Core Clinical Data Elements for Cancer Genomic Repositories: A Multi-stakeholder Consensus.

The Center for Medical Technology Policy and the Molecular Evidence Development Consortium gathered a diverse group of more than 50 stakeholders to develop consensus on a core set of data elements and values essential to understanding the clinical utility of molecularly targeted therapies in oncology.

The Role of Suprapubic Superficial Fascial System Reconstruction During Repair of Adult-Acquired Buried Penis.

BACKGROUND: Adult-Acquired Buried Penis is a disorder associated with systemic obesity that confers increased risks of malignancy, sexual dysfunction, urinary abnormalities, and psychological distress. Surgical correction improves patient-reported functional and psychological outcomes and often requires collaboration between plastic and urologic surgeons. To improve postoperative cosmetic outcomes and decrease wound complications following adult-acquired buried penis repair, we performed an anatomic and histologic study of the superficial fascial layers providing support to the external male genitalia and describe our approach for fascial reconstruction. METHODS: We characterized the superficial fascial anatomy in three patients undergoing adult-acquired buried penis repair, including two patients with Wisconsin Type II disease and one patient with Wisconsin Type IV disease. Gross specimens were sent from two patients histologic analysis using H&E and elastin-specific stains to characterize the identity of the superficial fibrofatty tissue. RESULTS: In all three patients, the fundiform ligament overlying the suspensory ligament was identified, isolated, and transected for removal with the suprapubic specimen. We found that reapproximation of this ligament following transection at the time of escutcheonectomy provided significant lift to the penis and genitals via improved support of dartos fascia. Histologic analysis of the superficial fibrofatty tissue located beneath the dermis revealed histologic similarities with the superficial fascial system described previously in abdominal and breast tissue. CONCLUSIONS: Reapproximation of the fundiform ligament and superficial fascial tissue following suprapubic/lower abdominal fat pad removal during adult-acquired buried penis may improve postoperative cosmesis by reducing strain on the dermal closure. LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors http://www.springer.com/00266 .

Surgical Outcomes and Prediction of Complications Following High-complexity Buried Penis Reconstruction.

PURPOSE: With uniform modern approaches to adult acquired buried penis reconstruction, this study provides updated results on surgical outcomes for complex cases while evaluating the relative influence of medical, surgical, and socioeconomic factors on these results. MATERIALS AND METHODS: Retrospective review was conducted of all patients undergoing initial buried penis reconstruction including escutcheonectomy and penile skin grafting at 1 tertiary center from 2015 through 2022. Summary scores for frailty and socioeconomic status were calculated with the Modified Frailty Index and Area Deprivation Index, respectively. RESULTS: The cohort included 103 patients. Median age was 51 years (IQR 44-65), and median BMI was 43 (IQR 38-49). Frail patients (≥2 Modified Frailty Index risk factors) accounted for 27% of the population while socioeconomic disadvantage (≥85th percentile on Area Deprivation Index) affected 33% of patients. Twenty-eight percent of repairs included a panniculectomy. Rate of revision for a poor outcome was 3.9% with median follow-up of 11 months. Complications were frequent (50%) with most being Clavien I or II (41%) and related to wound dehiscence (31%) or infection (30%). Frail patients had a higher rate of complication (71% vs 41%, P = .01) and were 6 times more likely to experience a complication on multivariable logistic regression (OR 6.41, 95% CI: 1.77-23.22, P = .005). CONCLUSIONS: The modern approach to complex buried penis reconstruction results in a low revision rate; however, low-grade complications are frequent. Patient frailty identifies those at highest risk for complication, offering an opportunity for counseling and preoperative preparation.

An institutional review of genomic sequencing in pediatric solid tumors.

