DNMT1 Deficiency Impacts on Plasmacytoid Dendritic Cells in Homeostasis and Autoimmune Disease.

Dendritic cells (DCs) are heterogeneous immune regulators involved in autoimmune diseases. Epigenomic mechanisms orchestrating DC development and DC subset diversification remain insufficiently understood but could be important to modulate DC fate for clinical purposes. By combining whole-genome methylation assessment with the analysis of mice expressing reduced DNA methyltransferase 1 levels, we show that distinct DNA methylation levels and patterns are required for the development of plasmacytoid DC and conventional DC subsets. We provide clonal in vivo evidence for DC lineage establishment at the stem cell level, and we show that a high DNA methylation threshold level is essential for Flt3-dependent survival of DC precursors. Importantly, reducing methylation predominantly depletes plasmacytoid DC and alleviates systemic lupus erythematosus in an autoimmunity mouse model. This study shows how DNA methylation regulates the production of DC subsets and provides a potential rationale for targeting autoimmune disease using hypomethylating agents.

Analysis of mutational signatures with yet another package for signature analysis.

Different mutational processes leave characteristic patterns of somatic mutations in the genome that can be identified as mutational signatures. Determining the contributions of mutational signatures to cancer genomes allows not only to reconstruct the etiology of somatic mutations, but can also be used for improved tumor classification and support therapeutic decisions. We here present the R package yet another package for signature analysis (YAPSA) to deconvolute the contributions of mutational signatures to tumor genomes. YAPSA provides in-built collections from the COSMIC and PCAWG SNV signature sets as well as the PCAWG Indel signatures and employs signature-specific cutoffs to increase sensitivity and specificity. Furthermore, YAPSA allows to determine 95% confidence intervals for signature exposures, to perform constrained stratified signature analyses to obtain enrichment and depletion patterns of the identified signatures and, when applied to whole exome sequencing data, to correct for the triplet content of individual target capture kits. With this functionality, YAPSA has proved to be a valuable tool for analysis of mutational signatures in molecular tumor boards in a precision oncology context. YAPSA is available at R/Bioconductor (http://bioconductor.org/packages/3.12/bioc/html/YAPSA.html).

Febrile urinary tract infections after ureteroneocystostomy and subureteral injection of dextranomer/hyaluronic acid for vesicoureteral reflux--do choice of procedure and success matter?

PURPOSE: Despite success rates favoring ureteroneocystostomy over subureteral injection of dextranomer/hyaluronic acid for correction of vesicoureteral reflux, the reported incidence of postoperative febrile urinary tract infection favors the latter. We evaluated contemporary treatment cohorts for an association between correction of vesicoureteral reflux and risk of postoperative febrile urinary tract infection. MATERIALS AND METHODS: We retrospectively reviewed the records of 396 consecutive patients who underwent ureteroneocystostomy or subureteral injection of dextranomer/hyaluronic acid between 1994 and 2008. Time to event multivariate analyses included preoperative grade of vesicoureteral reflux and bladder/bowel dysfunction. RESULTS: Of 316 patients meeting study criteria 210 underwent ureteroneocystostomy (356 ureters) and 106 underwent subureteral injection of dextranomer/hyaluronic acid (167). Median patient age was 5.7 years (IQR 3.4 to 8.3). Median followup was 28 months (IQR 8 to 61). Ureteral success was significantly greater after ureteroneocystostomy (88%, 314 of 356 cases) vs subureteral injection of dextranomer/hyaluronic acid (74%, 124 of 167, p = 0.0001). When controlling for preoperative grade of vesicoureteral reflux and bladder/bowel dysfunction, the risk of persistent reflux was 2.8 times greater after subureteral injection of dextranomer/hyaluronic acid (95% CI 1.7-4.7, p <0.0001). The incidence of febrile urinary tract infection did not significantly differ between ureteroneocystostomy (8%, 16 of 210 cases) and subureteral injection of dextranomer/hyaluronic acid (4%, 4 of 106; HR 1.96, 95% CI 0.64-5.9, p = 0.24) even when controlling for preoperative grade of vesicoureteral reflux, a predictor of postoperative febrile urinary tract infection on multivariate analysis (HR 2.2 per increase in grade, 95% CI 1.3-3.6, p = 0.0022). Persistent reflux was not a predictor of postoperative febrile urinary tract infection (HR 0.81, 95% CI 0.22-2.9, p = 0.75 for ureteroneocystostomy vs HR 1.8, 95% CI 0.2-17.3, p = 0.6 for subureteral injection of dextranomer/hyaluronic acid and HR 1.8, 95% CI 0.3-3.3, p = 0.6 for both). CONCLUSIONS: The incidence of postoperative febrile urinary tract infection may be independent of radiographic procedural success.

