Developmental basis of SHH medulloblastoma heterogeneity.

Many genes that drive normal cellular development also contribute to oncogenesis. Medulloblastoma (MB) tumors likely arise from neuronal progenitors in the cerebellum, and we hypothesized that the heterogeneity observed in MBs with sonic hedgehog (SHH) activation could be due to differences in developmental pathways. To investigate this question, here we perform single-nucleus RNA sequencing on highly differentiated SHH MBs with extensively nodular histology and observed malignant cells resembling each stage of canonical granule neuron development. Through innovative computational approaches, we connect these results to published datasets and find that some established molecular subtypes of SHH MB appear arrested at different developmental stages. Additionally, using multiplexed proteomic imaging and MALDI imaging mass spectrometry, we identify distinct histological and metabolic profiles for highly differentiated tumors. Our approaches are applicable to understanding the interplay between heterogeneity and differentiation in other cancers and can provide important insights for the design of targeted therapies.

Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has made it clear that combating coronavirus outbreaks benefits from a combination of vaccines and therapeutics. A promising drug target common to all coronaviruses-including SARS-CoV, MERS-CoV, and SARS-CoV-2-is the papain-like protease (PLpro). PLpro cleaves part of the viral replicase polyproteins into non-structural protein subunits, which are essential to the viral replication cycle. Additionally, PLpro can cleave both ubiquitin and the ubiquitin-like protein ISG15 from host cell substrates as a mechanism to evade innate immune responses during infection. These roles make PLpro an attractive antiviral drug target. Here we demonstrate that ubiquitin variants (UbVs) can be selected from a phage-displayed library and used to specifically and potently block SARS-CoV-2 PLpro activity. A crystal structure of SARS-CoV-2 PLpro in complex with a representative UbV reveals a dimeric UbV bound to PLpro at a site distal to the catalytic site. Yet, the UbV inhibits the essential cleavage activities of the protease in vitro and in cells, and it reduces viral replication in cell culture by almost five orders of magnitude.

A versatile toolkit for CRISPR-Cas13-based RNA manipulation in Drosophila.

Advances in CRISPR technology have immensely improved our ability to manipulate nucleic acids, and the recent discovery of the RNA-targeting endonuclease Cas13 adds even further functionality. Here, we show that Cas13 works efficiently in Drosophila, both ex vivo and in vivo. We test 44 different Cas13 variants to identify enzymes with the best overall performance and show that Cas13 could target endogenous Drosophila transcripts in vivo with high efficiency and specificity. We also develop Cas13 applications to edit mRNAs and target mitochondrial transcripts. Our vector collection represents a versatile tool collection to manipulate gene expression at the post-transcriptional level.

Polypharmacy, Medication Possession, and Deprescribing of Potentially Non-Beneficial Drugs in Hospice Patients.

Patients frequently have comorbidities that when combined with their primary diagnosis qualifies the patient for hospice. Consequently, patients are at risk for polypharmacy due to the number of medications prescribed to treat both the underlying conditions and the related symptoms. Polypharmacy is associated with negative consequences, including increased risk for adverse drug events, drug-drug and drug-disease interactions, reduced functional status and falls, multiple geriatric syndromes, medication nonadherence, and increased mortality. Polypharmacy also increases the complexity of medication management for caregivers and contributes to the cost of prescription drugs for hospices and patients. Deprescribing or removing nonbeneficial or ineffective medications can reduce polypharmacy in hospice. We study medication possession ratios and rates of deprescribing of commonly prescribed but potentially nonbeneficial classes of medication using a large hospice pharmacy database. Prevalence of some classes of potentially inappropriate medications is high. We report possession ratios for 10 frequently prescribed classes, and, because death and prescription termination are competing events, we calculate prescription termination rates using Cumulative Incidence Functions. Median duration of antifungal and antiviral medications is brief (5 and 7 days, respectively), while statins and diabetes medications have slow discontinuance rates (median termination durations of 93 and 197 days). Almost all patients with a proton pump inhibitor prescription have the drug for their entire hospice stay. Data from this study identify those drug classes that are commonly deprescribed slowly, suggesting drug classes and diagnoses that hospices may wish to focus on more closely, as they act to limit polypharmacy and reduce prescription costs.

A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.

High-throughput screening and gene signature analyses frequently identify lead therapeutic compounds with unknown modes of action (MoAs), and the resulting uncertainties can lead to the failure of clinical trials. We developed an approach for uncovering MoAs through an interpretable machine learning model of transcriptomics, epigenomics, metabolomics, and proteomics. Examining compounds with beneficial effects in models of Huntington's Disease, we found common MoAs for compounds with unrelated structures, connectivity scores, and binding targets. The approach also predicted highly divergent MoAs for two FDA-approved antihistamines. We experimentally validated these effects, demonstrating that one antihistamine activates autophagy, while the other targets bioenergetics. The use of multiple omics was essential, as some MoAs were virtually undetectable in specific assays. Our approach does not require reference compounds or large databases of experimental data in related systems and thus can be applied to the study of agents with uncharacterized MoAs and to rare or understudied diseases.

