Systematic analysis of variants escaping nonsense-mediated decay uncovers candidate Mendelian diseases

Protein-truncating variants (PTVs) near the 3' end of genes may escape nonsense-mediated decay (NMD). PTVs in the NMD-escape region (PTVescs) can cause Mendelian disease but are difficult to interpret given their varying impact on protein function. Previously, PTVesc burden was assessed in an epilepsy cohort, but no large-scale analysis has systematically evaluated these variants in rare disease. We performed a retrospective analysis of 29,031 neurodevelopmental disorder (NDD) parent-offspring trios referred for clinical exome sequencing to identify PTVesc de novo mutations (DNMs). We identified 1,376 PTVesc DNMs and 133 genes that were significantly enriched (binomial p < 0.001). The PTVesc-enriched genes included those with PTVescs previously described to cause dominant Mendelian disease (e.g., SEMA6B, PPM1D, and DAGLA). We annotated ClinVar variants for PTVescs and identified 948 genes with at least one high-confidence pathogenic variant. Twenty-two known Mendelian PTVesc-enriched genes had no prior evidence of PTVesc-associated disease. We found 22 additional PTVesc-enriched genes that are not well established to be associated with Mendelian disease, several of which showed phenotypic similarity between individuals harboring PTVesc variants in the same gene. Four individuals with PTVesc mutations in RAB1A had similar phenotypes including NDD and spasticity. PTVesc mutations in IRF2BP1 were found in two individuals who each had severe immunodeficiency manifesting in NDD. Three individuals with PTVesc mutations in LDB1 all had NDD and multiple congenital anomalies. Using a large-scale, systematic analysis of DNMs, we extend the mutation spectrum for known Mendelian disease-associated genes and identify potentially novel disease-associated genes.

Der Einfluß glykolytischer Fermente auf den Stoffwechsel von Tumorzellen

Es wird über Versuche berichtet, durch mechanische und chemische Behandlung mikrosomengebundene G-6-Pase in Lösung zu bringen. Während diese Versuche nicht zum Ziel führten, gelang es durch kombinierte Behandlung mit Natriumdesoxycholat und Digitonin die G-6-Pase zu lösen.

Outcome and life satisfaction of adults with myelomeningocele

BACKGROUND

Myelomeningocele (MMC) commonly causes impairments in body structure and functions as well as cognitive disabilities that can have an adverse effect on adult life. Improved medical care has resulted in increased numbers of individuals with MMC surviving to adulthood, however little is known about the impact of MMC on the lives of adults age 25 years or older.

OBJECTIVE

To gain a better understanding of outcomes in education, employment, relationships, reproduction and life satisfaction of adults with MMC.

METHODS

A primarily quantitative multiple-choice questionnaire designed to capture outcomes in education, employment, relationships and reproduction, along with a previously validated life satisfaction checklist (LiSat-11), was completed by adults with MMC. Relationships between demographic variables, outcomes and life satisfaction were determined using cross tabulation analysis, logistic regression and linear regression.

RESULTS

Ninety adults with MMC, age 25-85 years (median age 32), reported a diverse range of outcomes in education, employment, relationships and reproduction. The most consistent variable associated with difficulty attaining adult milestones was hydrocephalus, the presence of which reduced the likelihood of living independently (p ≤ 0.001), having a partner (p = 0.003) and reproducing (p ≤ 0.001), but did not contribute to reduced life satisfaction.

CONCLUSIONS

Adults with MMC, especially those without hydrocephalus, can obtain gainful employment, live independently, form partner relationships and have children, and these achievements contribute to life satisfaction. While MMC does not affect overall reported life satisfaction for adults, attention should be paid to specific domains with less reported satisfaction.

HLA phenotypes of ESRD patients are risk factors in the panel-reactive antibody (PRA) response

