Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis

Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.

SOCS1 Haploinsufficiency Presenting as Severe Enthesitis, Bone Marrow Hypocellularity, and Refractory Thrombocytopenia in a Pediatric Patient with Subsequent Response to JAK Inhibition

Haploinsufficiency of suppressor of cytokine signaling 1 (SOCS1) is a recently discovered autoinflammatory disorder with significant rheumatologic, immunologic, and hematologic manifestations. Here we report a case of SOCS1 haploinsufficiency in a 5-year-old child with profound arthralgias and immune-mediated thrombocytopenia unmasked by SARS-CoV-2 infection. Her clinical manifestations were accompanied by excessive B cell activity, eosinophilia, and elevated IgE levels. Uniquely, this is the first report of SOCS1 haploinsufficiency in the setting of a chromosomal deletion resulting in complete loss of a single SOCS1 gene with additional clinical findings of bone marrow hypocellularity and radiologic evidence of severe enthesitis. Immunologic profiling showed a prominent interferon signature in the patient's peripheral blood mononuclear cells, which were also hypersensitive to stimulation by type I and type II interferons. The patient showed excellent clinical and functional laboratory response to tofacitinib, a Janus kinase inhibitor that disrupts interferon signaling. Our case highlights the need to utilize a multidisciplinary diagnostic approach and consider a comprehensive genetic evaluation for inborn errors of immunity in patients with an atypical immune-mediated thrombocytopenia phenotype.

Same-day discharge vs. observation after laparoscopic pediatric appendectomy: a prospective cohort study

Background

Through 2015, the practice at our university based free-standing children's hospital was to admit uncomplicated appendicitis patients for overnight observation post-operatively. Given the increasing body of evidence suggesting the safety and feasibility of same-day discharge after appendectomy for uncomplicated appendicitis, we elected to perform a prospective study evaluating the complication rates of same-day discharge compared to overnight observation at our institution, given our large volume of appendicitis.

Methods

Pediatric patients who underwent laparoscopic appendectomies for uncomplicated appendicitis in 2016 were analyzed. Data regarding demographics, admission, and discharge times and outcomes of complications, as well as readmissions, return to the emergency department, and nonscheduled clinic visits were collected and analyzing using chi-square and multivariate regression. Cost of stay data was obtained and analyzed using Mann-Whitney U test to compare non-parametric variables.

Results

Eight hundred and forty-nine laparoscopic appendectomies were performed for uncomplicated appendicitis during the study period, of which 382 resulted in same-day discharge and 467 in an admission for observation. Univariate analysis revealed no statistical difference between readmission rates for same day vs. observation (2 vs. 6 patients; P=0.21) or in emergency department visits within 30 days (22 vs. 27 patients; P=0.98). There was no difference in the number of surgical site infections or extra clinic visits. There was a significantly lower median cost of stay for patients discharged home the same day at 29,150 dollars (25,644, 32,276, IQR) compared to a median of 34,827 dollars (31,154, 39,457, IQR) (P<0.0001).

Conclusions

Same-day discharge for laparoscopic uncomplicated appendectomy should be the new standard of care. This study found no differences in outcomes between the timing of discharge, with a significantly lower cost of stay for patients discharged home the same day.

[Pseudohyperkalemia and thrombocytosis]

INTRODUCTION

Hyperkalemia is common in medicine and requires rapid management. Besides the easily evoked causes such as renal failure, adrenal insufficiency, cell lysis or iatrogenic causes, false or pseudo-hyperkalemia should not be forgotten.

OBSERVATIONS

Three patients (1 man, 2 women, aged 78, 84, 88) were managed for thrombocytosis (between 1306 and 2404 G/L) and non-symptomatic hyperkalemia (between 6.1 and 7.7mmol/L) are reported. Kalemia on blood collected in heparin tube was normal (4.4-4.6mmol/L). Therefore, no specific treatment for this pseudohyperkalemia was required.

CONCLUSION

The combination of thrombocytosis and non-symptomatic hyperkalemia should suggest the diagnosis of pseudohyperkalemia and should prompt for a control of kalemia on blood collected in heparin tube. The recognition of this diagnosis is important in order to avoid unnecessary and potentially deleterious treatment of hyperkalemia.