BACKGROUND: Although tumor genomic profiling has aided the advancement of targeted genetic therapy, its clinical integration remains a challenge in pediatric cancers due to lower mutation frequency and less available targeted drugs. There have been multiple novel studies examining molecular sequencing in pediatrics; however, many of these studies primarily utilized large-scale, genome-wide screening applications that limit applicable use due to the availability of testing. This study examined the institutional use of a targeted, clinically available approach to tumor genomic sequencing. METHODS: A retrospective chart review was performed on pediatric patients with solid tumors who were managed at Roswell Park Comprehensive Cancer Center and underwent molecular testing of their tumor biopsy via OmniSeq from August 2016 to July 2021. Results were reviewed for mutations considered to be "actionable" by targeted therapy. Patients with actionable mutations were further examined to evaluate treatment course, receival of targeted therapy, and clinical outcomes. RESULTS: We identified 64 pediatric patients consisting of 20 (31%) with CNS tumors and 44 (69%) with non-CNS tumors, ranging in age from 9 months to 21 years. Thirty-five total actionable mutations were identified amongst 27 patients (42%). Of these 27, 12 patients (44%) received at least 1 targeted drug against a respective actionable mutation, of which 6 patients (50%) achieved clinical benefit to therapy, including 1 complete response. CONCLUSIONS: The use of a clinically focused and readily available targeted molecular sequencing panel identified actionable mutations at a comparable rate to the large-scale, less readily available sequencing panels utilized in other studies. Half of our patients who received targeted therapy achieved a complete response or clinical benefit from therapy. Although targeted therapy has a role in pediatric cancer treatment, many newer drugs require further research on their safety and efficacy.

Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist.

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) affect 150 million people annually. Despite effective antibiotic therapy, 30-50% of patients experience recurrent UTIs. In addition, the growing prevalence of UPEC that are resistant to last-line antibiotic treatments, and more recently to carbapenems and colistin, make UTI a prime example of the antibiotic-resistance crisis and emphasize the need for new approaches to treat and prevent bacterial infections. UPEC strains establish reservoirs in the gut from which they are shed in the faeces, and can colonize the periurethral area or vagina and subsequently ascend through the urethra to the urinary tract, where they cause UTIs. UPEC isolates encode up to 16 distinct chaperone-usher pathway pili, and each pilus type may enable colonization of a habitat in the host or environment. For example, the type 1 pilus adhesin FimH binds mannose on the bladder surface, and mediates colonization of the bladder. However, little is known about the mechanisms underlying UPEC persistence in the gut. Here, using a mouse model, we show that F17-like and type 1 pili promote intestinal colonization and show distinct binding to epithelial cells distributed along colonic crypts. Phylogenomic and structural analyses reveal that F17-like pili are closely related to pilus types carried by intestinal pathogens, but are restricted to extra-intestinal pathogenic E. coli. Moreover, we show that targeting FimH with M4284, a high-affinity inhibitory mannoside, reduces intestinal colonization of genetically diverse UPEC isolates, while simultaneously treating UTI, without notably disrupting the structural configuration of the gut microbiota. By selectively depleting intestinal UPEC reservoirs, mannosides could markedly reduce the rate of UTIs and recurrent UTIs.

Chaos controlled: discovery of a powerful amyloid inhibitor.

In this issue of Molecular Cell, Evans et al. (2015) report that the hitherto largely unstudied CsgC protein is responsible for the suppression of premature amyloidogenesis within the cellular periplasm, preventing early aggregation and cellular toxicity.

Current Policy Challenges in Genomic Medicine.

