Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples.

HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows. Key points: HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.

Single nucleotide polymorphism within chromosome 8q24 is associated with prostate cancer development in Saudi Arabia.

Objective: Genome-wide association studies have demonstrated that single nucleotide polymorphisms (SNPs) are important risk factors for the development of prostate cancer (PCa). Preliminary studies have suggested that the incidence of PCa in Saudi males is low but is probably familial or genetically related. Methods: To identify any possible association of SNP with PCa development in Saudi patients, we investigated a group of SNPs in Saudi PCa patients (n=85) and compared the outcomes to healthy normal controls (n=115) and nodular hyperplasia patients (n=120). DNA was extracted from paraffin-embedded formalin fixed tissue or whole blood from both patients' groups and healthy control group. A total of thirteen SNPs were genotyped using TaqMan® minor groove binder polymerase chain reaction assay. Results: The rs16901979A, s629242T and rs1447295A alleles were found at significantly higher frequency in PCa patients than controls (p<0.05). The rs16901979 CA genotype was found at significantly greater frequency in PCa patients than in healthy controls (43% vs. 14%, odds ratio=4.6, p=0.0001) and benign hyperplasia group (43% vs. 25%, odds ratio=2.2, p=0.009). Conclusion: Our study has highlighted the association of rs16901979 SNP with PCa in Saudi males. Such findings have important implications in the PCa diagnosis and in screening unaffected family members of Saudi patients.

Polypyrimidine Tract Binding Protein: A Universal Player in Cancer Development.

OBJECTIVES: Polypyrimidine tract binding protein is a 57-Kda protein located in the perinucleolar compartment where it binds RNA and regulates several biological functions through the regulation of RNA splicing. Numerous research articles have been published that address the cellular network and functions of PTB and its isoforms in various disease states. METHODOLOGY: Through an extensive PubMed search, we attempt to summarize the relevant research into this biomolecule. RESULTS: Besides its roles in embryonic development, neuronal cell growth, RNA metabolism, apoptosis, and hematopoiesis, PTB can affect cancer growth via several metabolic, proliferative, and structural mechanisms. PTB overexpression has been documented in several cancers where it plays a role as a novel prognostic factor. CONCLUSION: The diverse carcinogenic effect opens an argument into its potential role in inhibitory targeted therapy.

There's More Than Meets the Eye: Wolfram Syndrome in a Type I Diabetic Patient.

Wolfram syndrome (WS) is a rare neurodegenerative and genetic disorder, also known by the synonym DIDMOAD, which stands for diabetes insipidus (DI), childhood-onset diabetes mellitus (DM), optic atrophy (OA), and deafness (D). We present a case of a 25-year-old diabetic patient, using insulin for 15 years, who had increasing polyuria and polydipsia, along with progressive hearing and vision loss. Laboratory tests revealed elevated hemoglobin A1c (HbA1c) and blood sugar levels. Optic nerve, optic chiasm, pons, and brain stem atrophy was seen on magnetic resonance imaging (MRI) of brain. After workup, a diagnosis of DI was made. Once the diagnosis was reached, treatment with subcutaneous insulin and nasal desmopressin improved patient's symptoms. In juvenile diabetic patients presenting with new onset or worsening polyuria and polydipsia, the possibility of WS should be considered. Early diagnosis and initiation of appropriate management leads to improved outcomes and the quality of life.

Encephalitis as a Clinical Manifestation of COVID-19: A Case Series.

COVID-19 is a novel virus which causes a variety of clinical manifestations in the body, some of which are yet to be discovered. The main aim of our study is to highlight the neurological manifestations of COVID-19 as it is still new to the medical world, and to emphasize the fact that the physicians have to be wary of the possibility that patients affected by COVID-19 can present with encephalitis. Only a few studies are available so far regarding the neurological manifestations of this novel virus which highlights the need for this study. We present a case series of 4 patients who were found to have COVID-19 encephalitis. There is still no disease-defining test for diagnosis so the mainstay of diagnosis is exclusion of all the common causes of encephalitis. Brain magnetic resonance imaging and cerebrospinal fluid analysis performs an ancillary in the diagnostic tools. Our study also supports the use of IV tocilizumab (4-8 mg/kg) and IV methylprednisolone (0.5-2 mg/kg) as possible treatment options with good results, as the patients described in our case series responded well to these medications.