Parental satisfaction with same-day discharge after laparoscopic appendectomy for uncomplicated appendicitis

Objectives

Recent studies suggest that same-day discharge is safe for the paediatric population after various laparoscopic procedures. Same-day discharge is increasingly common after laparoscopic surgery for uncomplicated appendicitis although it is not standard practice. This prospective study aims to assess parental satisfaction with same-day discharge after laparoscopic appendectomy for uncomplicated appendicitis.

Methods

At our institution, 849 patients with uncomplicated acute appendicitis underwent laparoscopic appendectomy in 2016; of which, 382 were discharged on the same calendar day. Postdischarge surveys assessing parental satisfaction were administered by telephone at the 2-week follow-up.

Results

Approximately 65% of 185 total parental responses reported initial satisfaction with same-day discharge. About 30% were nervous at that time, and 5% did not feel ready to go home yet. Upon reflection, a higher proportion of parents (81.6%) felt same-day discharge was the appropriate course of action, 11.4% were unsure, and 7.0% would not do it again. Some parents cited concerns regarding pain control and incongruous expectations from conversations with staff or surgical experiences of their own.

Conclusions

The majority of parents recalled being happy at discharge, with an increase to 82% retrospectively. Only 7% of parents would not elect to go home on the same day again. Opportunities for improvement include a unified plan from all providers with expectations of same-day discharge if appendicitis is intraoperatively confirmed to be uncomplicated and better analgesic instructions at discharge.

Safety and feasibility of same-day discharge for uncomplicated appendicitis: A prospective cohort study

BACKGROUND

Appendicitis is the most common gastrointestinal pediatric surgical emergency. With the introduction of laparoscopic techniques in the 1990s, recovery, pain, and hospital stay after laparoscopic procedures have been significantly reduced. While many laparoscopic procedures are performed as outpatient surgeries, pediatric appendectomy patients continue to be hospitalized for postoperative observation. Our goal was to evaluate the safety and feasibility of same day discharge after laparoscopic appendectomy for uncomplicated appendicitis.

METHODS

After IRB approval, all pediatric patients undergoing laparoscopic appendectomy during 2016 for noncomplicated appendicitis were eligible for the study. Decision for same day discharge was based on surgeon preference and parental agreement. Data regarding demographics, admission and discharge times, outcomes of complications, readmissions, return to the ED, and nonscheduled clinic visits were collected.

RESULTS

A total of 1321 appendectomies were performed during the study period, of which 849 were uncomplicated and 382 were discharged same day. There were 2 readmissions, 4 superficial surgical site infections, 10 patients with nausea or vomiting, and 33 patients with pain control issues, 9 of whom presented to the ED.

CONCLUSIONS

Same day discharge for laparoscopic noncomplicated appendectomy is a safe and feasible alternative to postoperative admission and observation. This has the potential to yield significant healthcare cost savings.

LEVEL OF EVIDENCE

Level II, Prospective Cohort Study.

DNA methylation of Th2 lineage determination genes at birth is associated with allergic outcomes in childhood

BACKGROUND

There is now increasing evidence that asthma and atopy originate in part in utero, with disease risk being associated with the altered epigenetic regulation of genes.

OBJECTIVE AND METHODS

To determine the relationship between variations in DNA methylation at birth and the development of allergic disease, we examined the methylation status of CpG loci within the promoter regions of Th1/2 lineage commitment genes (GATA3, IL-4, IL-4R, STAT4 and TBET) in umbilical cord DNA at birth in a cohort of infants from the Southampton Women's Survey (n = 696) who were later assessed for asthma, atopic eczema and atopy.

RESULTS

We found that higher methylation of GATA3 CpGs -2211/-2209 at birth was associated with a reduced risk of asthma at ages 3 (median ratio [median methylation in asthma group/median methylation in non-asthma group] = 0.74, P = .006) and 6-7 (median ratio 0.90, P = .048) years. Furthermore, we demonstrated that the GATA3 CpG loci associated with later risk of asthma lie within a NF-κB binding site and that methylation here blocks transcription factor binding to the GATA3 promoter in the human Jurkat T-cell line. Associations between umbilical cord methylation of CpG loci within IL-4R with atopic eczema at 12 months (median ratio 1.02, P = .028), and TBET with atopy (median ratio 0.98, P = .017) at 6-7 years of age were also observed.

CONCLUSIONS AND CLINICAL RELEVANCE

Our findings provide further evidence of a developmental contribution to the risk of later allergic disorders and suggest that involvement of epigenetic mechanisms in childhood asthma is already demonstrable at birth.