BACKGROUND: Molecular genetic testing has raised a variety of policy issues, ranging from privacy to reimbursement. Recently, payment policies have become of paramount importance as Medicare implemented the first significant change to test pricing since 1984 and announced a broad national coverage policy for the use of next-generation sequencing (NGS) in cancer patients that contains significant restrictions. Regulatory and oversight concerns have been important topics for discussion as the US Food and Drug Administration (FDA), Congress, and stakeholders have focused on new approaches to regulation of laboratory-developed tests (LDTs). Patents on gene sequences and relationships between genetic variants and clinical phenotypes have been points of contention since the field's inception. Two Supreme Court cases invalidated patents on gene sequences and biological relationships, ushering in the era of NGS and precision medicine. However, a recent legislative proposal threatens to reverse these gains and restore gene patents as barriers to progress in genetic and genomic testing and the implementation of genomic medicine. CONTENT: This review discusses current issues in payment policy, laboratory oversight, and gene patenting and their potential impacts on genetic and genomic testing. SUMMARY: Coverage and reimbursement policies present serious challenges to genetic and genomic testing. The potential for FDA regulation of LDTs looms as a significant threat to diagnostic innovation, patient access, and the viability of molecular genetic testing laboratories. Changes in patent law could cause gene patents to reemerge as barriers to the advancement of genomic medicine.

Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel ß-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation.

Role of copper efflux in pneumococcal pathogenesis and resistance to macrophage-mediated immune clearance.

In bacteria, the intracellular levels of metals are mediated by tightly controlled acquisition and efflux systems. This is particularly true of copper, a trace element that is universally toxic in excess. During infection, the toxic properties of copper are exploited by the mammalian host to facilitate bacterial clearance. To better understand the role of copper during infection, we characterized the contribution of the cop operon to copper homeostasis and virulence in Streptococcus pneumoniae. Deletion of either the exporter, encoded by copA, or the chaperone, encoded by cupA, led to hypersensitivity to copper stress. We further demonstrated that loss of the copper exporter encoded by copA led to decreased virulence in pulmonary, intraperitoneal, and intravenous models of infection. Deletion of copA resulted in enhanced macrophage-mediated bacterial clearance in vitro. The attenuation phenotype of the copA mutant in the lung was found to be dependent on pulmonary macrophages, underscoring the importance of copper efflux in evading immune defenses. Overall, these data provide insight into the role of the cop operon in pneumococcal pathogenesis.

Evidence synthesis and guideline development in genomic medicine: current status and future prospects.

PURPOSE: With the accelerated implementation of genomic medicine, health-care providers will depend heavily on professional guidelines and recommendations. Because genomics affects many diseases across the life span, no single professional group covers the entirety of this rapidly developing field. METHODS: To pursue a discussion of the minimal elements needed to develop evidence-based guidelines in genomics, the Centers for Disease Control and Prevention and the National Cancer Institute jointly held a workshop to engage representatives from 35 organizations with interest in genomics (13 of which make recommendations). The workshop explored methods used in evidence synthesis and guideline development and initiated a dialogue to compare these methods and to assess whether they are consistent with the Institute of Medicine report "Clinical Practice Guidelines We Can Trust." RESULTS: The participating organizations that develop guidelines or recommendations all had policies to manage guideline development and group membership, and processes to address conflicts of interests. However, there was wide variation in the reliance on external reviews, regular updating of recommendations, and use of systematic reviews to assess the strength of scientific evidence. CONCLUSION: Ongoing efforts are required to establish criteria for guideline development in genomic medicine as proposed by the Institute of Medicine.

Anti-electrostatic hydrogen bonds.

Ab initio and hybrid density functional techniques were employed to characterize a surprising new class of H-bonded complexes between ions of like charge. Representative H-bonded complexes of both anion-anion and cation-cation type exhibit appreciable kinetic stability and the characteristic theoretical, structural, and spectroscopic signatures of hydrogen bonding, despite the powerful opposition of Coulomb electrostatic forces. All such "anti-electrostatic" H-bond (AEHB) species confirm the dominance of resonance-type covalency ("charge transfer") interactions over the inessential (secondary or opposing) "ionic" or "dipole-dipole" forces that are often presumed to be essential for numerical modeling or conceptual explanation of the H-bonding phenomenon.

A Single-resident Experience of Overnight Call Activity at a Multi-site Academic Health System.

