Genetic analysis of IRF2BPL in a Taiwanese dystonia cohort: The genotype and phenotype correlation

OBJECTIVE

IRF2BPL mutation has been associated with a rare neurodevelopmental disorder with abnormal movements, including dystonia. However, the role of IRF2BPL in dystonia remains elusive. We aimed to investigate IRF2BPL mutations in a Taiwanese dystonia cohort.

METHODS

A total of 300 unrelated patients with molecularly unassigned isolated (n = 256) or combined dystonia (n = 44) were enrolled between January 2015 and July 2023. The IRF2BPL variants were analyzed based on whole exome sequencing. The in silico prediction of the identified potential pathogenic variant was performed to predict its pathogenicity. We also compared the clinical and genetic features to previous literature reports.

RESULTS

We identified one adolescent patient carrying a de novo heterozygous pathogenic variant of IRF2BPL, c.379C>T (p.Gln127Ter), who presented with generalized dystonia, developmental regression, and epilepsy (0.33% of our dystonia cohort). This variant resides within the polyglutamine (poly Q) domain before the first PEST sequence block of the IRF2BPL protein, remarkably truncating the protein structure. Combined with other patients with IRF2BPL mutations in the literature (n = 60), patients with variants in the poly Q domain have a higher rate of nonsense mutations (p < 0.001) and epilepsy (p = 0.008) than patients with variants in other domains. Furthermore, as our index patient, carriers with substitutions before the first PEST sequence block have significantly older age of onset (p < 0.01) and higher non-epilepsy symptoms, including generalized dystonia (p = 0.003), and ataxia (p = 0.003).

INTERPRETATION

IRF2BPL mutation is a rare cause of dystonia in our population. Mutations in different domains of IRF2BPL exhibit different phenotypes.

Cost-Effectiveness Analysis from a Societal Perspective of Recurrence Index for Distant Recurrence (RecurIndex) in Women with Hormone Receptor-Positive and HER2-Negative Early-Stage Breast Cancer

Purpose

A clinical-genomic prognostic multigene panel (RI-DR assay, RecurIndex^®), predicting the risk level of distant recurrence (DR) in early-stage breast cancer (EBC) patients with an Asian background, has been validated as a valuable tool for identifying high-risk patients to develop distant recurrence (metastasis). Although the clinical benefit of adjuvant chemotherapy from the assay’s prediction is already proved, its affordability remains uncertain. This study is the first time in which the long-term cost-effectiveness of the RI-DR assay is evaluated.

Patients and Methods

A lifetime Markov decision-analytic model was developed from a societal perspective to estimate the life-years gained (LYGs), quality-adjusted life-years (QALYs), medical costs, and incremental cost-effectiveness ratios (ICERs), comparing EBC women with and without RI-DR genomic testing. A decision tree was used to classify patients in one of the fifteen end nodes (by order, each arm was stratified by a patient being tested or not with the RI-DR assay, being treated or not with adjuvant chemotherapy and had no, minor, major, or fatal toxicity after adjuvant chemotherapy). Health utilities, costs, transition probabilities, and survival data were extracted from the scientific literature. Deterministic sensitivity analysis (DSA) and probabilistic sensitivity analysis (PSA) were performed on variables to assess the robustness of the model. A willingness-to-pay (WTP) threshold of 790,000 NT$ per QALY gained was considered as a cost-effectiveness criterion.

Results

The incremental cost per QALY gained under base-case assumptions of the model was 173,842 NT$. Findings on the variation in model input parameters were robust and confirmed that every key variable was cost-effective for the benefit of RI-DR testing.

Conclusion

The clinical-genomic RI-DR assay is cost-effective in guiding adjuvant chemotherapy decisions compared to current clinical practice guidelines.

A Clinicogenetic Prognostic Classifier for Prediction of Recurrence and Survival in Asian Breast Cancer Patients

Background

Several prognostic factors affect the recurrence of breast cancer in patients who undergo mastectomy. Assays of the expression profiles of multiple genes increase the probability of overexpression of certain genes and thus can potentially characterize the risk of metastasis.

Methods

We propose a 20-gene classifier for predicting patients with high/low risk of recurrence within 5 years. Gene expression levels from a quantitative PCR assay were used to screen 473 luminal breast cancer patients treated at Taiwan Hospital (positive for estrogen and progesterone receptors, negative for human epidermal growth factor receptor 2). Gene expression scores, along with clinical information (age, tumor stage, and nodal stage), were evaluated for risk prediction. The classifier could correctly predict patients with and without relapse (logistic regression, P<0.05).

Results

A Cox proportional hazards regression analysis showed that the 20-gene panel was prognostic with hazard ratios of 5.63 (95% confidence interval 2.77-11.5, univariate) and 5.56 (2.62-11.8, multivariate) for the “genetic” model, and of 8.02 (3.52-18.3, univariate) and 19.8 (5.96-65.87, multivariate) for the “clinicogenetic” model during a 5-year follow-up.