To determine whether recipient HLA phenotypes are correlated with an increased or decreased risk of alloantibody sensitization in end-stage renal disease (ESRD) candidates for first or repeat kidney transplantation; we analyzed 19440 kidney allograft recipients consisting of 13,216 Caucasians and 6224 non-Caucasians transplanted between 10/87 and 11/98 at South-Eastern Organ Procurement Foundation (SEOPF) member institutions. Relative risk values and 95% confidence limits were obtained using Wolfe's method. Logistic regression was used to adjust for covariates that influence sensitization, i.e. ethnicity, gender, age, pregnancies, transfusions, primary/repeat transplant and living versus cadaver donor. Univariate analysis of the entire cohort indicated that nine HLA allelotypes (DR1,4,7; B8,12,40; A1,2,11) were associated with a significantly reduced risk of sensitization, and five allelotypes (B42,B53; A 10,19,36) were associated with an increased risk of PRA responses. Corrected for the number of statistical comparisons, recipients with DR1, DR4, A1 or A2 were 15% less likely to be sensitized per allelotype. Recipients with B42, B53 or A36 were at increased risk of preformed antibodies, after correction of the P value, for an average of 38% increased risk per allelotype. In the multivariate analysis, HLA phenotypes identified as independent risk factors associated with protection against sensitization were DR1,4,7; B12(44,45); and A1,2, with an average reduced risk of 9% per allelotype. The only independent susceptibility allelotype was A36 with an increased risk of 29%. The A10 (25,26,34,66) group reached borderline significance. We also looked for HLA-DR,-B,-A combinations that could potentially represent protective or at risk haplotypes/genotypes. Stepwise logistic regression identified five combinations associated with protection: DR1-B35-A3; DR1-B35-A2; DR1-B44-A2; DR4-B44-A2; DR7-B57-A1 (RR range 0.83-0.63) with 27% average reduced risk per combination. Phenotype combinations associated with an increased risk of sensitization were: DR2-B44-A2; DR2B53-A2; DR3-B8-A1: DR3-B42-A30; DR6-B42-A30; DR11-B53-A30 (RR range 2.76-1.48) with an average increased risk of 70% per combination. This study provides strong evidence that HLA-linked genes influence the anti-HLA PRA response. The magnitude of the altered PRA response risk in DR-B-A combinations was approximately twice that of the allelotypes at individual loci. HLA-DR genes seemed to contribute most of the altered risk. The correlations between DR types and PRA responsiveness are consistent with the DR types previously regarded as predictors of kidney graft survival. The magnitude of increased PRA risk attributable to an allelotype or combination was approximately twice that associated with a decreased risk. We conclude that some HLA class II-linked genes modulate the PRA response in a clinically significant manner. This immune response gene (Ir) regulation probably operates through polymorphic HLA molecules in their physiologic roles of antigen processing and presentation to helper T cells.

Taste and olfactory disturbances after treatment for acne with isotretinoin, a 13-cis-isomer of retinoic acid

We report an olfactory disturbance after acne treatment with isotretinoin. A disturbance in taste was also reported by the patient. Examination of the nose showed no pathological findings. A CT scan was done to exclude a tumor or a lesion at the lamina cribrosa. Taste and smell examinations were performed and verified the lost qualities.

Leukoencephalopathy after cisplatin therapy

Cisplatin is a neurotoxic chemotherapeutic agent known to cause sensory peripheral neuropathy or ototoxicity. We report a patient with an oropharynx carcinoma who developed a multifocal, necrotizing leukoencephalopathy after cisplatin treatment. This indicates that cisplatin can induce, similar to other chemotherapeutic agents, demyelinating, necrotizing lesions in the white matter of the cerebrum.

Activation of the estrogen receptor from N-nitrosomethylurea-induced rat mammary tumors

The activation of the estrogen receptor (ER) from N-nitrosomethylurea (NMU)-induced rat mammary tumors was studied in vitro. The activation of the receptor induced by heating of the cytosol containing occupied ER was measured by a 3-4-fold increase of receptor binding to nuclei in comparison with the nuclear binding of the nonactivated ER. The activation of the ER was further shown by alteration of the elution profile from DEAE-cellulose. A shift of the receptor peak from 234 mM (Peak II, nonactivated ER) to 70 mM (Peak I, activated ER) phosphate buffer could be obtained. The overall recoveries of activated ER following chromatography on DEAE-cellulose were significantly lower than the recoveries of the nonactivated ER, 71 and 85%, respectively. Binding of the activated ER to nuclei and chromatography of the supernatant which is not able to bind to nuclei on DEAE-cellulose resulted in a decrease of Peak I and in an increase of the overall recovery. These findings suggest that the nuclear bound ER consists of two parts. One is represented partially by Peak I of the elution profile and the other one by that part of the receptor which can not be eluted from the column under the conditions used. Furthermore, the dissociation of tritiated estradiol (E3H) from the nonactivated ER followed a two component exponential function whereas after activation a monophasic dissociation curve could be observed. The mean half times for the dissociation of E3H from the activated and nonactivated ER were 101 and 7.2 min, respectively. Finally, the nonactivated molybdate stabilized ER sedimented in 5-20% sucrose density gradients as two peaks, one at 9.5 S and the other at 4 S. After activation of the ER only the smaller 4 S peak was evident. Molybdate inhibited the activation of the ER measured by nuclear binding assays, sucrose density gradient analysis, dissociation kinetics or ion exchange chromatography but not completely in every case.