OBJECTIVE: To characterize urology resident on-call activities overnight at a multi-site academic medical center and model the expected volume of clinical activity using inpatient beds, emergency room visits, and attendings covered. MATERIALS AND METHODS: On-call activities for 70 13-hour overnight shifts spanning 5 nonconsecutive months between May 2022 and February 2023 were recorded. Clinical coverage included 5 academic hospitals encompassing 1761 staffed inpatient beds and an expected nightly volume of 255 Emergency Department (ED) visits. The time, source, and clinical features of every call were documented. RESULTS: An average of 15 unique calls were received during each shift. Of these, 35% required an in-person evaluation and 12% required a bedside or operative procedure. Approximately a third of calls (36%) were received after midnight. An in-person evaluation occurred within the first hour of 53% of shifts and every shift required at least 1 evaluation. When normalized for inpatient bed volume, an average of 7 unique patient communications occurred per 1000 beds, leading to 2 in-person evaluations. When normalized for an expected number of overnight ED visits, an average of 1 new ED consultation occurred per 100 ED visits. CONCLUSION: After-hours clinical coverage models vary significantly by specialty and institution, and coverage decisions must balance quality clinical care with safe provider workload. Patient needs were appropriately addressed by a single overnight on-call resident, providing a robust clinical experience. The volume of patient care activities in this experience supports the practice of a "night-float" resident with the clear expectation on-site care is required.

Minimally Invasive Management of Posterior Urethral Stricture/Stenosis with DVIU and Mitomycin C Injection.

OBJECTIVE: To demonstrate a technique for minimally invasive endoscopic management of posterior urethral strictures, including those at the bladder neck and vesicourethral anastomosis. METHODS: Herein, we have included endoscopic video footage from 3 patients with posterior urethral strictures, including 1 at the bladder neck, 1 at the vesicourethral anastomosis, and 1 in the bulbomembranous urethra. In each patient, we perform a direct visualization internal urethrotomy (DVIU) with incisions at the 5 and 7 o'clock positions to widen the urethral lumen, followed by injection of 2 mg mitomycin C (MMC) in a total volume of 5 mL sterile water. RESULTS: Herein, we describe our technique for the endoscopic management of posterior urethral strictures, including those in the prostatic urethra and bladder neck. MMC injection, in conjunction with traditional DVIU, adds minimally to the complexity and length of the procedure but may substantially improve long-term surgical outcomes. CONCLUSION: Bladder outlet obstruction due to stenosis or stricture of the posterior urethra is a common urologic diagnosis whose etiology can often be traced to prior urethral manipulation or iatrogenic trauma. While Americal Urological Assicuation (AUA) guidelines state that dilation or direct visualization internal urethrotomy (DVIU) should be offered for bulbar strictures measuring less than 2 cm in length, recent evidence suggests that DVIU with or without MMC injection may have utility in the management of bladder neck or vesicourethral anastomotic contractures. We have found that DVIU with subsequent MMC injection is a viable minimally invasive approach for the treatment of posterior urethral strictures. While more data are needed to better understand the long-term success rates of these procedures, this approach should be considered for patients with a bladder outlet obstruction secondary to a short stricture of the posterior urethra, bladder neck, or vesicourethral anastomosis.

No-Opioid Discharge Following Artificial Urinary Sphincter Placement Does Not Significantly Increase Health Care System Burden.

