Urachal carcinoma: A novel staging system utilizing the National Cancer Database.

BACKGROUND: Urachal carcinoma (UrC) is a rare, aggressive cancer with a poor prognosis that is frequently diagnosed in advanced stages. Due to its rarity, the current staging systems, namely Sheldon, Mayo, and Ontario were established based on relatively small patient cohorts, necessitating further validation. We used a large patient population from the National Cancer Database to model a novel staging system based on the Tumor (T), Node(N), and Metastasis (M) (TNM) staging system and compared it to established staging systems. METHODS: We identified patients diagnosed with UrC between the years of 2004-2016. To determine median overall survival (OS), a Kaplan-Meier (KM) curve was generated using the Sheldon, Mayo, Ontario, and TNM staging system. A cox proportional-hazards regression model was developed to highlight predictors of overall survival. RESULTS: A total of 626 patients were included in the analysis. The OS for the entire cohort was 58.2 months (50.1-67.8) with survival rates at 12, 24, and 60 months of 83%, 70%, and 49%, respectively (p < 0.0001). As compared to the Sheldon, Mayo, and Ontario staging system, our TNM staging system had a more balanced sample and survival distribution per stage and no overlap among stages on KM survival curves. The Mayo, Ontario, and TNM staging systems were more accurate in terms of stage-survival correlation than the Sheldon staging system (p < 0.05 for all stages). CONCLUSIONS: The proposed novel TNM staging system for UrC has a more balanced sample distribution and a more accurate stage-survival correlation than the traditional Mayo, Sheldon, and Ontario staging systems. It is clinically applicable and enables better risk stratification, prognosis, and therapeutic decision-making.

Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair.

DNA repair by homologous recombination (HR) is critical for the maintenance of genome stability. Germline and somatic mutations in HR genes have been associated with an increased risk of developing breast (BC) and ovarian cancers (OvC). However, the extent of factors and pathways that are functionally linked to HR with clinical relevance for BC and OvC remains unclear. To gain a broader understanding of this pathway, we used multi-omics datasets coupled with machine learning to identify genes that are associated with HR and to predict their sub-function. Specifically, we integrated our phylogenetic-based co-evolution approach (CladePP) with 23 distinct genetic and proteomic screens that monitored, directly or indirectly, DNA repair by HR. This omics data integration analysis yielded a new database (HRbase) that contains a list of 464 predictions, including 76 gold standard HR genes. Interestingly, the spliceosome machinery emerged as one major pathway with significant cross-platform interactions with the HR pathway. We functionally validated 6 spliceosome factors, including the RNA helicase SNRNP200 and its co-factor SNW1. Importantly, their RNA expression correlated with BC/OvC patient outcome. Altogether, we identified novel clinically relevant DNA repair factors and delineated their specific sub-function by machine learning. Our results, supported by evolutionary and multi-omics analyses, suggest that the spliceosome machinery plays an important role during the repair of DNA double-strand breaks (DSBs).

Objective determination of peripheral edema in heart failure patients using short-wave infrared molecular chemical imaging.

SIGNIFICANCE: Peripheral pitting edema is a clinician-administered measure for grading edema. Peripheral edema is graded 0, 1 + , 2 + , 3 + , or 4 + , but subjectivity is a major limitation of this technique. A pilot clinical study for short-wave infrared (SWIR) molecular chemical imaging (MCI) effectiveness as an objective, non-contact quantitative peripheral edema measure is underway. AIM: We explore if SWIR MCI can differentiate populations with and without peripheral edema. Further, we evaluate the technology for correctly stratifying subjects with peripheral edema. APPROACH: SWIR MCI of shins from healthy subjects and heart failure (HF) patients was performed. Partial least squares discriminant analysis (PLS-DA) was used to discriminate the two populations. PLS regression (PLSR) was applied to assess the ability of MCI to grade edema. RESULTS: Average spectra from edema exhibited higher water absorption than non-edema spectra. SWIR MCI differentiated healthy volunteers from a population representing all pitting edema grades with 97.1% accuracy (N = 103 shins). Additionally, SWIR MCI correctly classified shin pitting edema levels in patients with 81.6% accuracy. CONCLUSIONS: Our study successfully achieved the two primary endpoints. Application of SWIR MCI to monitor patients while actively receiving HF treatment is necessary to validate SWIR MCI as an HF monitoring technology.

Visible near infrared reflectance molecular chemical imaging of human ex vivo carcinomas and murine in vivo carcinomas.