Binding of estrogen receptor from N-nitrosomethylurea-induced rat mammary tumors to nuclei

The binding of the cytoplasmic estrogen receptor (ERc) from N-nitrosomethylurea (NMU)-induced rat mammary tumors to the nucleus using a cell-free system is described. All tumors studied were estrogen-receptor-positive and most of them were hormone-dependent. Sixty-two percent of all tumors investigated (n = 134) decreased in size more than 30% 4-5 days after ovariectomy. Brief heating of the cytosol loaded with tritiated estradiol induced activation of the ERc measured by an increase of nuclear binding activity. Temperature-dependent activation was evident in every case. The optimal time and temperature of activation were 15-60 min at 30 degrees C. After denaturation of the ERc by heating for 20 min at 56 degrees C only small parts of free estradiol could be bound to nuclei. Mg2+ ions and EDTA inhibited the nuclear binding of the receptor. The nuclear binding assay was performed for 1 hr at 0-4 degrees C. After this time the activated ERc was bound nearly maximally to nuclei. Under optimized conditions 50-60% of the ERc could be bound to nuclei maximally. Using the same medium for the preparation of crude and purified nuclei the binding of the receptor to both kinds of nuclei was similar. Na2MoO4 prevented the activation of the ERc from NMU-tumors completely but did not influence the binding of the previously activated receptor to nuclei.

Spontaneous and aggregated IgG induced rheumatoid factor producing cells in rheumatoid arthritis

Seropositive rheumatoid arthritis (RA) patients were found to have high numbers of spontaneously occurring cells making rheumatoid factor (RF) reactive with human IgG as measured by a RF plaque forming cell (RF-PFC) assay. There was a significant positive correlation between the number of RF-PFC and both disease activity measured by the sedimentation rate and RF titer measured by the RA latex test. Aggregated IgG and pokeweed mitogen were equally effective stimulators of RF-PFC in cultures of RA peripheral blood mononuclear leukocytes. The rheumatoid ratio of helper (T4): suppressor (T8) T lymphocytes was also significantly increased over the ratio of normal controls, but this ratio did not correlate with the number of RF-PFC. Aggregated IgG or immune complexes may be responsible for stimulating RA RF-PFC in vivo.

Kinetic data of cytoplasmic estradiol receptor

Association and dissociation equilibrium constants and rate constants have been determined in human breast cancer tissues, human lymph node metastases, experimentally induced rat mammary tumors and pooled uteri of normal rats. When the dissociation constants gained from the Scatchard plot applying the Chamness correction were compared to those calculated as the quotient of the rate constants, relatively large differences were found, predominantly due to the values of measured association rate constants. In contrast, there were no specific differences between the constants of distinct tissues. The differences among the association rate constants were presumably caused by a contamination of cytosols by steroid binding proteins of serum. Increasing amounts of serum added to tissue samples resulted in an increasing interference with the determination of the dissociation constants using the Scatchard analysis.

Studies of random Black and White populations in North Carolina: hla antigen profile

As HLA testing is becoming a major vehicle for parentage determination with non-excluded, alleged fathers being compared to their racial peers, it is important to ensure that the population data used accurately reflect the genetic profile of the region from which the alleged fathers are drawn. This paper presents data on the HLA profile of Black and White residents of North Carolina. Significant differences were observed for certain antigens when the North Carolina data were compared to nationally derived population tables. Differences were observed for B7 (increase) and Bw16 (decrease) in Whites and A10 (decrease), B7 (increase) and Bw42 (decrease) in Blacks. Internal controls comparing the testing from the two participating centers showed complete agreement for White persons, but a significant difference for B5 between the two Black populations.