Conclusions

The proposed 20-gene classifier can successfully separate the patients into two risk groups, and the two risk group had significantly different relapse rate and prognosis. This 20-gene classifier can provide better estimation of prognosis, which can help physicians to make better personalized treatment plans.

The smut fungus Ustilago esculenta has a bipolar mating system with three idiomorphs larger than 500 kb

Zizania latifolia Turcz., which is mainly distributed in Asia, has had a long cultivation history as a cereal and vegetable crop. On infection with the smut fungus Ustilago esculenta, Z. latifolia becomes an edible vegetable, water bamboo. Two main cultivars, with a green shell and red shell, are cultivated for commercial production in Taiwan. Previous studies indicated that cultivars of Z. latifolia may be related to the infected U. esculenta isolates. However, related research is limited. The infection process of the corn smut fungus Ustilago maydis is coupled with sexual development and under control of the mating type locus. Thus, we aimed to use the knowledge of U. maydis to reveal the mating system of U. esculenta. We collected water bamboo samples and isolated 145 U. esculenta strains from Taiwan's major production areas. By using PCR and idiomorph screening among meiotic offspring and field isolates, we identified three idiomorphs of the mating type locus and found no sequence recombination between them. Whole-genome sequencing (Illumina and PacBio) suggested that the mating system of U. esculenta was bipolar. Mating type locus 1 (MAT-1) was 552,895 bp and contained 44% repeated sequences. Sequence comparison revealed that U. esculenta MAT-1 shared high gene synteny with Sporisorium reilianum and many repeats with Ustilago hordei MAT-1. These results can be utilized to further explore the genomic diversity of U. esculenta isolates and their application for water bamboo breeding.

Identification of the human crooked neck gene by comparative gene identification

Drosophila melanogaster serves as a useful model organism for functional genomic studies, and its genome project was recently completed. We previously described a comparative-gene-identification approach to assist human ortholog gene identification that involves applying an entire proteome as an alignment template. Analysis of the available 14100 Drosophila protein sequences revealed that 37% of them (5228 sequences) might lead to discoveries of novel human genes. Upon further database interrogations, we found several putative full-length human gene transcripts, including the human crooked neck (crn) gene. Based on sequence gap-closure experiments using reverse transcriptase-polymerase chain reaction as well as bioinformatic analysis, we found that the assembled human cDNA contig of crooked neck gene was at least 3903 base pairs in length with alternative splicing variations which encoded mainly for a 687-amino-acid residue protein. The human crooked neck gene was located on chromosome 20 with at least 15 exons. The unique features of the 16 copies of the tetratrico peptide repeat (TPR) motif were conserved in the yeast, fly and human crooked neck orthologous proteins, which were important for spliceosome assembly in cells.

Quantitative evaluation of pork adulteration in raw ground beef by radial immunodiffusion and enzyme-linked immunosorbent assay

Quantitative estimates are important to establish whether pork adulteration in ground beef is accidental or intentional. A standard agar gel radial immunodiffusion (RID) test using forensic-grade antiserum to porcine albumin and an enzyme-linked immunosorbent assay (ELISA) using forensic-grade anti-porcine glycoprotein immunoglobulin were used to determine from 1 to 75% raw pork in raw ground beef. The RID test, which incorporated 1.5% anti-pork serum in 1% immunodiffusion agar, formed precipitin rings with pork albumin in agar wells. A linear standard curve was obtained by plotting the diffusion area against standard pork concentrations ranging from 0 to 80%. For the ELISA the endpoint optical density increased linearly versus log % pork between 0.0625% and 2% pork. In spiked samples, the RID test had a detection limit of 3 to 5%, a coefficient of variation (CV) of 22%, and a recovery of 105%. The ELISA had a detection limit of 1%, a CV of 18%, and a recovery of 114%. The mean recovery from the spiked samples by the ELISA and RID test was not significantly different (P > 0.05) from the known sample amounts. Quantitation by RID of 28 ground beef samples (27 of which were DTEK ELISA-positive for pork adulteration) revealed a wide range of pork content, with values as high as 48%.

Selective Procedure for Detection of Salmonellae from Poultry and Sausage Products

The efficacy of lactose preenrichment and various selective enrichment and differential plating media were evaluated to determine the optimal procedure for detecting salmonellae from fresh chicken or frozen turkey, pork sausage, and cured chicken. Salmonellae were most frequently recovered from fresh poultry or pork sausage when samples were preenriched in lactose broth incubated at 35°C, selectively enriched in TT broth at 43°C, and streaked onto a new differential plating medium, modified lysine iron agar (MLIA/USDA). Enrichment of cured chicken in selenite brilliant green broth incubated at 43°C was more productive than in TT incubated at 43°C. When poultry and sausage samples were first preenriched at 35°C, selectively enriched at 43°C, and then streaked onto MLIA/USDA greater than 75% of all CFUs on the MLIA/USDA plates were typical of salmonellae. Different procedures are recommended for maximal recovery of salmonellae from fresh, frozen or cured poultry products.