Population-based comparison of laparoscopic and open pyeloplasty in paediatric pelvi-ureteric junction obstruction.

OBJECTIVE: To describe the extent of use and in-hospital outcomes of open and laparoscopic pyeloplasty for paediatric pelvi-ureteric junction (PUJ) obstruction in the USA. PATIENTS AND METHODS: Using the 2004-2008 Nationwide Inpatient Sample, we identified 4590 paediatric patients (≤18 years old) who underwent open or laparoscopic pyeloplasty for PUJ obstruction at 195 hospitals. Multivariable regression models were used to test the associations between hospital and patient covariates (age, gender, race, primary health insurance), type of admission (emergent vs elective), and hospital characteristics (teaching vs non-teaching status; rural vs urban location) with complications, length of stay (LOS), and total hospitalization costs. RESULTS: During the 5-year study interval, 4426 (96.4%) and 164 (3.6%) paediatric patients diagnosed with PUJ obstruction underwent open and laparoscopic pyeloplasty, respectively. The proportion of patients undergoing laparoscopic pyeloplasty gradually increased from 2.4% in 2004 to 4.4% in 2008, but this increase was not significant (P = 0.22 for trend). On multivariable analysis, laparoscopic pyeloplasty was observed to have rates of postoperative complications (2.51 vs 5.00; P = 0.67), LOS (2.42 vs 2.75; P = 0.33) and total hospitalization cost ($9755 vs $8537; P = 0.24) similar to those of open pyeloplasty. CONCLUSIONS: While laparoscopic pyeloplasty was generally an infrequent operation performed for paediatric PUJ obstruction during the period studied, this minimally invasive surgery provided similar outcomes in terms of in-hospital complications, LOS and total hospitalization costs. The results of this study inform policymakers about the comparative effectiveness of laparoscopic and open pyeloplasty.

mPEG-PAMAM-G4 nucleic acid nanocomplexes: enhanced stability, RNase protection, and activity of splice switching oligomer and poly I:C RNA.

Dendrimer chemistries have virtually exploded in recent years with increasing interest in this class of polymers as gene delivery vehicles. An effective nucleic acid delivery vehicle must efficiently bind its cargo and form physically stable complexes. Most importantly, the nucleic acid must be protected in biological fluids and tissues, as RNA is extremely susceptible to nuclease degradation. Here, we characterized the association of nucleic acids with generation 4 PEGylated poly(amidoamine) dendrimer (mPEG-PAMAM-G4). We investigated the formation, size, and stability over time of the nanoplexes at various N/P ratios by gel shift and dynamic light scatter spectroscopy (DLS). Further characterization of the mPEG-PAMAM-G4/nucleic acid association was provided by atomic force microscopy (AFM) and by circular dichroism (CD). Importantly, mPEG-PAMAM-G4 complexation protected RNA from treatment with RNase A, degradation in serum, and various tissue homogenates. mPEG-PAMAM-G4 complexation also significantly enhanced the functional delivery of RNA in a novel engineered human melanoma cell line with splice-switching oligonucleotides (SSOs) targeting a recombinant luciferase transcript. mPEG-PAMAM-G4 triconjugates formed between gold nanoparticle (GNP) and particularly manganese oxide (MnO) nanorods, poly IC, an anticancer RNA, showed enhanced cancer-killing activity by an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cell viability assay.

Dynamic DNA methylation reveals novel cis-regulatory elements in mouse hematopoiesis.

Differentiation of hematopoietic stem and progenitor cells to terminally differentiated immune cells is accompanied by large-scale remodeling of the DNA methylation landscape. Although significant insights into the molecular mechanisms of hematopoietic tissue regeneration were derived from mouse models, profiling of DNA methylation has been hampered by high cost or low resolution using available methods. The recent development of the Infinium Mouse Methylation BeadChip (MMBC) array facilitates methylation profiling of the mouse genome at a single CpG resolution at affordable cost. We extended the RnBeads package to provide a computational framework for the analysis of MMBC data. This framework was applied to a newly generated reference map of mouse hematopoiesis encompassing nine different cell types. Analysis of dynamically regulated CpG sites showed progressive and unidirectional DNA methylation changes from hematopoietic stem and progenitor cells to differentiated hematopoietic cells and allowed the identification of lineage- and cell type-specific DNA methylation programs. Comparison with previously published catalogs of cis-regulatory elements (CREs) revealed 12,856 novel putative CREs that were dynamically regulated by DNA methylation (mdCREs). These mdCREs were predominantly associated with patterns of cell type-specific DNA hypomethylation and could be identified as epigenetic control regions regulating the expression of key hematopoietic genes during differentiation. In summary, we established an analysis pipeline for MMBC data sets and provide a DNA methylation atlas of mouse hematopoiesis. This resource allowed us to identify novel putative CREs involved in hematopoiesis and will serve as a platform to study epigenetic regulation of normal and malignant hematopoiesis.