[Agranulocytosis related to fluindione: A case report]

INTRODUCTION

While in most countries warfarin is the preferred anti-vitamin K, fluindione, a molecule with a prolonged half-life remains largely prescribed in France. Some of its side effects, including immuno-allergic complications, remain poorly understood.

CASE REPORT

A 77-year-old woman presented with a febrile severe neutropenia of immunoallergic mechanism with a favourable outcome associated with fluindione, introduced 25 days earlier for the treatment of atrial fibrillation.

CONCLUSION

This rare side effect is a reminder of the importance of biological monitoring in the first weeks following the introduction of fluindione and key diagnostic elements and therapeutic aspects of iatrogenic agranulocytosis.

Delivery of intraocular triamcinolone acetonide in the treatment of macular edema

Macular edema (ME) is one of the eventual outcomes of various intraocular and systemic pathologies. The pathogenesis for ME is not yet entirely understood; however, some of the common risk factors for its development have been identified. While this investigation will not discuss the numerous etiologies of ME in detail, it appraises the two most widely studied delivery modalities of intraocular corticosteroids in the treatment of ME—intravitreal injection (IVI) and sub-Tenon’s infusion (STI). A thorough review of the medical literature was conducted to identify the efficacy and safety of IVI and STI, specifically for the administration of triamcinolone acetonide (TA), in the setting of ME in an attempt to elucidate a preferred steroid delivery modality for treatment of ME.

Time taken to produce dispensing labels in hospital pharmacies, and factors affecting it

The time taken in hospital pharmacies to produce labels for individual patients' medication was measured, and factors affecting the labelling process investigated. Labelling time was measured by direct observation using a stopclock at randomly chosen semi-stratified time periods. Four combinations of major London hospitals and computer systems were studied. The time to produce 2,167 labels was measured and 59 operators were observed. There were significant differences in average labelling time between the studied hospitals/systems (16.6 to 39.3 seconds per label). Operators' experience with their system and the occurrence of interruptions were found to affect labelling significantly (P&lt;0.0001 in both cases). There was an overall trend for labelling time to decrease with increasing experience (P&lt;0.0001), and interruptions added 11 to 12 seconds on average. Operator experience also affected the rate and duration of interruptions, which subsequently affected labelling time. Fewer interruptions occurred with more experienced staff (P=0.0015) and when interrupted, they took less time than inexperienced staff to complete the labelling process. A performance indicator of person-days per 100,000 labels varied from 62.3 to 147.6. Pharmacy managers should be aware that there are significant differences in performance using different labelling systems and that staff training and systems of work may have a marked effect on labelling time.

Large-scale phenotypic analysis reveals identical contributions to cell functions of known and unknown yeast genes

Sequencing of the yeast genome has shown that about one-third of the yeast ORFs code for unknown proteins. Many other have similarity to known genes, but still the cellular functions of the gene products are unknown. The aim of the B1 Consortium of the EUROFAN project was to perform a qualitative phenotypic analysis on yeast strains deleted for functionally orphan genes. To this end we set up a simple approach to detect growth defects of a relatively large number of strains in the presence of osmolytes, ethanol, high temperature, inhibitory compounds or drugs affecting protein biosynthesis, phosphorylation level or nucleic acids biosynthesis. We have now developed this procedure to a semi-quantitative level, we have included new inhibitors, such as hygromycin B, benomyl, metals and additional drugs interfering with synthesis of nucleic acids, and we have performed phenotypic analysis on the deleted strains of 564 genes poorly characterized in respect to their cellular functions. About 30% of the deleted strains showed at least one phenotype: many of them were pleiotropic. For many gene deletions, the linkage between the deletion marker and the observed phenotype(s) was studied by tetrad analysis and their co-segregation was demonstrated. Co-segregation was found in about two-thirds of the analysed strains showing phenotype(s).

Description and application of a rapid method for genomic DNA direct sequencing

We describe a rapid method for determining nucleotide sequences directly from total genomic DNA. This technique was used to determine genomic DNA sequences in various prokaryotic and eukaryotic microorganisms with a G+C content between 40 and 50%, e.g. Escherichia coli, Vibrio cholerae, Bacillus subtilis and Saccharomyces cerevisiae. Furthermore, the method was applied to accurately sequence up to 300 DNA base pairs in Photorhabdus luminescens, whose genome sequencing is currently under way. Taken together, these results provide evidence that our technique can be widely used to easily and efficiently determine genomic DNA sequences.

