Multiplexed Functional Assessment of Genetic Variants in CARD11

Genetic testing has increased the number of variants identified in disease genes, but the diagnostic utility is limited by lack of understanding variant function. CARD11 encodes an adaptor protein that expresses dominant-negative and gain-of-function variants associated with distinct immunodeficiencies. Here, we used a "cloning-free" saturation genome editing approach in a diploid cell line to simultaneously score 2,542 variants for decreased or increased function in the region of CARD11 associated with immunodeficiency. We also described an exon-skipping mechanism for CARD11 dominant-negative activity. The classification of reported clinical variants was sensitive (94.6%) and specific (88.9%), which rendered the data immediately useful for interpretation of seven coding and splicing variants implicated in immunodeficiency found in our clinic. This approach is generalizable for variant interpretation in many other clinically actionable genes, in any relevant cell type.

GB virus C infection in children with perinatal human immunodeficiency virus infection

BACKGROUND

GB virus C (GBV-C) infection occurs in 20-40% of human immunodeficiency virus (HIV)-infected adults, and coinfection is associated with improved HIV disease outcome.

METHODS

To determine the prevalence of GBV-C infection in children who were perinatally infected with HIV, we conducted a cross-sectional prevalence survey in a cohort of perinatally infected HIV-positive children selected from a large, multicenter observational protocol. A blood specimen was obtained and tested for GBV-C viremia with the use of a qualitative GBV-C RNA assay and screened for past GBV-C infection with enzyme-linked immunosorbent assay to detect antibodies to the GBV-C envelope protein E2 (E2 Ab).

RESULTS

The 354 children who participated in the substudy were relatively healthy, with a median CD4 of 784 cells/mm and median HIV-1 viral load of 1055 copies/mL. The prevalence of GBV-C viremia was 20 of 353 or 5.7% (95% confidence interval, 3.5-8.6%), and the prevalence of E2 Ab was 12 of 354 or 3.4% (95% confidence interval, 1.8-5.8%). GBV-C viremic patients were older than patients without past GBV-C infection (median age, 12.8 years versus 10.7 years). Median CD4 lymphocyte counts were highest in subjects without GBV-C infection and lowest in those with E2 Ab.

CONCLUSIONS

GBV-C prevalence rates are lower in children with perinatal HIV infection than those reported for HIV-infected adults. With the exception of evidence that GBV-C viremic children had lower rates of Centers for Disease Control and Prevention HIV disease category C disease before GBV-C testing, we did not find evidence of improved HIV disease outcome in coinfected patients, but the number of HIV/GBV-C-coinfected children was small.

Hepatitis C Prevalence in Children With Perinatal Human Immunodeficiency Virus Infection Enrolled in a Long-term Follow-up Protocol

OBJECTIVE

To evaluate the prevalence of hepatitis C virus (HCV) infection in children with perinatal human immunodeficiency virus (HIV) infection.

DESIGN

Cross-sectional substudy.

SETTING

Multicenter study from 41 sites in the United States.

PATIENTS

Children with perinatal HIV infection were randomly selected from a large, long-term, follow-up protocol.

MAIN OUTCOME MEASURE

Hepatitis C infection was defined as having positive test results on both HCV antibody and HCV RNA assays.

RESULTS

Five hundred thirty children enrolled in the substudy; definitive HCV test results were available for 525 children. Eighty-three percent were of a minority race or ethnicity. They were equally distributed by sex, had a median age of 10.7 years, and were relatively healthy, with 75% having CD4+ lymphocyte counts greater than 500 cells/mm3. Eight of 525 children (1.5%; 95% confidence interval [CI], 0.7%-3.0%) infected with HIV were coinfected with HCV. In contrast, the rate of HCV infection in a serosurvey of more than 2700 children aged 6 to 11 years from the National Health and Nutrition Examination Survey was 0.2% (95% CI, 0.04%-0.6%). In our study, there were no differences between children coinfected with HIV and HCV and those without HCV infection in terms of demographic characteristics, CD4+ or CD8+ T-lymphocyte counts, HIV 1 RNA levels, preterm or mode of delivery, or liver disease; however, the number of children coinfected with HIV and HCV was small.

CONCLUSION

While HCV prevalence infection rates are low in children with perinatal HIV infection, they are 8 to 10 times higher than reported in HCV serosurveys of children in the United States.