Perinucleolar Compartment (PNC) Prevalence as an Independent Prognostic Factor in Pediatric Ewing Sarcoma: A Multi-Institutional Study.

The perinucleolar compartment (PNC) is a small nuclear body that plays important role in tumorigenesis. PNC prevalence correlates with poor prognosis and cancer metastasis. Its expression in pediatric Ewing sarcoma (EWS) has not previously been documented. In this study, we analyzed 40 EWS tumor cases from Caucasian and Hispanic patients for PNC prevalence by immunohistochemical detection of polypyrimidine tract binding protein and correlated the prevalence with dysregulated microRNA profiles. EWS cases showed staining ranging from 0 to 100%, which were categorized as diffuse (≥77%, n = 9, high PNC) or not diffuse (<77%, n = 31) for low PNC. High PNC prevalence was significantly higher in Hispanic patients from the US (n = 6, p = 0.017) and in patients who relapsed with metastatic disease (n = 4; p = 0.011). High PNC was associated with significantly shorter disease-free survival and early recurrence compared to those with low PNC. Using NanoString digital profiling, high PNC tumors revealed upregulation of eight and downregulation of 18 microRNAs. Of these, miR-320d and miR-29c-3p had the most significant differential expression in tumors with high PNC. In conclusion, this is the first study that demonstrates the presence of PNC in EWS, reflecting its utility as a predictive biomarker associated with tumor metastasis, specific microRNA profile, Hispanic ethnic origin, and poor prognosis.

Analysis of Orthopaedic In-Training Examination Trauma Questions: 2017 to 2021.

INTRODUCTION: The Orthopaedic In-Training Examination (OITE) is a multiple-choice examination developed by the American Academy of Orthopaedic Surgeons annually since 1963 to assess orthopaedic residents' knowledge. This study's purpose is to analyze the 2017 to 2021 OITE trauma questions to aid orthopaedic residents preparing for the examination. METHODS: The 2017 to 2021 OITEs on American Academy of Orthopaedic Surgeons' ResStudy were retrospectively reviewed to identify trauma questions. Question topic, references, and images were analyzed. Two independent reviewers classified each question by taxonomy. RESULTS: Trauma represented 16.6% (204/1,229) of OITE questions. Forty-nine percent of trauma questions included images (100/204), 87.0% (87/100) of which contained radiographs. Each question averaged 2.4 references, of which 94.9% were peer-reviewed articles and 46.8% were published within 5 years of the respective OITE. The most common taxonomic classification was T1 (46.1%), followed by T3 (37.7%) and T2 (16.2%). DISCUSSION: Trauma represents a notable portion of the OITE. Prior OITE trauma analyses were published greater than 10 years ago. Since then, there has been an increase in questions with images and requiring higher cognitive processing. The Journal of Orthopaedic Trauma (24.7%), Journal of the American Academy of Orthopaedic Surgeons (10.1%), and Journal of Bone and Joint Surgery, American Volume (9.3%) remain the most cited sources.

Impact of Duodenal Pathology on Oral Drug Bioavailability and Disease Outcomes in Pediatric Crohn's Disease.

BACKGROUND: Crohn's disease with upper gastrointestinal tract involvement occurs more often in children than adults and has the potential to interfere with oral drug absorption. We aimed to compare disease outcomes in children receiving oral azathioprine for the treatment of Crohn's disease with (DP) and without (NDP) duodenal pathology at diagnosis. METHODS: Duodenal villous length, body mass index (BMI), and laboratory studies were compared in DP vs. NDP during the first year post-diagnosis, using parametric/nonparametric tests and regression analysis (SAS v9.4); the data are reported as the median (interquartile range) or the mean ± standard deviation. Thiopurine metabolite concentration (pmol/8 × 108 erythrocytes) 230-400 was considered therapeutic for 6-thioguanine nucleotides (6-TGN), and >5700 was considered hepatotoxic for 6-methylmercaptopurine (6-MMPN). RESULTS: Twenty-six of the fifty-eight children enrolled (29 DP, 29 NDP) started azathioprine for standard medical care, including nine DP and ten NDP who had normal thiopurine methyltransferase activity. Duodenal villous length was significantly shorter in DP vs. NDP (342 ± 153 vs. 460 ± 85 µm; p < 0.001) at diagnosis; age, sex, hemoglobin, and BMI were comparable between groups. A trend toward lower 6-TGN was observed in the DP vs. NDP subset receiving azathioprine (164 (117, 271) vs. 272 (187, 331); p = 0.15). Compared to NDP, DP received significantly higher azathioprine doses (2.5 (2.3, 2.6) vs. 2.2 (2.0, 2.2) mg/kg/day; p = 0.01) and had an increased relative risk of sub-therapeutic 6-TGN. At 9 months post-diagnosis, children with DP had significantly lower hemoglobin (12.5 (11.7, 12.6) vs. 13.1 (12.7, 13.3) g/dL; p = 0.01) and BMI z-scores (-0.29 (-0.93, -0.11) vs. 0.88 (0.53, 0.99); p = 0.02) than children with NDP. CONCLUSION: For children with Crohn's disease, duodenal pathology, marked by villous blunting, increased the risk of sub-therapeutic 6-TGN levels, despite higher azathioprine dosing during the first year post-diagnosis. Lower hemoglobin and BMI z-scores at 9 months post-diagnosis suggest the impaired absorption/bioavailability of nutrients, as well as oral drugs, in children with duodenal disease.

