, and their allelic frequencies correlated well with those determined by NGS. The results from this unaffected cohort will be added to the RET MEN2 database.

Analysis of the factor V Leiden mutation using the READIT Assay.

BACKGROUND: A variety of methods exist for the detection of single-nucleotide polymorphisms (SNPs) present in amplified segments of genomic DNA. We show the application of a novel SNP scoring tool for analysis of the factor V Leiden mutation. METHODS AND RESULTS: We have developed a novel method for analyzing SNPs. The luciferase-based technique, known as the READIT Technology (Promega Corp, Madison, WI), was used to analyze 510 residual human samples sent for factor V Leiden testing from three independent testing laboratories. A blinded retrospective analysis of the factor V Leiden mutation was used to determine the accuracy and throughput capabilities of the technology. One hundred percent concordance was observed between the READIT Assay and genotype assignments made in the testing laboratories. In addition, greater than 6 SDs of separation were observed between the means of wild-type and heterozygote sample populations. Repetitive sample measurements with representative wild-type, heterozygote, and mutant samples showed that greater than 9 SDs separated the means of heterozygote and homozygote sample populations. Confidence intervals based on the means of wild-type, heterozygote, and mutant sample populations were determined. CONCLUSION: Perfect concordance using the READIT Assay showed its effectiveness as a SNP scoring tool. The design of the factor V READIT Assay was straightforward, requiring the design of two unmodified oligonucleotides that differ at the 3' penultimate position to form perfect hybrids with the wild-type or Leiden form of the factor V sequence. The use of previously published amplification primers and conditions minimized the time needed to optimize and validate the assay. The READIT Calculator supplied with the assay allowed automated genotype assignments and statistical analysis from the READIT Assay data. Confidence-interval analysis validated the ability to distinguish between wild-type, heterozygote, and mutant samples using the READIT Assay.

Molecular diagnosis of hereditary hemochromatosis.

Hereditary hemochromatosis (HH) is an autosomal recessive disorder of iron metabolism with a frequency of homozygosity in the Caucasian population of 1 in 200-400. The pathophysiologic hallmark of HH is chronic, increased absorption of dietary iron beyond that required for normal iron homeostasis. The excess absorption leads to progressive iron accumulation in parenchymal cells that can manifest in adulthood as multiple end-organ damage (1). In 1996, the gene responsible for the majority of cases of HH was identified. Designated HFE, the HH gene resides on the short arm of chromosome 6 telomeric of the major histocompatibility complex (MHC) and encodes a 343 amino acid protein (HFE) that shares sequence and structural homology to class I MHC proteins. Approximately 85% of unrelated HH patients are homozygous for a point mutation involving a G to A change at nucleotide 845 in the HFE cDNA sequence (G845A) that converts cysteine, at amino acid position 282, to tyrosine (Cys282Tyr or C282Y) (2).

Analytical evaluation of primer engineered multiplex polymerase chain reaction-restriction fragment length polymorphism for detection of factor V Leiden and prothrombin G20210A.

Factor V Leiden and prothrombin G20210A are clinically relevant genetic risk factors for venous thrombosis. Analysis for both mutations is increasingly being performed on patients exhibiting hypercoagulability. The goal of the current study was to evaluate the performance of primer-engineered multiplex polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for the simultaneous detection of factor V Leiden and prothrombin G20210A. Primer-engineered multiplex PCR-RFLP methods for the detection of factor V Leiden and prothrombin G20210A from the medical literature were reviewed. A modified method was optimized in which both mutations generate HindIII RFLPs and the prothrombin amplicon contains an invariant HindIII recognition site to assess the completeness of endonuclease digestion. Digested amplification products were analyzed by agarose gel electrophoresis in a single gel lane and visualized by ethidium bromide. Primer-engineered multiplex PCR-RFLP was used to analyze 205 human genomic DNA samples whose factor V Leiden genotypes had been previously determined by MnlI PCR-RFLP. Complete concordance for factor V Leiden genotypes was observed between the two methods in the 205-sample cohort comprising 139 wild-type, 62 heterozygous mutant, and four homozygous mutant individuals. For prothrombin G20210A, primer-engineered multiplex PCR-RFLP identified 196 wild-type and nine heterozygous mutant individuals in the 205-sample cohort. To independently verify prothrombin genotypes, the nine heterozygous mutants and an additional 11 wild-type patient samples (representing 10% of patient samples) were subjected to DNA sequencing. Complete concordance was observed between DNA sequencing and primer-engineered multiplex PCR-RFLP results. In further validation, 123 of the DNA samples consisting of four heterozygous mutant and 119 wild type individuals were genotyped with the Invader Assay for Factor II (prothrombin G20210A). Results showed 100% concordance between the Invader Assay and primer-engineered multiplex PCR-RFLP. A primer-engineered multiplex PCR-RFLP based on single restriction endonuclease digestion has been evaluated and shown to simultaneously and accurately detect factor V Leiden and prothrombin G20210A mutations. The method is robust and readily adaptable to the clinical molecular diagnostic laboratory.