Genetic predictors of patient response and side effects in the treatment of rheumatoid arthritis with a high dose nonsteroidal antiinflammatory drug regimen

Clinical, laboratory, genetic, and radiologic studies were evaluated for 18 patients with rheumatoid arthritis who were treated for a mean of 16.6 months with a regimen involving supplementary aspirin and piroxicam, an investigational, nonsteroidal antiinflammatory agent. Although improvement in disease activity was seen, progression was evident on successive radiographs. Disease activity was not associated with the presence of any of the genetic markers. Peptic ulcers developed in 33% of patients, all of whom had type O blood. ABO blood typing may therefore be useful in patients with rheumatoid arthritis before consideration of therapy with potentially ulcerogenic drugs.

Insulin binding and response to insulin of adipocytes from thyroxine-treated rats

Insulin binding to isolated fat cells from rats rendered hyperthyroid by daily injections of T4 (1 mg/kg) for 5 days was approximately doubled. The Scatchard curves reflected a large increase in receptor number, as well as an elevation in affinity of the high affinity binding sites. The response to insulin of the fat cells, however, was not increased accordingly: glucose incorporation into lipid in the presence of insulin did not differ significantly from that observed in the control group, whereas the effect of insulin on the lipolytic response to isoprenaline (isoproterenol) was even reduced in the T4-treated animals. T4 treatment had thus dissociated insulin binding from the metabolic effects of insulin, since the increase in membrane receptors was not paralleled by an enhanced effect of the hormone. Since levels of serum insulin were increased in the treated animals, the increase in number of insulin receptors was not mediated by reduced exposure to insulin. Propranolol failed to fully antagonize the effect of T4 on insulin binding, and reserpine treatment even enhanced it. It seems unlikely, therefore, that the increase in insulin receptors of adipocytes results from an augmented response to endogenous catecholamines in T4-treated rats.

Estradiol receptor activity in human breast cancer, disease free interval and survival time

Disease-free interval and survival time of breast cancer patients were investigated in regard to the estradiol receptor (ER) status as measured in the corresponding primary tumours. Disease-free interval and survival time of patients with ER positive breast cancers were found to be significantly longer than those of patients with ER negative tumours. The percentage of ER positive tumours in patients with finished free interval, or that died as a consequence of their disease, is lower than that found in an unselected material. The ER concentrations did not, however, differ significantly. Patients with ER positive breast cancers of stage IV did not survive longer than patients with ER negative tumours. No correlations could be found between disease-free interval and survival time of the patients, and the ER concentrations measured in their corresponding tumours individually. The menopausal status of the patients influenced the disease free interval regardless the ER status of the primary tumours. The survival time of postmenopausal patients with ER positive breast cancers were found to be significantly longer than that of premenopausal patients with ER negative cancers. The average ER concentration of breast cancers of postmenopausal patients with finished free interval is significantly higher than the valve found in cancers of premenopausal patients.

Estradiol receptor in human breast cancers throughout the menstrual cycle

The existence and the concentration of the estradiol receptor (ER) in breast cancers of pre- and postmenopausal patients were measured. ER status and concentration are significantly higher in cancers of postmenopausal women. Breast cancers operated at various phases of the menstrual cycle showed remarkable differences in ER incidence and concentration. The highest values were found in the early proliferative phase, whereas the ER incidence is lowest in cancers which were operated at early secretory phase. ER concentrations found in late proliferative and late secretory phases are significantly lower than those found in cancers of postmenopausal patients. Statistically significant differences of the ER concentrations between the various phases of the menstrual cycle could not be secured.

Comparison of estradiol receptor investigations and histochemical investigations on enzymes in human mammary cancers

The best way to predict the responsiveness of human breast carcinomas to hormone therapy is to investigate the estradiol receptor-binding abilities of these tumors. This binding induces many hormone-regulated changes in the activities of several enzymes. Therefore, enzyme activities after short-term organ culture exposed to added hormones were tested to see whether a correlation of enzyme activities exists with estradiol receptor binding. The results from both the estradiol receptor investigations and histochemical investigations on enzymes revealed a high degree of conformity, which confirms the existence of such a correlation. However, for this reason histochemical investigations on enzymes cannot eliminate the discrepancy between the experimentally verified existence of estradiol receptor binding and the response of mammary tumors to hormone therapy, which is not higher than 50-60%.