Autologous Transplantation of Skin-Derived Precursor Cells in a Porcine Model.

BACKGROUND: Hirschprung's disease is characterized by aganglionic bowel and often requires surgical resection. Cell-based therapies have been investigated as potential alternatives to restore functioning neurons. Skin-derived precursor cells (SKPs) differentiate into neural and glial cells in vitro and generate ganglion-like structures in rodents. In this report, we aimed to translate this approach into a large animal model of aganglionosis using autologous transplantation of SKPs. METHODS: Juvenile pigs underwent skin procurement from the shoulder and simultaneous chemical denervation of an isolated colonic segment. Skin cells were cultured in neuroglial-selective medium and labeled with fluorescent dye for later identification. The cultured SKPs were then injected into the aganglionic segments of colon, and the specimens were retrieved within seven days after transplantation. SKPs in vitro and in vivo were assessed with histologic samples for various immunofluorescent markers of multipotency and differentiation. SKPs from the time of harvest were compared to those at the time of injection using PCR. RESULTS: Prior to transplantation, 72% of SKPs stained positive for nestin and S100b, markers of neural and glial precursor cells of neural crest origin, respectively. Markers of differentiated neurons and gliocytes, TUJ1 and GFAP, were detected in 47% of cultured SKPs. After transplantation, SKPs were identified in both myenteric and submucosal plexuses of the treated colon. Nestin co-expression was detected in the SKPs within the aganglionic colon in vivo. Injected SKPs appeared to migrate and express early neuroglial differentiation markers. CONCLUSIONS: Autologous SKPs implanted into aganglionic bowel demonstrated immunophenotypes of neuroglial progenitors. Our results suggest that autologous SKPs may be potentially useful for cell-based therapy for patients with enteric nervous system disorders. TYPE OF STUDY: Basic science.

Glycogen branching enzyme controls cellular iron homeostasis via Iron Regulatory Protein 1 and mitoNEET.

Iron Regulatory Protein 1 (IRP1) is a bifunctional cytosolic iron sensor. When iron levels are normal, IRP1 harbours an iron-sulphur cluster (holo-IRP1), an enzyme with aconitase activity. When iron levels fall, IRP1 loses the cluster (apo-IRP1) and binds to iron-responsive elements (IREs) in messenger RNAs (mRNAs) encoding proteins involved in cellular iron uptake, distribution, and storage. Here we show that mutations in the Drosophila 1,4-Alpha-Glucan Branching Enzyme (AGBE) gene cause porphyria. AGBE was hitherto only linked to glycogen metabolism and a fatal human disorder known as glycogen storage disease type IV. AGBE binds specifically to holo-IRP1 and to mitoNEET, a protein capable of repairing IRP1 iron-sulphur clusters. This interaction ensures nuclear translocation of holo-IRP1 and downregulation of iron-dependent processes, demonstrating that holo-IRP1 functions not just as an aconitase, but throttles target gene expression in anticipation of declining iron requirements.

Intestinal lengthening via multiple in-continuity springs.

BACKGROUND: Short bowel syndrome is a debilitating condition with few effective treatments. Spring-mediated distraction enterogenesis can be used to lengthen intestine. The purpose of this study is to determine whether multiple springs in series can safely increase the total amount of lengthening. METHODS: Juvenile mini-Yucatan pigs each received three nitinol springs placed within their jejunum. Plication was used to narrow the intestine around each spring to secure them. Compressed springs were used in the experimental group, while uncompressed springs were used in the control group. The intestine was examined 3 weeks later for lengthening and histologic changes. RESULTS: All pigs tolerated diets postoperatively with continued weight gain, and no dilation or obstruction of the intestine was observed. Segments of intestine that contained compressed springs had a significant increase in length from 2.5 cm to 3.9 ±â€¯0.2 cm per spring, compared to segments containing control springs that showed no change (p < 0.001). CONCLUSIONS: Intestinal plication can be safely used to secure multiple springs in series to achieve intestinal lengthening without compromising intestinal function. Using several springs at once allows for a greater amount of total lengthening. This is a promising model that has potential in the treatment of short bowel syndrome.

Double plication for spring-mediated in-continuity intestinal lengthening in a porcine model.