Management of chronic myeloid leukemia during pregnancy with leukapheresis.

We describe the successful treatment of a pregnant patient with chronic myelogenous leukemia in chronic phase by using only leukapheresis. Following 20 leukapheresis procedures initiated during the 13th week of gestation and performed over approximately 7 weeks, the patients white blood cell count dropped from 242,000/microl to 19,300/microl. The WBC remained stable over the ensuing 17 weeks until the time of delivery. The patient gave birth by cesarean section to a healthy 2,640 g boy at 37.5 weeks of gestation. This is the second report of the successful use of leukapheresis alone for chronic myelogenous leukemia in chronic phase during the first half of pregnancy. We conclude that where leukapheresis is available, it may provide an alternative treatment to chemotherapy or alpha-interferon, especially in light of their potential teratogenic and leukemogenic side-effects.

Assessment of SNRPN expression as a molecular tool in the diagnosis of Prader-Willi syndrome.

BACKGROUND: Prader-Willi syndrome (PWS) is associated with lesions of the paternal chromosome 15q11- 13. Recently, loss of expression of a paternally expressed gene in this region, SNRPN, has been proposed as a molecular hallmark of PWS. The goal of this study was to determine the diagnostic accuracy of SNRPN expression in a well-characterized cohort of PWS patients. METHODS: SNRPN expression was analyzed by reverse transcription coupled to polymerase chain reaction (RT-PCR). RNA was isolated from peripheral blood leukocytes and subjected to multiplex RT-PCR in which expression of SNRPN and a constituitively expressed internal control gene were analyzed. The amplified products were electrophoresed in agarose gels and visualized by ethidium bromide staining. RESULTS: Multiplex RT-PCR was applied to RNAs isolated from 30 normal control subjects and 30 well- characterized PWS patients. All control patients expressed the SNRPN and internal control genes. In contrast, all 30 PWS patients demonstrated loss of SNRPN expression, with integrity of RNA being demonstrated by the presence of internal control gene expression. CONCLUSIONS: Loss of SNRPN expression appears to be a consistent finding in PWS. Expression analysis of SNRPN offers a novel approach for the diagnostic evaluation of PWS that is robust and can be performed in a single day.

Activated protein C resistance assay performance: improvement by sample dilution with factor V-deficient plasma.

OBJECTIVE: To evaluate a modification of a commercially available reagent kit (COATEST APC Resistance Kit) for functional activated protein C (APC) resistance testing, and to determine the ability of the modified assay to demonstrate APC resistance in patients receiving warfarin. DESIGN: Functional APC resistance testing was performed using both the first-generation COATEST APC Resistance Kit and a modified, or second-generation, version of the COATEST assay that uses predilution of the patient sample with factor V-deficient plasma. Factor V genotyping for APC resistance (FV R506Q) was performed using a well-characterized polymerase chain reaction-restriction fragment length polymorphism method. SETTING: University medical center. PATIENTS: Seventy-three individuals referred for hypercoagulability testing who were not receiving warfarin therapy and 29 patients with a history of venous thrombosis who were receiving warfarin therapy. MAIN OUTCOME MEASURE: Sensitivity and specificity as determined by comparing functional APC resistance to the FV R506Q genotype. RESULTS: In 73 patients referred for hypercoagulability testing, but not receiving warfarin therapy, a sensitivity of 0.86 and a specificity of 0.75 were obtained with the first-generation COATEST assay. In contrast, a sensitivity and specificity of 1.0 were obtained when the second-generation COATEST assay was employed. In 29 patients receiving warfarin, the first-generation assay exhibited a sensitivity and specificity of 0.88 and 0.95, respectively, whereas the sensitivity and specificity for the second-generation assay was 1.0. CONCLUSIONS: Predilution of patient plasma with factor V-deficient plasma results in improved sensitivity and specificity of the COATEST APC Resistance Kit, thus offering a simple modification to enhance APC resistance determination in the routine clinical laboratory setting.