Virologic testing in the management of perinatal HIV exposure

Over the last several years, virologic assays for the detection and measurement of HIV-1 RNA have become important in the diagnosis and management of perinatal HIV infection. Since AIDS Clinical Trials Group 076, a number of prospective and retrospective analyses have investigated the role of viral load in perinatal transmission. Although no universal virologic threshold for perinatal HIV transmission has been established, much has been learned about the timing of perinatal transmission and the relationship between maternal viral load and disease progression in HIV-infected neonates. Virologic assays have become accepted as standards of care in monitoring viral load during pregnancy, diagnosing neonatal infection, and establishing prognosis and response to therapy in infected infants.

Human immunodeficiency virus infection and multilocular thymic cysts

PURPOSE

Pathologic changes of the thymus, often seen in children with the human immunodeficiency virus (HIV), reflect direct invasion by the virus, followed by involution of the gland. A previously unknown form of thymic response to HIV infection, that of a multilocular thymic cyst, is reported.

MATERIALS AND METHODS

Findings were examined in three HIV-positive patients, two children and one adult first seen with large thymic masses.

RESULTS

All three had large, septate low-attenuation areas at computed tomography consistent with multilocular thymic cysts. The cystic nature of the lesions was confirmed with magnetic resonance imaging in two. Histopathologic examination, performed in two instances, helped establish the diagnosis. All patients remained in clinically stable condition. They all had parotid gland enlargement and lymphocytic interstitial pneumonia.

CONCLUSION

Multilocular thymic cysts are probably another manifestation of the diffuse infiltrative lymphocytosis syndrome, usually associated with a milder course of acquired immunodeficiency syndrome.

Flow cytometric analysis of natural killer cell function as a clinical assay

The 51Cr release assay has been the method of choice in analyzing natural killer cell (NK) function. Previous FCM cytotoxicity assays of NK activity have had numerous disadvantages that discouraged clinicians from attempting to evaluate NK function by flow cytometry. We demonstrate the effectiveness of using PKH-26, a stable membrane dye, to label the K562 target cells and propidium iodide intercalation into killed target cell DNA to determine the percentage of target cells killed by effector NK cells from the peripheral blood or bone marrow. This method compares favorably with the 51Cr release assay and is quicker and easier to perform. The percentage of cytotoxicity of NK cells (CD3- CD56+ and/or CD16+) from 10 normal subjects and 10 HIV-infected children are reported to demonstrate the feasibility of studying NK function in clinical populations by FCM. The potentiation of cytolysis by alpha-interferon and interleukin 2 in vitro was also compared between these two study groups. In addition, a patient whose leukemic blasts expressed CD56+ was also studied for NK activity using this flow cytometric assay. The benefits of using this flow cytometric approach to clinically assess NK function are discussed.

Dysfunction of natural killer cells in human immunodeficiency virus-infected children with or without Pneumocystis carinii pneumonia

The development of Pneumocystis carinii pneumonia (PCP) in human immunodeficiency virus (HIV)-infected children with normal T-cell numbers is contrary to previous experience with HIV-infected adults, in whom low CD4+ T-cell numbers predict susceptibility to PCP. To determine whether PCP in HIV-infected children reflects a qualitative T-cell or other immune defect, we studied four HIV-infected children who also had PCP and 10 others without PCP for T-cell and natural killer (NK) cell function. Most of the HIV-infected children had normal T-cell numbers for age, and all had CD4+ T-cell numbers greater than those predictive of PCP in HIV-infected adults. All HIV-infected children had normal T-cell function in vitro. The HIV-infected children as a whole had deficient NK cell cytolysis. We obtained a significant interactive effect of age by health status for NK cell function between patients and age-matched control subjects. All HIV-infected children with defective NK cell function failed to enhance their NK cell cytolysis when their mononuclear cells were stimulated with recombinant interferon alfa (r-IFN-alpha). This NK cell defect in HIV-infected children may facilitate the development of secondary infection.

Cytomegalovirus and Pneumocystis carinii pneumonia in children with acquired immunodeficiency syndrome

To ascertain the effect of cytomegalovirus (CMV) infection on the course of Pneumocystis carinii pneumonia (PCP) in children with acquired immunodeficiency syndrome (AIDS), we reviewed the charts of all children with AIDS who also had a lung biopsy specimen or a bronchoalveolar lavage specimen cultured for CMV at the time PCP was diagnosed. The data indicate that children with AIDS and PCP whose cultures are positive for CMV do not have a poorer prognosis during a first episode of PCP compared with children whose cultures are negative for CMV.