Attrition of X Chromosome Inactivation in Aged Hematopoietic Stem Cells.

During X chromosome inactivation (XCI), the inactive X chromosome (Xi) is recruited to the nuclear lamina at the nuclear periphery. Beside X chromosome reactivation resulting in a highly penetrant aging-like hematopoietic malignancy, little is known about XCI in aged hematopoietic stem cells (HSCs). Here, we demonstrate that LaminA/C defines a distinct repressive nuclear compartment for XCI in young HSCs, and its reduction in aged HSCs correlates with an impairment in the overall control of XCI. Integrated omics analyses reveal higher variation in gene expression, global hypomethylation, and significantly increased chromatin accessibility on the X chromosome (Chr X) in aged HSCs. In summary, our data support the role of LaminA/C in the establishment of a special repressive compartment for XCI in HSCs, which is impaired upon aging.

Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response.

Somatic mutations in DNA methyltransferase 3A (DNMT3A) are among the most frequent alterations in clonal hematopoiesis (CH) and acute myeloid leukemia (AML), with a hotspot in exon 23 at arginine 882 (DNMT3AR882). Here, we demonstrate that DNMT3AR882H-dependent CH and AML cells are specifically susceptible to the hypomethylating agent azacytidine (AZA). Addition of AZA to chemotherapy prolonged AML survival solely in individuals with DNMT3AR882 mutations, suggesting its potential as a predictive marker for AZA response. AML and CH mouse models confirmed AZA susceptibility specifically in DNMT3AR882H-expressing cells. Hematopoietic stem cells (HSCs) and progenitor cells expressing DNMT3AR882H exhibited cell autonomous viral mimicry response as a result of focal DNA hypomethylation at retrotransposon sequences. Administration of AZA boosted hypomethylation of retrotransposons specifically in DNMT3AR882H-expressing cells and maintained elevated levels of canonical interferon-stimulated genes (ISGs), thus leading to suppressed protein translation and increased apoptosis.

ShinyButchR: Interactive NMF-based decomposition workflow of genome-scale datasets.

Non-negative matrix factorization (NMF) has been widely used for the analysis of genomic data to perform feature extraction and signature identification due to the interpretability of the decomposed signatures. However, running a basic NMF analysis requires the installation of multiple tools and dependencies, along with a steep learning curve and computing time. To mitigate such obstacles, we developed ShinyButchR, a novel R/Shiny application that provides a complete NMF-based analysis workflow, allowing the user to perform matrix decomposition using NMF, feature extraction, interactive visualization, relevant signature identification, and association to biological and clinical variables. ShinyButchR builds upon the also novel R package ButchR, which provides new TensorFlow solvers for algorithms of the NMF family, functions for downstream analysis, a rational method to determine the optimal factorization rank and a novel feature selection strategy.

Increasing prevalence and associated risk factors for methicillin resistant Staphylococcus aureus bacteriuria.

PURPOSE: Infections due to methicillin resistant Staphylococcus aureus are becoming increasingly prevalent in hospitals and in the community. We reviewed our institutional experience to determine whether methicillin resistant S. aureus is becoming a more common cause of bacteriuria and to determine if there are specific risk factors that may predict the development of methicillin resistant S. aureus bacteriuria. MATERIALS AND METHODS: We reviewed all urine cultures with a pure growth of a single organism obtained at our institution from 1997 and 2007. Patients with urine cultures positive for methicillin resistant S. aureus were compared to a cohort with cultures positive for methicillin sensitive S. aureus, and to a third cohort with cultures positive for Escherichia coli to determine patient characteristics and associated risk factors. RESULTS: We identified 7,100 and 9,985 positive urine cultures performed in 1997 and 2007, respectively. The most common urinary organism was E. coli. The number of patients with methicillin resistant S. aureus bacteriuria increased from 18 (0.3%) to 74 (0.8%) (p <0.001). On multivariate analysis older age (p = 0.004), catheter use (p = 0.004), hospital exposure (p <0.001) and patient comorbidity (p <0.001) were associated with methicillin resistant S. aureus bacteriuria compared with E. coli bacteriuria. CONCLUSIONS: Methicillin resistant S. aureus remains rare as a cause of bacteriuria but its incidence has increased during the last decade. Risk factors for methicillin resistant S. aureus bacteriuria include increased age, patient comorbidity, hospital exposure and catheter use. For patients with these risk factors and new onset urinary symptoms, methicillin resistant S. aureus should be considered a possible cause of urinary tract infection.