SIGNIFICANCE: A key risk faced by oncological surgeons continues to be complete removal of tumor. Currently, there is no intraoperative imaging device to detect kidney tumors during excision. AIM: We are evaluating molecular chemical imaging (MCI) as a technology for real-time tumor detection and margin assessment during tumor removal surgeries. APPROACH: In exploratory studies, we evaluate visible near infrared (Vis-NIR) MCI for differentiating tumor from adjacent tissue in ex vivo human kidney specimens, and in anaesthetized mice with breast or lung tumor xenografts. Differentiation of tumor from nontumor tissues is made possible with diffuse reflectance spectroscopic signatures and hyperspectral imaging technology. Tumor detection is achieved by score image generation to localize the tumor, followed by application of computer vision algorithms to define tumor border. RESULTS: Performance of a partial least squares discriminant analysis (PLS-DA) model for kidney tumor in a 22-patient study is 0.96 for area under the receiver operating characteristic curve. A PLS-DA model for in vivo breast and lung tumor xenografts performs with 100% sensitivity, 83% specificity, and 89% accuracy. CONCLUSION: Detection of cancer in surgically resected human kidney tissues is demonstrated ex vivo with Vis-NIR MCI, and in vivo on mice with breast or lung xenografts.

Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes.

The homologous recombination repair (HRR) pathway repairs DNA double-strand breaks in an error-free manner. Mutations in HRR genes can result in increased mutation rate and genomic rearrangements, and are associated with numerous genetic disorders and cancer. Despite intensive research, the HRR pathway is not yet fully mapped. Phylogenetic profiling analysis, which detects functional linkage between genes using coevolution, is a powerful approach to identify factors in many pathways. Nevertheless, phylogenetic profiling has limited predictive power when analyzing pathways with complex evolutionary dynamics such as the HRR. To map novel HRR genes systematically, we developed clade phylogenetic profiling (CladePP). CladePP detects local coevolution across hundreds of genomes and points to the evolutionary scale (e.g., mammals, vertebrates, animals, plants) at which coevolution occurred. We found that multiscale coevolution analysis is significantly more biologically relevant and sensitive to detect gene function. By using CladePP, we identified dozens of unrecognized genes that coevolved with the HRR pathway, either globally across all eukaryotes or locally in different clades. We validated eight genes in functional biological assays to have a role in DNA repair at both the cellular and organismal levels. These genes are expected to play a role in the HRR pathway and might lead to a better understanding of missing heredity in HRR-associated cancers (e.g., heredity breast and ovarian cancer). Our platform presents an innovative approach to predict gene function, identify novel factors related to different diseases and pathways, and characterize gene evolution.

SHLD2/FAM35A co-operates with REV7 to coordinate DNA double-strand break repair pathway choice.

DNA double-strand breaks (DSBs) can be repaired by two major pathways: non-homologous end-joining (NHEJ) and homologous recombination (HR). DNA repair pathway choice is governed by the opposing activities of 53BP1, in complex with its effectors RIF1 and REV7, and BRCA1. However, it remains unknown how the 53BP1/RIF1/REV7 complex stimulates NHEJ and restricts HR to the S/G2 phases of the cell cycle. Using a mass spectrometry (MS)-based approach, we identify 11 high-confidence REV7 interactors and elucidate the role of SHLD2 (previously annotated as FAM35A and RINN2) as an effector of REV7 in the NHEJ pathway. FAM35A depletion impairs NHEJ-mediated DNA repair and compromises antibody diversification by class switch recombination (CSR) in B cells. FAM35A accumulates at DSBs in a 53BP1-, RIF1-, and REV7-dependent manner and antagonizes HR by limiting DNA end resection. In fact, FAM35A is part of a larger complex composed of REV7 and SHLD1 (previously annotated as C20orf196 and RINN3), which promotes NHEJ and limits HR Together, these results establish SHLD2 as a novel effector of REV7 in controlling the decision-making process during DSB repair.

T regulatory lymphocytes and endothelial function in pediatric obstructive sleep apnea.