Update of pediatric bone tumors-other mesenchymal tumors of bone, hematopoietic neoplasms of bone, and WHO classification of undifferentiated small round cell sarcomas of bone.

There are numerous bone tumors in the pediatric population, with imaging playing an essential role in diagnosis and management. Our understanding of certain bone tumors has rapidly evolved over the past decade with advancements in next-generation genetic sequencing techniques. This increased level of understanding has altered the nomenclature, management approach, and prognosis of certain lesions. We provide a detailed update of bone tumors that occur in the pediatric population with emphasis on the recently released nomenclature provided in the 5th edition of the World Health Organization Classification of Soft Tissue and Bone Tumours. We discuss other mesenchymal tumors of bone, hematopoietic neoplasms of bone, and WHO classification of undifferentiated small round cell sarcomas of bone. We have detailed osteogenic tumors and osteoclastic giant cell-rich tumors, as well as notochordal tumors, chondrogenic tumors, and vascular tumors of the bone in separate manuscripts.

Appearance Says It All; A Rare Case Of Hypohidrotic Ectodermal Dysplasia.

Ectodermal Dysplasia (ED) is a rare genetic condition characterized by the involvement of ectoderm derivatives such as hair, nail, sweat glands, and teeth. It has many variants, but the two most common ones are hypohidrotic/anhidrotic ectodermal dysplasia and hidrotic ectodermal dysplasia. Herein, we present a case of a 20-year-old female with hypohidrotic ectodermal dysplasia who had anodontia, hypohidrosis, and hypotrichosis, and her condition went unrecognized until she was seen for gastroenteritis at a tertiary care center. This case report will help spread education and awareness regarding such a rare and under-recognized condition. Early diagnosis and intervention help improve the quality of life.

Do Histologic Features of the Proximal Margin of Resected Specimens Predict Clinical Outcomes in Hirschsprung Disease?

Objective Patients with Hirschsprung disease (HSCR) can experience obstructive symptoms despite adequate resection. We sought to determine if submucosal nerve thickness or length of ganglionated bowel in the resected specimen correlated with functional outcomes. Methods A retrospective study of patients who underwent surgery between 2015-2019 was performed. The resected specimen was scanned to measure areas of the thickest submucosal nerves and the length of the ganglionated segment. Functional outcomes were collected via chart review. Results Thirty patients were included. The median age at pull-through was 4.5 months (interquartile range {IQR} 0.5 - 6.7 months); 70% were male, and 57% had a Swenson pull-through. The median size of the thickest nerves was 28 micrometers (IQR 24, 32). Three specimens had a nerve thickness of >40 micrometers. The median length of the resected ganglionated segment was 4.4 cm (IQR 2.2, 7.2). Out of the total, 53% of patients experienced post-operative enterocolitis; 13% required further surgery. At a median of 25.3 months (IQR 17.6, 42.2 months) from pull-through, 33% did not require any bowel regimen therapy. Utilizing logistic regression, neither submucosal nerve thickness nor length of the resected ganglionic segment correlated with outcomes. Conclusion While continued bowel management therapy was common, no correlation was found between histologic findings and functional outcomes.

Modern vaccine strategies for emerging zoonotic viruses.