Cytochrome P450 4A, peroxisomal enzymes and nicotinamide cofactors in koala liver

We have examined hepatic levels of microsomal lauric acid hydroxylase activity and cyanide-insensitive palmitoyl coenzyme A oxidative activity in koala (Phascolarctos cinereus) and tammar wallaby (Macropus eugenii) and compared our results to those determined in rat. Microsomal lauric acid hydroxylation was significantly higher in koala than in tammar wallaby or rat. However, cyanide-insensitive palmitoyl-CoA oxidation was absent in the koala. We have also determined the hepatic nicotinamide cofactors in these species. Hepatic nicotinamide-adenine dinucleotide (NAD) and the ratio of NAD/nicotinamide-adenine dinucleotide phosphate (NADP) were higher in koala than in tammar wallaby and rat liver. Reverse transcription of koala liver mRNA, followed by polymerase chain reaction using primers based on highly conserved areas in the CYP4A family led to the cloning of a partial, near full length, cDNA clone with approximately 70% nucleotide and deduced amino acid sequence identity to human CYP4A11. The CYP has been named CYP4A15.

Fetal serum beta2-microglobulin predicts postnatal renal function in bilateral uropathies

BACKGROUND

Predicting postnatal renal function is crucial for the prenatal evaluation of fetal bilateral uropathies. Prenatal ultrasound can identify intrauterine terminal renal failure, but is not sensitive enough to identify those infants who would survive with an impaired renal function. Because it reflects fetal glomerular filtration, fetal serum beta2-microglobulin is a potential predictor of postnatal renal function.

METHODS

Fetal serum beta2-microglobulin (beta2m) was assayed in 61 cases of bilateral or low obstructive uropathy, 74 controls, and 17 cases of bilateral renal agenesis, and was correlated with renal function.

RESULTS

Fetal serum beta2m was 3.2 mg/L (range 1.5 to 4.7) in controls (N = 74), 9.5 mg/L (range 6.7 to 11.3) in bilateral renal agenesis (N = 17), 7 mg/L (5.1 to 10.6) in uropathy in which terminal renal failure resulted in termination of pregnancy (N = 26), and 3.7 mg/L (range 2.3 to 11.2) in live births with uropathy (N = 35). In the latter subgroup, fetal serum beta2m was significantly and positively correlated (r2 = 0.91) with postnatal serum creatinine. All survivors with a postnatal serum creatinine < or =50 micromol/L ha a fetal serum beta2m lower than 5 mg/L. Four of 6 survivors with a postnatal serum creatinine> 50 micromol/L had a fetal serum beta2m greater than 5 mg/L.

CONCLUSION

Fetal serum beta2-microglobulin is a marker for renal function and predicts postnatal serum creatinine in bilateral or low fetal obstructive uropathy.

Isolation and characterization of vicH, encoding a new pleiotropic regulator in Vibrio cholerae

During the last decade, the hns gene and its product, the H-NS protein, have been extensively studied in Escherichia coli. H-NS-like proteins seem to be widespread in gram-negative bacteria. However, unlike in E. coli and in Salmonella enterica serovar Typhimurium, little is known about their role in the physiology of those organisms. In this report, we describe the isolation of vicH, an hns-like gene in Vibrio cholerae, the etiological agent of cholera. This gene was isolated from a V. cholerae genomic library by complementation of different phenotypes associated with an hns mutation in E. coli. It encodes a 135-amino-acid protein showing approximately 50% identity with both H-NS and StpA in E. coli. Despite a low amino acid conservation in the N-terminal part, VicH is able to cross-react with anti-H-NS antibodies and to form oligomers in vitro. The vicH gene is expressed as a single gene from two promoters in tandem and is induced by cold shock. A V. cholerae wild-type strain expressing a vicHDelta92 gene lacking its 3' end shows pleiotropic alterations with regard to mucoidy and salicin metabolism. Moreover, this strain is unable to swarm on semisolid medium. Similarly, overexpression of the vicH wild-type gene results in an alteration of swarming behavior. This suggests that VicH could be involved in the virulence process in V. cholerae, in particular by affecting flagellum biosynthesis.