BACKGROUND: Obstructive sleep apnea (OSA) is a low-grade inflammatory disease affecting the cardiovascular and metabolic systems. Increasing OSA severity reduces T-regulatory lymphocytes (Tregs) in OSA children. Since Tregs modulate endothelial activation, and attenuate insulin resistance, we hypothesized that Tregs are associated with endothelial and metabolic dysfunction in pediatric OSA. METHODS: 50 consecutively recruited children (ages 4.8-12 years) underwent overnight polysomnography and fasting homeostatic model (HOMA) of insulin resistance was assessed. Percentage of Tregs using flow cytometry, and endothelial function, expressed as the time to peak occlusive hyperemia (Tmax), were examined. In a subgroup of children (n = 21), in vitro Treg suppression tests were performed. RESULTS: Circulating Tregs were not significantly associated with either BMI z score or HOMA. However, a significant inverse correlation between percentage of Tregs and Tmax emerged (p<0.0001, r = -0.56). A significant negative correlation between Tregs suppression and the sleep pressure score (SPS), a surrogate measure of sleep fragmentation emerged (p = 0.02, r = -0.51) emerged, but was not present with AHI. CONCLUSIONS: Endothelial function, but not insulin resistance, in OSA children is strongly associated with circulating Tregs and their suppressive function, and appears to correlate with sleep fragmentation. Thus, alterations in T cell lymphocytes may contribute to cardiovascular morbidity in pediatric OSA.

Obstructive sleep apnea in children is associated with severity-dependent deterioration in overnight endothelial function.

BACKGROUND: Restorative sleep is expected to promote improved endothelial function (EF) in the morning compared to the evening. However, in adults with obstructive sleep apnea (OSA) EF is not only adversely affected, but it worsens during the night. Data in pediatric OSA are scarce, and overnight changes have not been explored. Therefore, we sought to examine potential associations between pediatric OSA and overnight changes in EF. METHODS: 59 habitually snoring children with various degrees of sleep-disordered breathing (age range, 4-16 years) underwent EF assessment (reactive hyperemia test by EndoPAT, Itamar Medical, Israel) in the evening before and the morning after an overnight polysomnography (PSG). Two brachial occlusion periods (1 min and 5 min) also were tested. Potential associations between evening-to-morning changes in EF and polysomnographic parameters were explored. RESULTS: Evening-to-morning changes in children with OSA displayed severity-dependent deterioration of EF, and occlusions lasting 1 or 5 min during the reactive hyperemia test yielded similar findings. CONCLUSIONS: In children deterioration in EF during the night significantly correlated with the severity of OSA. Furthermore, the reactive hyperemia test can be reliably performed with only 60 seconds of arterial flow occlusion in children. These findings support our hypothesis that similarly to adults, sleep apnea in children results in endothelial dysfunction (ED). We speculate that pediatric OSA is less commonly associated with cardiovascular complications possibly due to the shorter duration of the syndrome.

Urinary neurotransmitters are selectively altered in children with obstructive sleep apnea and predict cognitive morbidity.

BACKGROUND: Pediatric obstructive sleep apnea (OSA) is associated with cognitive dysfunction, suggesting altered neurotransmitter function. We explored overnight changes in neurotransmitters in the urine of children with and without OSA. METHODS: Urine samples were collected from children with OSA and from control subjects before and after sleep studies. A neurocognitive battery assessing general cognitive ability (GCA) was administered to a subset of children with OSA. Samples were subjected to multiple enzyme-linked immunosorbent assays for 12 neurotransmitters, and adjusted for creatinine concentrations. RESULTS: The study comprised 50 children with OSA and 20 control subjects. Of the children with OSA, 20 had normal GCA score (mean ± SD) (101.2 ± 14.5) and 16 had a reduced GCA score (87.3 ± 13.9; P < .001). Overnight increases in epinephrine, norepinephrine, and γ-aminobutyric acid (GABA) levels emerged in children with OSA; taurine levels decreased. Using combinatorial approaches and cutoff values for overnight changes of these four neurotransmitters enabled prediction of OSA (area under the curve [AUC]: 0.923; P < .0001). Furthermore, GABA and taurine alterations, as well as overnight reductions in phenylethylamine, were more prominent in children with OSA and low GCA than in children with OSA and normal GCA (P < .001), and they reliably discriminated GCA status (AUC: 0.977; P < .0001). CONCLUSIONS: Pediatric OSA is associated with overnight increases in urinary concentrations of catecholamines indicative of heightened sympathetic outflow. Increases in GABA levels and decreases in taurine levels could underlie mechanisms of neuronal excitotoxicity and dysfunction. Combinatorial approaches using defined cutoffs in overnight changes in concentrations of selected neurotransmitters in urine may not only predict OSA but also the presence of cognitive deficits. Larger cohort studies appear warranted to confirm these findings.