INTRODUCTION: Postoperative opioid prescriptions are associated with an increased risk of opioid dependance. While studies on no-opioid discharge strategies have been assessed following many urologic procedures, the effect of no-opioid discharges on health care utilization following artificial urinary sphincter placement is unknown. We performed a single-surgeon retrospective comparison of health care system interactions following artificial urinary sphincter implantation between patients who received an opioid prescription on discharge to those who did not. METHODS: We identified 101 male patients who underwent 3-piece artificial urinary sphincter placement or revision by 1 provider between 2015 and 2022. All patients were discharged with acetaminophen and ibuprofen; none received intraoperative local anesthetic. Demographic information, preprocedural opioid use, opioid prescriptions following the procedure, postoperative office communications, unplanned office visits, and emergency department (ED) visits were recorded for each patient for 90 days. RESULTS: Forty-five patients (45%) were discharged without an opioid prescription and 56 patients (55%) were discharged with an opioid prescription. No differences in age, race, BMI, operative time, or presence of a preoperative opioid prescription were observed. Discharge without an opioid did not significantly increase the number of office communications (55% vs 40%, P = .11), unplanned office visits (36% vs 23%, P = .19), or ED visits (20 vs 12, P = .41) within 90 days of implantation/revision. CONCLUSIONS: Opioids can be omitted from the discharge analgesic regimen following artificial urinary sphincter placement without increasing burden to surgical office staff or local EDs. Providers should consider no-opioid discharges for patients undergoing uncomplicated sphincter placement to limit risk of opioid-related morbidity.

Patient Interaction With the Health Care System Following a Nonopioid Discharge Strategy for Anterior Urethroplasty.

INTRODUCTION: Continued efforts have been made to minimize postoperative opioids following urologic interventions. Studies show that patient-reported pain outcomes are similar between those patients discharged with and without opioids following anterior urethroplasty, but we do not know what impact this has on health care utilization. We aim to show that a nonopioid discharge following anterior urethroplasty does not increase postoperative health care utilization. METHODS: Five hundred patients who underwent anterior urethroplasty from January 2016 to October 2022 were identified from retrospective chart review. Patient demographic information, surgical characteristics, and postoperative interactions with the health care system were extracted from the electronic medical record. We then compared these outcomes by discharge opioid prescription status. RESULTS: A total of 253 patients were discharged without an opioid prescription. Patients who received an opioid were more likely to have had a perineal incision (73% vs 64%, P = .02), more likely to have had an overnight hospital stay (30% vs 14%, P < .01), and were more likely to have been prescribed an opioid preoperatively (13% vs 7%, P = .03). There were overall low rates of interaction with the health system in both groups with no significant difference in 30-day unplanned office visits, emergency department visits, or office phone calls. Overall, by the end of our study period 97% were discharged without an opioid and 94% of patients were discharged the same day. CONCLUSIONS: Patients undergoing anterior urethroplasty can safely be discharged home without opioids following surgery without undue postoperative burden on the health care system.

Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update.

To provide an update on recent revisions to Evaluation of Genomic Applications in Practice and Prevention (EGAPP) methods designed to improve efficiency, and an assessment of the implications of whole genome sequencing for evidence-based recommendation development. Improvements to the EGAPP approach include automated searches for horizon scanning, a quantitative ranking process for topic prioritization, and the development of a staged evidence review and evaluation process. The staged process entails (i) triaging tests with minimal evidence of clinical validity, (ii) using and updating existing reviews, (iii) evaluating clinical validity prior to analytic validity or clinical utility, (iv) using decision modeling to assess potential clinical utility when direct evidence is not available. EGAPP experience to date suggests the following approaches will be critical for the development of evidence based recommendations in the whole genome sequencing era: (i) use of triage approaches and frameworks to improve efficiency, (ii) development of evidence thresholds that consider the value of further research, (iii) incorporation of patient preferences, and (iv) engagement of diverse stakeholders. The rapid advances in genomics present a significant challenge to traditional evidence based medicine, but also an opportunity for innovative approaches to recommendation development.

Transcorporal Artificial Urinary Sphincter Technique Video.