Correlation of alkaline phosphatase (ALP) determination and analysis of the tissue non-specific ALP gene in prenatal diagnosis of severe hypophosphatasia

Prenatal diagnosis of severe hypophosphatasia by mutation analysis of the tissue non-specific alkaline phosphatase (TNSALP) gene is reliable and mostly informative. However, alkaline phosphatase (ALP) assay of CVS may be a useful complementary and independent method, especially when a mutation is unidentified and DNA from the index case is unavailable, rendering impossible the use of DNA polymorphisms as genetic markers of the disease. We report here mutation analysis of the TNSALP gene and ALP assay in nine cases of prenatal diagnosis of severe hypophosphatasia. The results showed a good correlation between ALP assay and DNA analysis in all but one case, which suggested that in at least some cases low values of ALP may correspond to affected fetuses as well as to heterozygotes.

Evaluation of the Abbott system in maternal serum screening for Down syndrome: the AxSym analyzer, AFP and hCG reagents and Maciel Prenatal Interpretive Software

Multi-marker maternal serum screening for Down syndrome in the second trimester is now part of routine care in many centers. Most protocols use a combination of hCG (or its free beta-subunit) and alpha-fetoprotein (AFP) or unconjugated estriol (UE3), or both. Risk calculation is based on these maternal serum marker values combined with maternal age and trisomy 21 maternal age-related risk. Computer programs are therefore necessary. Both technical and statistical efficiency are included in the final risk evaluation. We studied the Abbott system, comprising AxSym analyzer, AFP and hCG kits and Prenatal Interpretive Software (Maciel). Median values were established between 14 and 18 weeks of amenorrhea in a population of 1822 patients and in twin pregnancies in 157 cases. Forty maternal sera from trisomy 21 affected pregnancies were analyzed. Software was evaluated in a population of 429 patients and in 124 cases of trisomy 21. We conclude that this system constitutes an accurate and efficient method of maternal serum screening for Down syndrome.

Diverse signaling pathways modulate nuclear receptor recruitment of N-CoR and SMRT complexes

Several lines of evidence indicate that the nuclear receptor corepressor (N-CoR) complex imposes ligand dependence on transcriptional activation by the retinoic acid receptor and mediates the inhibitory effects of estrogen receptor antagonists, such as tamoxifen, suppressing a constitutive N-terminal, Creb-binding protein/coactivator complex-dependent activation domain. Functional interactions between specific receptors and N-CoR or SMRT corepressor complexes are regulated, positively or negatively, by diverse signal transduction pathways. Decreased levels of N-CoR correlate with the acquisition of tamoxifen resistance in a mouse model system for human breast cancer. Our data suggest that N-CoR- and SMRT-containing complexes act as rate-limiting components in the actions of specific nuclear receptors, and that their actions are regulated by multiple signal transduction pathways.

Role of Escherichia coli histone-like nucleoid-structuring protein in bacterial metabolism and stress response--identification of targets by two-dimensional electrophoresis

The histone-like nucleoid-structuring protein, H-NS, is a major bacterial chromatin component which influences DNA structure and gene expression. Mutations in hns, the structural gene of H-NS protein, have been shown to result in highly pleiotropic effects in Escherichia coli cells. In this study, we have initiated an index of the proteins whose synthesis is, directly or indirectly regulated by H-NS. Using two-dimensional gel electrophoresis, we have examined the global changes in gene expression which occured in an hns background compared with its wild-type parent. In addition, we analysed the effects of mutations in two other genes i.e. lrp and pta, which are also involved in global regulatory pathways. Although these comparative analyses revealed several common differences, thus suggesting possible interactions between these regulatory mechanisms, i.e. H-NS, Lrp (leucine-responsive regulatory protein) and acetylphosphate, the most extensive modifications occurred in an hns mutant. Among the polypeptides whose level of synthesis was specifically altered in an hns mutant, several corresponded to H-NS targets previously identified by classical selection methods. Moreover, the present study allows us to characterize several H-NS targets, which were identified either by comparison with the E. coli two-dimensional reference maps or by microsequencing procedure. Many of these newly identified polypeptides are involved in adaptation of E. coli cells to environmental challenges, and one of them could be involved in bacterial virulence. Finally, synthesis of several proteins belonging to the heat-shock regulon, more particularly molecular chaperones, was induced in an hns mutant.