Factor V R506Q gene mutation analysis by PCR-RFLP: optimization, comparison with functional testing for resistance to activated protein C, and establishment of cell line controls.

Resistance to activated protein C (APC) has been recently identified as a highly prevalent risk factor for the development of venous thrombosis. In the majority of cases, APC resistance correlates with the presence of a single point mutation in the factor V gene (FV R506Q). The mutation is present in 3% to 5% of the general population and in up to 50% of patients with a personal and family history of venous thrombosis. In the current study, the authors have optimized and implemented for clinical diagnosis a method for detection of FV R506Q using the polymerase chain reaction coupled with restriction fragment length polymorphism analysis (PCR-RFLP). Forty-one healthy adults and 139 patients referred for hypercoagulability testing were genotyped and their APC resistance ratios determined using commercially available reagents (COATEST APC Resistance Kit). Comparative analysis indicated that if functional APC resistance was defined as per manufacturer's guidelines, a significant number of individuals with a normal factor V genotype were categorized as APC resistant and conversely, a significant number of individuals heterozygous for FV R506Q were categorized as non-APC resistant. These results indicate that comparative functional and genotypic analyses in the individual clinical laboratory setting are critical for establishing normal ranges and cut-off values for functional APC resistance due to FV R506Q. To facilitate molecular evaluation of APC resistance, Epstein-Barr virus (EBV) immortalized B-lymphocyte cell lines were established from individuals heterozygous and homozygous for FV R506Q.

Resistance to activated protein C and a novel factor V gene mutation.

A novel mutation in the factor V gene of the blood coagulation cascade has been identified recently. The mutation confers a lifelong hypercoagulable state, and carriers of the mutation have an approximate eightfold increase in relative risk for the development of venous thrombosis. Carriers of the mutation manifest a laboratory coagulation defect termed resistance to activated protein C (APC). This article reviews the discovery of APC resistance, the identification of the factor V gene mutation, and laboratory approaches to their diagnosis.

Extensive amplification of bcr/abl fusion genes clustered on three marker chromosomes in human leukemic cell line K-562.

Using fluorescence in situ hybridization (FISH), we were able to demonstrate 22-24-fold amplification of the bcr/abl fusion gene in the human leukemic cell line K-562. About 60% of the amplified sequences are localized to a large acrocentric marker chromosome, with another 30% clustered on a small acrocentric chromosome. In addition to these two masked Ph chromosomes, the remaining bcr/abl fusion genes are located on a der(2) distal to band q33. G- and C-banding analysis revealed similar unique banding patterns in both masked Ph chromosomes and suggests that amplification occurred by tandem duplication of the bcr/abl fusion site. Because the number of bcr/abl fusion genes may be increasing over time, it is critical that researchers using K-562 cells should be aware of this extensive amplification.

Post-transcriptional regulation of the p53 tumor suppressor gene during growth-induction of human peripheral blood mononuclear cells.