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma.

Chordomas are rare bone tumors with few therapeutic options. Here we show, using whole-exome and genome sequencing within a precision oncology program, that advanced chordomas (n = 11) may be characterized by genomic patterns indicative of defective homologous recombination (HR) DNA repair and alterations affecting HR-related genes, including, for example, deletions and pathogenic germline variants of BRCA2, NBN, and CHEK2. A mutational signature associated with HR deficiency was significantly enriched in 72.7% of samples and co-occurred with genomic instability. The poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, which is preferentially toxic to HR-incompetent cells, led to prolonged clinical benefit in a patient with refractory chordoma, and whole-genome analysis at progression revealed a PARP1 p.T910A mutation predicted to disrupt the autoinhibitory PARP1 helical domain. These findings uncover a therapeutic opportunity in chordoma that warrants further exploration, and provide insight into the mechanisms underlying PARP inhibitor resistance.

Superficial genitourinary abscesses in children: emergence of methicillin resistant Staphylococcus aureus.

PURPOSE: The prevalence of methicillin resistant Staphylococcus aureus is increasing. However, little is known about methicillin resistant S. aureus in the genitourinary tract, particularly in children. We assessed the incidence of pediatric genitourinary methicillin resistant S. aureus superficial abscess requiring surgical intervention. MATERIALS AND METHODS: We reviewed the records of all children undergoing surgical debridement of superficial abscess at a single institution between 1995 and 2007. We assessed surgical site, organism identity, patient comorbidity, methicillin resistant S. aureus risk factors, number of procedures and patient outcome. RESULTS: Surgical debridement of a superficial genitourinary abscess was performed in 60 children. Patient age ranged from 29 days to 17 years (median 3 years). A single debridement was generally curative, with only 5 patients (8.3%) requiring more than 1 procedure. One patient (1.7%) died of sepsis postoperatively due to Pseudomonas infection. One patient had myelomeningocele, 1 had undergone renal transplant and 2 were undergoing chemotherapy at the time of debridement. None of these 3 patients had a methicillin resistant S. aureus infection. Methicillin resistant S. aureus was more common in the groin/genitalia and less common in the perineum (p = 0.007). The incidence of methicillin resistant S. aureus increased during the study period, accounting for none of 40 infections between 1995 and 2003, and 8 of 20 (40%) from 2004 to 2007 (p <0.001). CONCLUSIONS: Methicillin resistant S. aureus has become the predominant organism causing pediatric superficial genitourinary abscesses at our institution, accounting for three-quarters of all surgically managed infections in the last 2 years. Methicillin resistant S. aureus was more common at the groin and genitalia. One debridement was generally curative, and patient morbidity was low with aggressive treatment.

B7-H1 expression in Wilms tumor: correlation with tumor biology and disease recurrence.

PURPOSE: Despite tremendous gains in improving prognosis, 10% of patients with Wilms tumor will ultimately experience disease recurrence. The identification of novel prognostic markers and tumor associated targets for patients at risk could enable clinicians to treat recurrences more aggressively and, thus, optimize outcomes. We have previously shown that tumor expression of the T cell coregulatory ligand B7-H1 portends a poor prognosis for adults with renal cell carcinoma and represents a promising target to improve therapy. We hypothesize that this finding may be true for Wilms tumor. MATERIALS AND METHODS: We identified 81 patients with Wilms tumor treated at 1 institution between 1968 and 2004. Histopathological features, including Wilms tumor B7-H1 expression, were correlated with clinical observations and outcome. RESULTS: Tumor recurrences were noted in 22% of patients with Wilms tumor and 14% died. B7-H1 was expressed in 11 tumors (14%) and was more likely to occur in anaplastic Wilms tumor (p = 0.03). Tumor B7-H1 expression was associated with a 2.7-fold increased risk of recurrence, although this difference did not achieve statistical significance (p = 0.06). However, in favorable histology tumors B7-H1 expression was associated with a 3.7-fold increased risk of recurrence (p = 0.03). CONCLUSIONS: B7-H1 is expressed by Wilms tumor, correlates with tumor biology and is associated with an increased risk of recurrence in patients with favorable histology tumors. B7-H1 may prove useful in identifying high risk patients who could benefit from more aggressive initial treatment regimens, and may represent a promising therapeutic target. Multi-institutional studies to elucidate the role of B7-H1 in the treatment of Wilms tumor are warranted.

Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation.

The activity of proteins is dictated by their three-dimensional structure, the native state, and is influenced by their ability to remain in or return to the folded native state under physiological conditions. Backbone circularization is thought to increase protein stability by decreasing the conformational entropy in the unfolded state. A positive effect of circularization on stability has been shown for several proteins. Here, we report the development of a cloning standard that facilitates implementing the SICLOPPS technology to circularize proteins of interest using split inteins. To exemplify the usage of the cloning standard we constructed two circularization vectors based on the Npu DnaE and gp41-1 split inteins, respectively. We use these vectors to overexpress in Escherichia coli circular forms of the Bacillus subtilis enzyme family 11 xylanase that differ in the identity and number of additional amino acids used for circularization (exteins). We found that the variant circularized with only one additional serine has increased thermostability of 7 °C compared to native xylanase. The variant circularized with six additional amino acids has only a mild increase in thermostability compared to the corresponding exteins-bearing linear xylanase, but is less stable than native xylanase. However, this circular xylanase retains more than 50% of its activity after heat shock at elevated temperatures, while native xylanase and the corresponding exteins-bearing linear xylanase are largely inactivated. We correlate this residual activity to the fewer protein aggregates found in the test tubes of circular xylanase after heat shock, suggesting that circularization protects the protein from aggregation under these conditions. Taken together, these data indicate that backbone circularization has a positive effect on xylanase and can lead to increased thermostability, provided the appropriate exteins are selected. We believe that our cloning standard and circularization vectors will facilitate testing the effects of circularization on other proteins.

Diffuse large B-cell lymphoma in an adolescent male presenting as ureteral stricture.

Lymphoma may affect the ureter in cases of retroperitoneal involvement. We present a case of an adolescent male found to have non-Hodgkin lymphoma initially presenting as ureteral stricture evident on imaging. He was treated and responded to multiagent chemotherapy with resolution of both the lymphoma and the ureteral stricture. Although rare, non-Hodgkin lymphoma should be included in the differential diagnosis of pediatric patients with noncalculous, idiopathic ureteral strictures.

Vesicoureteral reflux in children with urachal anomalies.

OBJECTIVE: We report the largest known series of vesicoureteral reflux (VUR) in children with urachal anomalies (UA). METHODS: Two institutions' records were reviewed for children with UA (1951‒2007). RESULTS: Of 30 girls and 36 boys with UA (34 urachal cysts, 14 patent urachus, 10 urachal diverticula, 7 urachal sinuses, and 1 unknown), 57 (86%) underwent surgical resection or drainage. A voiding cystourethrogram was obtained in 22 (33%). VUR was demonstrated in 14 of the 22 children (64%), and rates were similar among the various types of UA. The median age with versus without VUR was not different (1.3 vs 1.7 years, P=0.97). Of 24 refluxing renal units, classification was grade≤3 in 71%, 4‒5 in 12%, and unspecified in 17%. Four children (26%) underwent ureteroneocystostomy and 10 observed patients resolved spontaneously. CONCLUSION: To our knowledge, this is the first series of VUR associated with UA. The increased incidence of VUR (64%) in this small subset of patients warrants prospective studies to determine if there is a positive correlation with UA. We believe thorough genitourinary and family histories are important when evaluating children with UA to help detect clinically significant VUR.

Precocious puberty in a 7-year-old boy: a novel case.

A 7-year-old boy was referred for evaluation of precocious puberty, evidenced by penile enlargement and pubic hair formation. His testicular size was prepubertal bilaterally. A comprehensive hormonal evaluation showed an elevated serum testosterone value (4.0 nmol/L) and a prepubertal gonadotropin value. A 0.9-cm heterogenous left testicular mass was detected on scrotal ultrasonography. Inguinal exploration was performed with ultrasound-guided open testicular biopsy and orchiectomy. Pathologic evaluation of the orchiectomy specimen showed the unclassified type of a mixed germ cell sex cord stromal tumor (MGCSCST), composed of neoplastic Sertoli cells and seminoma-like germ cells. Isolated previous reports of unclassified MGCSCSTs of the testis are now thought to be reports of sex cord stromal tumors with entrapped non-neoplastic germ cells. In our patient, the germ cells appeared to be neoplastic with aberrant expression of c-kit and placental alkaline phosphatase, a high proliferative rate, and DNA aneuploidy. Postoperatively, the patient's serum testosterone concentrations returned to prepubertal values (<0.2 nmol/L) and puberty was halted. This case represents a novel cause of precocious puberty.