INTRODUCTION: The significant increase in the emergence of notable zoonotic viruses in the previous decades has become a serious concern to global public health. Ninety-nine percent of infectious diseases have originated from zoonotic viruses with immense potential for dissemination, infecting the susceptible population completely lacking herd immunity. AREAS COVERED: Zoonotic viruses appear in the last two decades as a major health threat either newly evolved or previously present with elevated prevalence in the last few years are selected to explain their current prophylactic measures. In this review, modern generation vaccines including viral vector vaccines, mRNA vaccines, DNA vaccines, synthetic vaccines, virus-like particles, and plant-based vaccines are discussed with their benefits and challenges. Moreover, the traditional vaccines and their efficacy are also compared with the latest vaccines. EXPERT OPINION: The emergence and reemergence of viruses that constantly mutate themselves have greatly increased the chance of transmission and immune escape mechanisms in humans. Therefore, the only possible solution to prevent viral infection is the use of vaccines with improved safety profile and efficacy, which becomes the basis of modern generation vaccines.

Assessing the Quality of YouTube Videos on Adhesive Capsulitis.

Introduction  YouTube is the most popular video-based source of information on the Internet. It is accessed by over 1 billion users, which approximates to almost one-third of all Internet users. Orthopaedic video content published on YouTube is not screened and does not go through an editorial process, and most videos do not have information about authorship or appropriate references. Users who do not have the knowledge to assess the accuracy and reliability of the source may be misinformed about their medical condition. Previous studies have evaluated the quality of YouTube content for information in orthopaedics such as meniscus,kyphosis, and anterior cruciate ligament (ACL), but the quality of frozen shoulder videos on YouTube has not been investigated. The purpose of this study is to evaluate the quality and educational value of YouTube videos concerning adhesive capsulitis. Methods A YouTube search was performed using the term "frozen shoulder." Videos were excluded if they had no audio, were in a language other than English, or were longer than 10 minutes. A total of 70 videos were screened, and the first 50 videos that met the inclusion criteria were evaluated by three observers. Six video characteristics were extracted, and videos were categorized by source and content. Quality and educational value were assessed using the DISCERN (score range, 0-5), Global Quality score (GQS; score range, 0-4), and a Frozen Shoulder-Specific Score (FSSS; score range, 0-16). Results  The mean video duration was 242.46 ± 164.32 seconds. The mean number of views was 137,494 ± 262,756 and the total view count across 50 videos was 6,874,706. The mean DISCERN, GQS, and FSSS scores were 2.72 ± 0.85, 2.37 ± 0.895, and 4.42 ± 3.15, respectively. The video sources were primarily from non-physician healthcare professionals (32%), and most of the video content was focused on disease-specific information (50%). Significant between-group effects were observed for the DISCERN score and video source (P = .005), with videos from academic sources having the highest mean DISCERN score. DISCERN scores also differed significantly based on video content (P = .007), with disease content having the highest DISCERN score. Both GQS and FSSS scores differed significantly based on video content (both P < .001) but did not differ significantly based on the video source. Conclusions Information about frozen shoulder on YouTube is low quality and has limited educational value. Thus, providers for orthopaedic conditions should warn their patients and provide better alternatives for education.

Characterization of the Mucosally-Adherent Duodenal Microbiome in Children with and without Crohn's Disease.

Manipulation of the microbiome is a rational treatment strategy for inflammatory bowel disease (IBD). Compared to the colon and terminal ileum (TI), understanding of the microbial composition in the duodenum is sparse. This gap in knowledge is especially significant for children with Crohn's disease (CD) because the prevalence of duodenal CD is higher in children than in adults. Our aim was to characterize the bacterial composition of the mucosally-adherent duodenal microbiome in children with and without CD as a first step toward development of targeted IBD treatment strategies at this disease location. Fresh-frozen mucosal biopsies were obtained from the duodenum and TI of children with treatment-naïve CD and age- and sex-matched controls. Extracted DNA was analyzed for sequence variation in the 16S ribosomal RNA bacterial gene region V4 (Novogene; Beijing, China). Bacterial relative abundance, alpha and beta composition, and diversity, were compared across duodenal and TI samples from the controls and CD groups with and without chronic active inflammation (118 samples from 73 children total; approx. 50% CD), using UniFrac dissimilarity coefficients (α < 0.05), Linear Discriminant Analysis Effect Size (LEfSe) analysis (LDA score ≥ 2), and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis. The relationships between bacterial abundance, sex, age, concomitant medication use, and villous length were assessed. The microbial composition in the duodenum was significantly different from the TI in the control population(R-value = 0.558, p = 0.001) and in children with active CD (R-value = 0.301, p = 0.001). Significant differences in bacterial abundance were noted between the control and CD duodena (LDA > 4). The duodenum of children without CD was characterized by increased abundance in Pseudomonodales, whereas the actively inflamed duodenum in CD was characterized by increased abundance of Bacteroidales, specifically the family Prevotellaceae. This trend is opposite of previously published observations of microbial composition in the TI, where active inflammation was associated with a relative decrease in the abundance of Bacteroidetes and an increase in Proteobacteria, including Pseudomonadales. No statistically significant correlations were noted between abundance and age, sex, concomitant medication use or villous length, except for Bacteroidetes, which significantly decreased in abundance in the TI with age (p = 0.048). The pediatric duodenal microbiome is distinct from the TI and characterized by an increased abundance of Pseudomonodales and Spirochetes in healthy children, and an increased abundance of Bacteroidales in active CD patients.