Chloramphenicol-resistant Salmonella newport traced through hamburger to dairy farms. A major persisting source of human salmonellosis in California

Animal-to-human transmission of drug-resistant salmonella and the role of antimicrobial use in food animals in the emergence of these bacteria are controversial subjects. Investigation of a 4.9-fold increase in Salmonella newport isolations from Californians in 1985 showed that 87 percent of the isolates had an unusual antimicrobial-resistance pattern (including chloramphenicol resistance) and a single, identical plasmid. Interviews of 45 patients and 89 matched controls in Los Angeles County showed that illness was associated with penicillin or tetracycline use during the month before onset (P less than 0.001) and with eating ground beef during the week before onset (P = 0.052). The epidemic strain was isolated from hamburger products eaten by cases, abattoirs where the animals from which the meat came were slaughtered, dairies that sent cows for slaughter on days when culture-positive products were processed, and ill dairy cows. Isolation of salmonella from beef carcasses in abattoirs correlated with the proportion of dead or moribund animals received for slaughter (r = 0.60, P less than 0.05). Isolation of chloramphenicol-resistant salmonella from dairy farms was associated with the use of chloramphenicol at those dairies. We conclude that food animals are a major source of antimicrobial-resistant salmonella infections in humans and that these infections are associated with antimicrobial use on farms.

Toronto General Hospital controlled trial data plasma exchange therapy in Guillain-Barré' syndrome

The mechanism by which plasma exchange (PE) may benefit patients with acute Guillain-Barre' syndrome (AGBS) is unclear. It is possible, therefore, that the response of patients with AGBS is influenced by the choice of replacement solution (whole plasma vs. albumin or similar protein-containing solution). This report compares the outcome in 57 patients with AGBS treated at the Toronto General Hospital (TGH) using conventional therapy (27), PE with plasma replacement (15) and PE with albumin replacement (15). Fifteen patients (5 treated conventionally, 8 by PE with plasma replacement, 2 by PE with albumin replacement) were treated before the Baltimore coordinated multicenter trial. Forty-two patients (22 treated conventionally, 7 by PE with plasma replacement and 13 by PE with albumin replacement) were then entered at the TGH into the multicenter trial. The best outcome was observed in those patients (9) in whom PE was started within 14 days of the first neuropathic symptoms and plasma was used as replacement. The mean improvements in clinical grade in this subgroup of patients of 1.11 at four weeks after starting treatment and 1.71 at six weeks were significantly better than the corresponding improvements in the conventionally treated group of 0.35 (p less than 0.01) and 0.94 (p less than 0.05). The response of patients (9) exchanged within 14 days of onset, but replaced with albumin (grade change of 0.67 at four weeks and 0.86 at six weeks), was not significantly different from that of the conventionally treated patients. These data support the need for a randomized trial to compare PE using plasma replacement and PE using albumin replacement in patients with AGBS.(ABSTRACT TRUNCATED AT 250 WORDS)

Sampling Methods and Frozen Storage of Samples for Detection of Campylobacter jejuni on Freshly Processed Broiler Carcasses

Swab, rinse and excision sampling methods are commonly used for detection of microorganisms on poultry carcasses. Swabbing has been the most frequently reported sampling method for Campylobacter jejuni on poultry. We evaluated the three methods for C. jejuni detection on freshly processed poultry in the following ways: (a) the interior and exterior surfaces of half of a carcass were each thoroughly rubbed with separate swabs which were combined in a test tube containing 2 ml of appropriate medium; (b) 25 g of skin and tissue samples from neck and abdominal opening cut areas were deposited in a stomacher bag with 5 ml of brucella broth (BB) and stomached for 2 min; and (c) half carcasses were shaken for 1 min with 100 ml BB in plastic bags. One drop of each sample was streaked for isolation on brucella agar containing 10% defibrinated sheep blood and Skirrow antibiotics. Isolates were identified by microscopy and appropriate cultural tests. All three sampling techniques were essentially equivalent for detection of C. jejuni on fresh carcasses. However, when samples were stored frozen for 7 to 10 d to simulate transport conditions from sampling locations to the laboratory, the incidence of detection was significantly reduced. Use of cryoprotective agents was an effective method to preserve swab samples during frozen storage.

Importance of glutamate synthase in glutamate synthesis by soybean cell suspension cultures

The specific activities of glutamate synthase|EC 2.6.1.53, l-glutamine: alpha-ketoglutarate amino transferase (NADPH-oxidising)| and glutamine synthetase|EC 6.3.1.2, l-glutamate: ammonia ligase (ADP-forming)| extracted from soybean (Glycine max L.) cells grown in modified B5 medium were found to vary significantly in response to variations in the nitrogen content of the medium. The changes seen in specific activity levels could be correlated with similar patterns seen in the growth of the cells, in response to changes in the nitrogen content of the medium. By contrast, the specific activity of glutamate dehydrogenase|EC 1.4.1.2, l-glutamate: NAD(+) oxidoreductase (deaminating)|, was relatively low and invariant. Glutamate synthase was extracted from cells grown under optimal conditions, partially purified, and shown to have many properties in common with preparations of this enzyme extracted from other plant sources. Glutamate synthase was purified to homogeneity, using affinity chromatography on blue Sepharose.