HLA-B17 and the HLA-A1, B17 haplotype in acute myelogenous leukemia

Seventy-nine Caucasians with acute myelogenous leukemia (AML) were genotyped to determine whether AML, the induction of remission or patient survival were associated with particular HLA phenotypes or haplotypes. HLA-B17 and B27 were increased in AML patients over 40 years of age. Combined analysis of four independent studies indicates that HLA-B17 is significantly but weakly associated with AML, relative risk = 1.48 (.01 less than P less than .025). The A1, B17 and Aw24, Bw35 haplotypes occurred more frequently in the AML group as compared to racial and geographic controls (uncorrected P = 0.0068 and 0.0098, respectively Fisher's Exact Test). Induction of remission occurred less frequently in patients with the B17 phenotype as compared to patients lacking this antigen (P = 0.047). Patient survival was associated with remission status (P = 0.002) but was not significantly associated with particular HLA phenotypes or haplotypes. These results indicate that a gene or genes in the HLA-B region of the major histocompatibility complex can influence susceptibility to AML and also the response to chemotherapy.

Chemotherapeutic agents and estradiol receptor binding capacity

Cytotoxic agents used for the treatment of breast cancer did not inhibit the growth of uterus following estradiol injection to ovariectomized rats. They had no effect on the estradiol binding ability and on the dissociation constant of estradiol receptor binding of rat uterus. In addition, 1,2:5,6-dianhydrogalactitol, a highly active, proximal alkylating agent, applied in vitro did not alter the relative binding ability to tamoxifen to the cytoplasmic estradiol receptor of rat uterus and human breast cancer tissue. In summary, the present experiments did not reveal any disadvantageous interaction between simultaneously administered hormonal and cytotoxic drugs.

Der Einfluß glykolytischer Fermente auf den Stoffwechsel von Tumorzellen

Durch einen aus Rinderleber angereicherten FDPasehaltigen Extrakt kann in Kombination mit DPN die Glykolyse von Ascites-Tumorzellen stärker herabgesetzt werden als mit FDPase allein. Atmung und aerobe Glykolyse werden durch DPN nicht weiter beeinflußt. Durch DPNH wird die anaerobe Glykolyse vermindert, ein FDPase-Zusatz steigert diese Hemmwirkung nicht weiter.

Durch spektrophotometrische Untersuchungen konnte festgestellt werden, daß Leberextrakte DPN nicht hydrieren und FDPase-Lösungen nur wenig DPNH enthalten. Die Glykolysehemmung ist der FDPase-Aktivität und nicht dem DPNH-Gehalt proportional.

Über die Beeinflussung der Glykolyse von Ehrlich-Ascites-Tumorzellen durch phosphorylierte Fructosen

Fructose-1.6-diphosphat kann bei Tumor-Ascites-Zellen im glucosefreien Medium eine Glykolyse hervorrufen, die nur ca. 20% der Glykolyse unter normalen Bedingungen beträgt.

Die Milchsäurebildung verläuft bei geringen FDP-Konzentrationen proportional der Substratmenge. Höhere Konzentrationen als ca. 19 µMole FDP steigern die Glykolyse nicht weiter.

Enzymatisch hergestelltes Fructose-6-phosphat ruft eine größere Glykolyse als entsprechende FDP-Konzentrationen hervor. Dies scheint auf einer besseren Penetrationsfähigkeit des F6P durch die Zellmembran zu beruhen.

Zusatz von Insulin steigert die durch FDP induzierte Milchsäurebildung um ca. 100 Prozent.

Der Einfluß von Fructose-1.6-Diphosphatase auf die Glykolyse von Ehrlich-Ascites-Tumorzellen

Durch Fructose-1.6-Diphosphatase (FDPase) aus Rinderleber kann sowohl die anaerobe als auch die aerobe Glykolyse von Ehrlich-Ascites-Carcinomzellen um 50 — 60% gehemmt werden. FDPase setzt die Atmung dieser Zellen nur unwesentlich (5—7%) herab, Mg-Ionen haben keinen Einfluß auf die Glykolyse, Mn-Ionen setzen sie bis zu 20% herab. In Kombination mit FDPase wird diese Wirkung eliminiert. Durch O2-Durchströmung kann die Aktivität des Fermentes sehr stark herabgesetzt werden, ein Zusatz von Cystein stellt auch in der Wirkung auf die Glykolyse von Ascites-Zellen die ursprüngliche Fermentaktivität wieder her. Letzteres ist vermutlich auf die Notwendigkeit von freien Sulfhydrylgruppen für die Fermentaktivität zurückzuführen.