BACKGROUND: Short bowel syndrome is a condition with substantial morbidity and mortality, yet definitive therapies are lacking. Distraction enterogenesis uses mechanical force to "grow" new intestine. In this study, we examined whether intestinal plication can be used to safely achieve spring-mediated intestinal lengthening in a functioning segment of jejunum in its native position. METHODS: A total of 12 juvenile, miniature Yucatan pigs underwent laparotomy to place either compressed springs or expanded springs within a segment of jejunum (n = 6 per group). The springs were secured within the jejunum by performing intestinal plication to narrow the intestinal lumen around the spring. After 3 weeks, the jejunum was retrieved and examined for lengthening and for histologic changes. RESULTS: There were no intraoperative or postoperative complications, and the pigs tolerated their diets and gained weight. Segments of jejunum containing expanded springs showed no significant change in length over the 3 weeks. In contrast, jejunum containing compressed springs showed nearly a 3-fold increase in length (P < .001). Histology of the retrieved jejunum showed a significant increase in thickness of the muscularis propria and in crypt depth relative to normal jejunum. CONCLUSION: Intestinal plication is effective in securing endoluminal springs to lengthen the jejunum. This approach is a clinically relevant model because it allows for normal GI function and growth of animals during intestinal lengthening, which may be useful in lengthening intestine in patients with short bowel syndrome.

Subcutaneous cefazolin to reduce surgical site infections in a porcine model.

BACKGROUND: Surgical site infections (SSIs) pose a significant health and financial burden. A key aspect of appropriate prophylaxis is the administration of antibiotics intravenously (IV). However, subcutaneous administration of antibiotics is not well described in the literature. During surgery, we hypothesize that subcutaneous injection may provide better protection against SSIs. To better understand the kinetics after subcutaneous injection, we describe the serum concentrations of cefazolin in a porcine model. MATERIALS AND METHODS: Juvenile mini-Yucatan pigs were administered 20 mL of 25 mg/kg cefazolin subcutaneously, and serial blood samples were taken for 3 h. Blood samples were analyzed for cefazolin concentration using chromatography. Pharmacokinetic data were calculated based on the blood serum concentrations. RESULTS: Maximum serum concentrations of cefazolin were achieved 42.6 ± 2.0 min after the time of injection and were found to be 18.8 ± 7.4 µg/mL. The elimination rate constant was 0.0033 ± 0.0016 min-1 and the half-life was 266 ± 149 min. The area under the curve was 4940 ± 1030 µg × min/mL. The relative bioavailability of subcutaneous injection was 95% +5%/-20%. CONCLUSIONS: Subcutaneous administration of cefazolin achieves a significantly lower maximum serum concentration than IV injection. As a result, higher doses of antibiotic can be injected locally without incurring systemic toxicity. Subcutaneous administration will therefore result in higher concentrations of antibiotic for a longer time at the incision site compared with standard IV administration. This strategy of antibiotic delivery may be more effective in preventing SSIs. Further studies are needed to detail the exact effect of subcutaneous antibiotic injection on SSI rates.

Double plication for spring-mediated intestinal lengthening of a defunctionalized Roux limb.

BACKGROUND: Spring-mediated distraction enterogenesis has been shown to increase the length of an intestinal segment. The goal of this study is to use suture plication to confine a spring within an intestinal segment while maintaining luminal patency to the rest of the intestine. METHODS: Juvenile mini-Yucatan pigs underwent placement of nitinol springs within a defunctionalized Roux limb of jejunum. A 20 French catheter was passed temporarily, and sutures were used to plicate the intestinal wall around the catheter at both ends of the encapsulated spring. Uncompressed springs placed in plicated segments and springs placed in nonplicated segments served as controls. The intestine was examined approximately 3 weeks after spring placement. RESULTS: In the absence of plication, springs passed through the intestine within a week. Double plication allowed the spring to stay within the Roux limb for 3 weeks. Compared to uncompressed springs that showed no change in the length of plicated segments, compressed springs caused a significant 1.7-fold increase in the length of plicated segments. CONCLUSIONS: Intestinal plication is an effective method to confine endoluminal springs. The confined springs could lengthen intestine that maintains luminal patency. This approach may be useful to lengthen intestine in patients with short bowel syndrome. LEVEL OF EVIDENCE: Level I Experimental Study.

Clinical and socioeconomic factors associated with negative pediatric appendicitis.