OBJECTIVE: The artificial urethral sphincter (AUS) is the gold standard treatment for male stress urinary incontinence which commonly results from prostatectomy or pelvic radiation for prostate cancer. Patients with prior pelvic radiation history experience increased risk of developing urethral erosion. Transcorporal AUS (TAUS) placement can be used as an alternative for compromised urethras to incorporate a small portion of the corporal bodies for additional support. The inclusion of an additional tissue barrier has been shown to improve outcomes. Patients who undergo this technique require device explanation and AUS revision less often than those with AUS devices placed in the standard fashion. Additionally, TAUS placement has been shown to improve functional urinary outcomes such as postoperative Internal prostate symptom score (IPSS), and postoperative IPSS Quality of Life (QoL) scores. MATERIALS AND METHODS: A 67-year-old male with a past medical history of prostate cancer treated with surgery and radiation underwent a TAUS placement which was filmed to demonstrate placement technique and tips. Informed consent was obtained prior to filming this video. RESULTS: This technique can serve as a successful primary or salvage AUS placement technique as seen in this video. CONCLUSION: This video is used to demonstrate the technique of TAUS placement.

RNA Sequencing Identifies Novel NRG1 Fusions in Solid Tumors that Lack Co-Occurring Oncogenic Drivers.

NRG1 gene fusions are rare, therapeutically relevant, oncogenic drivers that occur across solid tumor types. To understand the landscape of NRG1 gene fusions, 4397 solid tumor formalin-fixed, paraffin-embedded samples consecutively tested by comprehensive genomic and immune profiling during standard care were analyzed. Nineteen NRG1 fusions were found in 17 unique patients, across multiple tumor types, including non-small-cell lung (n = 7), breast (n = 2), colorectal (n = 3), esophageal (n = 2), ovarian (n = 1), pancreatic (n = 1), and unknown primary (n = 1) carcinomas, with a cumulative incidence of 0.38%. Fusions were identified with breakpoints across four NRG1 introns spanning 1.4 megabases, with a mixture of known (n = 8) and previously unreported (n = 11) fusion partners. Co-occurring driver alterations in tumors with NRG1 fusions were uncommon, except colorectal carcinoma, where concurrent alterations in APC, BRAF, and ERBB2 were present in a subset of cases. The overall lack of co-occurring drivers highlights the importance of identifying NRG1 gene fusions, as these patients are unlikely to harbor other targetable alterations. In addition, RNA sequencing is important to identify NRG1 gene fusions given the variety of fusion partners and large genomic areas where breakpoints can occur.

Structure and catalytic mechanism of nicotinate (vitamin B3) degradative enzyme maleamate amidohydrolase from Bordetella bronchiseptica RB50.

The penultimate reaction in the oxidative degradation of nicotinate (vitamin B(3)) to fumarate in several species of aerobic bacteria is the hydrolytic deamination of maleamate to maleate, catalyzed by maleamate amidohydrolase (NicF). Although it has been considered a model system for bacterial degradation of N-heterocyclic compounds, only recently have gene clusters that encode the enzymes of this catabolic pathway been identified to allow detailed investigations concerning the structural basis of their mechanisms. Here, the Bb1774 gene from Bordetella bronchiseptica RB50, putatively annotated as nicF, has been cloned, and the recombinant enzyme, overexpressed and purified from Escherichia coli, is shown to catalyze efficiently the hydrolysis of maleamate to maleate and ammonium ion. Steady-state kinetic analysis of the reaction by isothermal titration calorimetry (ITC) established k(cat) and K(M) values (pH 7.5 and 25 °C) of 11.7 ± 0.2 s(-1) and 128 ± 6 µM, respectively. The observed K(D) of the NicF·maleate (E·P) complex, also measured by ITC, is approximated to be 3.8 ± 0.4 mM. The crystal structure of NicF, determined at 2.4 Å using molecular replacement, shows that the enzyme belongs to the cysteine hydrolase superfamily. The structure provides insight concerning the roles of potential catalytically important residues, most notably a conserved catalytic triad (Asp29, Lys117, and Cys150) observed in the proximity of a conserved non-proline cis-peptide bond within a small cavity that is likely the active site. On the basis of this structural information, the hydrolysis of maleamate is proposed to proceed by a nucleophilic addition-elimination sequence involving the thiolate side chain of Cys150.