Atretic Parietal Cephalocele With First Trimester Chiari Malformation and Sinus Pericranii Companion Case.

Encephaloceles are the type of dysraphism in which a skull defect allows for herniation of meninges, with or without the inclusion of neural tissue, and are commonly associated with agenesis of the corpus callosum. Encephaloceles are classified as frontal, occipital, or parietal, with parietal cephaloceles, or vertex cephaloceles (VC), being the least common. Despite this, VCs present as the most common cause of a midline scalp mass, displaying complex venous and neural malformations commonly referred to as the "tip of the iceberg." Atretic parietal encephaloceles (APC), a type of VC, are benign lesions arising from meningeal and vestigial tissue which have undergone fibrotic degeneration. As a result, prognosis will generally be better than other encephaloceles due to vestigial tissue involvement. Here, we report a neonate presenting with APC, corpus callosum agenesis, and a cingulate gyrus lesion, along with a sinus pericranii companion case for comparison.

NanoString Digital Molecular Profiling of Protein and microRNA in Rhabdomyosarcoma.

PURPOSE: Rhabdomyosarcoma (RMS) exhibits a complex prognostic algorithm based on histologic, biologic and clinical parameters. The embryonal (ERMS) and spindle cell-sclerosing RMS (SRMS) histologic subtypes warrant further studies due to their heterogenous genetic background and variable clinical behavior. NanoString digital profiling methods have been previously highlighted as robust novel methods to detect protein and microRNA expression in several cancers but not in RMS. METHODS/PATIENTS: To identify prognostic biomarkers, we categorized 12 ERMS and SRMS tumor cases into adverse (n = 5) or favorable (n = 7) prognosis groups and analyzed their signaling pathways and microRNA profiles. The digital spatial profiling of protein and microRNA analysis was performed on formalin-fixed, paraffin-embedded (FFPE) tumor tissue using NanoString technology. RESULTS: The detectable expression of several component members of the PI3K/AKT, MAPK and apoptosis signaling pathways was highlighted in RMS, including INPP4B, Pan-AKT, MET, Pan-RAS, EGFR, phospho-p90 RSK, p44/42 ERK1/2, BAD, BCL-XL, cleaved caspase-9, NF1, PARP and p53. Compared to cases with favorable prognosis, the adverse-prognosis tumor samples had significantly increased expression of INPP4B, which was confirmed with traditional immunohistochemistry. The analysis of microRNA profiles revealed that, out of 798 microRNAs assessed, 228 were overexpressed and 134 downregulated in the adverse prognosis group. Significant over-expression of oncogenic/tumor suppressor miR-3144-3p, miR-612, miR-302d-3p, miR-421, miR-548ar-5p and miR-548y (p < 0.05) was noted in the adverse prognosis group. CONCLUSION: This study highlights the utility of NanoString digital profiling methods in RMS, where it can detect distinct molecular signatures with the expression of signaling pathways and microRNAs from FFPE tumor tissue that may help identify prognostic biomarkers of interest. The overexpression of INPP4B and miR-3144-3p, miR-612, miR-302d-3p, miR-421, miR-548y and miR-548ar-5p may be associated with worse overall survival in ERMS and SRMS.

EPHB4 Mutation Suppresses PROX1 Expression and Disrupts Lymphatic Development in Neonatal Hydrops.

This case report highlights the importance of screening for mutations in EPHB4 and other genes that regulate lymphatic development in infants with the nonimmune hydrops fetalis.