Regulation of p53 gene expression at the post-transcriptional level was investigated during growth induction of human peripheral blood mononuclear cells (PBMCs). Freshly isolated PBMCs, which are in the Go phase of the cell cycle, were shown to express low levels of p53 mRNA that was rapidly degraded with a half life of 1 h. The rapid decay of p53 mRNA in quiescent PBMCs was dependent on global protein synthesis as treatment with cycloheximide resulted in stabilization of the p53 message. PBMCs were stimulated to enter the cell cycle by treatment with a combination of the mitogenic lectin phytohemagglutinin (PHA) and phorbol ester (TPA). Progressive stabilization of the p53 message occurred in PBMCs during growth induction. By 24 h of incubation in the presence of PHA and TPA, the half life of p53 mRNA was 6 h and p53 mRNA steady state levels were increased 4.5 to 5.0-fold. p53 protein was not detected in quiescent PBMCs, but was readily detected in PBMCs stimulated for 24 h with PHA and TPA. Stabilization of p53 mRNA was observed in PBMCs treated with either PHA or TPA, but to a lesser degree than when PHA and TPA were used as co-stimulants. These results indicate that differential degradation of p53 messenger RNA occurs in quiescent vs mitogen stimulated PBMCs and suggest that post-transcriptional regulation importantly contributes to increased p53 mRNA steady state levels as PBMCs enter the cell cycle.

Combined utility of gene rearrangement analysis and flow cytometry in the diagnosis of lymphoproliferative disease in the bone marrow.

The diagnosis of lymphoma involving bone marrow is often complicated by the presence of nonspecific lymphoid aggregates. Morphologic criteria may not permit the distinction of benign from malignant lymphoid aggregates with certainty in all cases. We combined morphology with immunophenotypic and immunogenotypic analyses of aspirated marrow cells to develop more reliable criteria for the diagnosis of marrow involvement by lymphoma. The presence of morphologically recognizable lymphoma cells in the bone marrow aspirate was always confirmed by immunogenotypic analysis. The yield of either immunophenotypic or immunogenotypic analyses on morphologically negative marrows was very low. Focal paratrabecular involvement by lymphoma was not always confirmed by immunophenotypic or immunogenotypic analyses, probably due to sampling error and factors interfering with aspiration of the lymphoid aggregates. Thus, the immunologic and molecular studies supported, but did not substantially improve upon the morphologic criteria that are in common usage for distinguishing benign from malignant lymphoid aggregates in the bone marrow. Finally, evidence of B-lymphocyte clonality was obtained in four of five cases in which there were nonspecific lymphoid aggregates in the bone marrow in the absence of otherwise clinically definable malignancy.

Plasma cell malignancy in the acquired immune deficiency syndrome. Association with Epstein-Barr virus.

The development of high-grade, malignant B-cell lymphoma is a well-recognized complication of human immunodeficiency virus (HIV) infection. Plasma cell neoplasms, however, have been rarely encountered in HIV-infected people. This study presents the morphologic and immunologic features of an unusual plasma cell tumor occurring in a 31-year-old HIV-antibody-positive male. The malignancy was characterized by widespread dissemination and hypercalcemia at presentation and a clinically aggressive course. Immunoperoxidase staining of tumor tissue obtained from biopsy and at autopsy had positive results for IgM and lambda. In the patient's serum, only an IgG kappa paraprotein was detected, indicating that the tumor was nonsecretory. DNA analysis of autopsy-derived tumor tissues demonstrated clonal rearrangements of the immunoglobulin (Ig) heavy chain gene locus and rearrangements in both kappa and lambda light chain gene loci. Furthermore, DNA hybridization studies revealed the presence of Epstein-Barr virus (EBV) genomes in tumor tissue but not in nontumor tissue from this patient.

Clonal B-cell proliferation in an infant with congenital HIV infection and immune thrombocytopenia.

An infant with congenital human immunodeficiency virus (HIV) infection had immune thrombocytopenic purpura (ITP) develop at four months of age. A bone marrow aspirate had normal results in morphologic characteristics and cellularity. Flow cytometry analysis of the marrow cells showed that the predominant cell in the "lymphocyte" cluster was of B-lineage and common acute lymphocytic leukemia antigen (CALLA) positive. Southern blot analysis of marrow DNA demonstrated gene rearrangements in both the immunoglobulin (Ig) heavy chain and kappa light chain loci, confirming the presence of a clonal B-cell lymphoid proliferation. At one year of age the patient is clinically well without evidence of malignant lympho-proliferative disease. This case exemplifies a limited clonal B-cell expansion in the bone marrow of a patient with HIV infection and a benign hematologic condition.