BACKGROUND: Misdiagnosing appendicitis may lead to unnecessary surgery. The study evaluates the risk factors for negative appendectomies, as well as the clinical and socioeconomic consequences of negative appendectomy across three states. MATERIALS AND METHODS: Data were obtained from the California, New York, and Florida State Inpatient Databases 2005-2011. Patients (<18 years) who underwent nonincidental appendectomies (n = 156,660) were evaluated with hierarchical and multivariate negative binomial regression analyses on outcomes including hospital cost, length of stay (LOS), and associated morbidity. RESULTS: From 2005 to 2011, there was a decrease in the rate of negative appendicitis and perforated appendicitis, whereas the rate of true acute nonperforated appendicitis increased. Whites, females, and privately insured patients were associated with higher negative appendicitis rates, whereas those at an increased risk for perforated appendicitis were African-Americans, males, and those with public or no insurance. Compared to patients with acute nonperforated appendicitis, those with negative appendicitis have significantly higher morbidity (2.5% versus 1.3%), longer LOS (3.4 versus 1.8 d), and greater hospital costs averaged over time ($6926 versus $6492 per patient). CONCLUSIONS: Despite a low incidence, negative appendicitis is associated with greater morbidity, longer LOS, and higher cost than acute nonperforated appendicitis. Certain subpopulations are at higher risk for undergoing surgery for negative appendicitis, whereas others are at greater risk for presenting with perforated appendicitis. Further research is needed to understand what drives such disparities and to inform efforts to improve quality of hospital care across all groups of patients.

Spring-mediated distraction enterogenesis in-continuity.

PURPOSE: Distraction enterogenesis has been investigated as a novel treatment for patients with short bowel syndrome (SBS) but has been limited by loss of intestinal length during restoration and need for multiple bowel surgeries. The feasibility of in-continuity, spring-mediated intestinal lengthening has yet to be demonstrated. METHODS: Juvenile mini-Yucatan pigs underwent in-continuity placement of polycaprolactone (PCL) degradable springs within jejunum. Methods used to anchor the spring ends to the intestine included full-thickness sutures and a high-friction surface spring. Spring constant (k) was 6-15N/m. Bowel was examined for length and presence of spring at 1 to 4weeks. RESULTS: Animals tolerated in-continuity lengthening without bowel obstruction for up to 29days. In-continuity jejunum with springs demonstrated intestinal lengthening by 1.47-fold ±0.11. Five springs had detached prematurely, and lengthening could not be assessed. Histologically, in-continuity jejunum showed significantly increased crypt depth and muscularis thickness in comparison to normal jejunum. CONCLUSION: Self-expanding endoluminal springs placed in continuity could lengthen intestine without obstruction in a porcine model. This is the first study showing safety and efficacy of a self-expanding endoluminal device for distraction enterogenesis. This is proof-of-concept that in-continuity spring lengthening is feasible and demonstrates its therapeutic potential in SBS. LEVEL OF EVIDENCE: Level 3.

Scalability of an endoluminal spring for distraction enterogenesis.

INTRODUCTION: Techniques of distraction enterogenesis have been explored to provide increased intestinal length to treat short bowel syndrome (SBS). Self-expanding, polycaprolactone (PCL) springs have been shown to lengthen bowel in small animal models. Their feasibility in larger animal models is a critical step before clinical use. METHODS: Juvenile mini-Yucatan pigs underwent jejunal isolation or blind ending Roux-en-y jejunojejunostomy with insertion of either a PCL spring or a sham PCL tube. Extrapolated from our spring characteristics in rodents, proportional increases in spring constant and size were made for porcine intestine. RESULTS: Jejunal segments with 7mm springs with k between 9 and 15N/m demonstrated significantly increased lengthening in isolated segment and Roux-en-y models. Complications were noted in only two animals, both using high spring constant k>17N/m. Histologically, lengthened segments in the isolated and Roux models demonstrated significantly increased muscularis thickness and crypt depth. Restoration of lengthened, isolated segments back into continuity was technically feasible after 6weeks. CONCLUSION: Self-expanding, endoluminal PCL springs, which exert up to 0.6N force, safely achieve significant intestinal lengthening in a translatable, large-animal model. These spring characteristics may provide a scalable model for the treatment of SBS in children.

Mechanical lengthening in multiple intestinal segments in-series.

PURPOSE: Current models of mechanical intestinal lengthening employ a single device in an isolated segment. Here we demonstrate that polycaprolactone (PCL) springs can be deployed in-series to lengthen multiple intestinal segments simultaneously to further increase overall intestinal length. METHODS: A Roux-en-y jejunojejunostomy with a blind Roux limb was created in the proximal jejunum of rats. Two encapsulated 10-mm PCL springs were placed in-series into the Roux limb and were secured with clips. After 4weeks, the lengthened segments were retrieved for histological analyses. RESULTS: Lengthening two intestinal segments simultaneously was achieved by placing two PCL springs in-series. The total combined length of the lengthened segments in-series was 45±4mm. The two jejunal segments with PCL springs (25±2 and 20±2mm) were significantly longer than control segments without the spring (14±1mm, p<0.05). CONCLUSION: Spring-mediated lengthening can be achieved using multiple springs placed sequentially. The use of the Roux-en-y surgical model allowed easy insertion of springs in a blind Roux limb and arrange them in-series. Combined with relengthening techniques, we can use these methods to increase the length of small intestine to reach clinical significance. LEVEL OF EVIDENCE: 1 Experimental.