Sonographically Determined Fecal Width: An Objective Indicator of Management of Bladder and Bowel Dysfunction in Children.

OBJECTIVE: To test whether sonographically determined fecal width (SDFW) correlates with symptom improvement in a population of children with bladder and bowel dysfunction (BBD) managed with standard urotherapy (SU), even for those patients lacking initial bowel complaints. METHODS: We retrospectively analyzed 200 pediatric BBD patients managed with SU for at least 3 months. Self-reported symptom improvement (complete, partial, no response) following International Children's Continence Society guidelines was tabulated. Patients with complex urologic diagnoses other than vesicoureteral reflux (VUR) were excluded. Pharmacotherapy choice, physical therapy (PT), urinary tract infection (UTI) occurrence, and VUR status were tabulated. SDFW was recorded. Non-parametric analysis of variants (ANOVA) and parametric/non-parametric t testing were used for analysis. RESULTS: Patients had a mean age of 9.5 years (4-12). Forty-eight patients had no gastrointestinal complaints at presentation. Urotherapy yielded complete, partial, and no responses in 14% (n = 27), 33% (n = 67), and 53% (n = 106) of patients, respectively. The average SDFW for those patients with complete response (2.6 cm) was smaller than the SDFW of those with a partial response (3.1 cm) or no response (3.3 cm) (P = .0001). Non-compliance led to greater SDFW compared to compliant patients (3.7 cm and 3.1 cm, respectively, P = .0001). Fecal width was unaffected by VUR, UTI, PT, or pharmacotherapy. CONCLUSION: SDFW correlates well with symptom improvement in pediatric patients managed for BBD, confirming our hypothesis. SDFW is reasonable as single objective parameter to identify successful management in patients with BBD, extending to those without bowel complaints at presentation.

Endometrial Carcinomas With Subclonal Loss of Mismatch Repair Proteins: A Clinicopathologic and Genomic Study.

Subclonal loss of mismatch repair (MMR) proteins has been described in a small subset of endometrial carcinomas (ECs), but the genomic basis for this phenomenon has received limited attention. Herein, we retrospectively evaluated all ECs with MMR immunohistochemistry (n=285) for subclonal loss, and in those (n=6), performed a detailed clinicopathologic and genomic comparison of the MMR-deficient and MMR-proficient components. Three tumors were FIGO stage IA, and one each stage IB, II, and IIIC2. Patterns of subclonal loss were as follows: (1) 3 FIGO grade 1 endometrioid carcinomas with subclonal MLH1/PMS2, MLH1 promoter hypermethylation, and no MMR gene mutations; (2) POLE -mutated FIGO grade 3 endometrioid carcinoma with subclonal PMS2, and PMS2 and MSH6 mutations limited to the MMR-deficient component; (3) dedifferentiated carcinoma with subclonal MSH2/MSH6, as well as complete loss of MLH1/PMS2, MLH1 promoter hypermethylation, and PMS2 and MSH6 mutations in both components; (4) dedifferentiated carcinoma with subclonal MSH6, and somatic and germline MSH6 mutations in both components, but with a higher allele frequency in MMR-deficient foci. Recurrences occurred in 2 patients, one consisted of the MMR-proficient component from a FIGO 1 endometrioid carcinoma, while the other was from the MSH6 -mutated dedifferentiated endometrioid carcinoma. At the last follow-up (median: 44 mo), 4 patients were alive and disease-free and 2 were alive with disease. In summary, subclonal MMR loss reflects subclonal and often complex genomic and epigenetic alterations, which may have therapeutic implications and therefore must be reported when present. In addition, subclonal loss can occur in both POLE -mutated and Lynch syndrome-associated ECs.

Clinicopathologic Evaluation and Molecular Profiling of Recurrent Stage IA Endometrial Endometrioid Carcinoma: A Case-control Study.

Most low-grade, early-stage endometrial endometrioid carcinomas (EEC) have an excellent prognosis; however, recurrences occur in a small subset with several studies reporting an increase in CTNNB1 exon 3 mutations in this population. Herein we evaluated 10 recurrent low-grade (FIGO 1 or 2), early-stage (FIGO IA) EECs matched to 10 nonrecurrent EECs to further characterize their clinicopathologic features and molecular phenotype. Cases were matched to controls based on size, grade, and depth of invasion. All tumors were evaluated for specific clinicopathologic parameters followed by next-generation sequencing using a 1213 gene panel. Recurrent EECs demonstrated no significant clinicopathologic differences when compared with nonrecurrent EECs, in terms of age, body mass index, pattern of invasion, presence of endometrial atypical hyperplasia/endometrioid intraepithelial neoplasia, associated metaplastic changes, peritumoral lymphocytes, mitoses, and tumor-infiltrating lymphocytes. Both cohorts also showed a similar number of pathogenic mutations, including CTNNB1 exon 3 mutations, as well as tumor mutational burden and microsatellite profiles. Although in this particular study, the lack of correlation between CTNNB1 exon 3 mutation and recurrence might be secondary to a small sample size, it also suggests the presence of other contributing factors. Thus, it helps set the foundation for larger series incorporating whole genome, transcriptome, proteome, and epigenome analyses to answer this clinically important question.

High Rates of Ultraviolet-Signature Mutations in Squamous Cell Carcinomas of the Parotid Gland and Prognostic Implications.

In the absence of clear pathologic differences, clinical history may differentiate potential primary parotid squamous cell carcinomas (SCC) from metastases. The presence of an ultraviolet (UV) signature can distinguish between tumors of cutaneous and non-cutaneous origin. This study aimed to investigate rates of UV signature mutations in squamous cell carcinomas of the parotid gland as well as differences in clinical features between tumors of cutaneous and non-cutaneous origin. Clinical and pathologic data were collected from 71 patients with SCC involving the parotid gland, of which 48 had cutaneous, 10 had mucosal, and 13 had no history of SCC. In 34 available cases, genomic DNA was isolated from formalin-fixed paraffin-embedded tissue specimens and sequenced using a targeted hybrid capture 1213 gene panel. Tumor mutational burden and COSMIC (Catalogue of Somatic Mutations in Cancer) mutational signatures were calculated. Most (74%) were UV-positive. Patients with UV-positive tumors were significantly older, white, and had higher rates of sun exposure. Patients with UV-negative tumors had a significantly higher mortality rate and shorter time to death: 6 (67%) died of disease with a median time to death of 9 months compared to 5 (20%) UV-positive patients who died of disease with a median time to death of 32 months. Pathologic features did not significantly vary by clinical history or UV status. The presence of a UV-signature combined with clinical history can be used to determine the primary source of SCC involving the parotid gland. UV-positivity may reflect a less aggressive disease course in an older population.

CDKN2A loss-of-function predicts immunotherapy resistance in non-small cell lung cancer.

Immune checkpoint blockade (ICB) improves outcomes in non-small cell lung cancer (NSCLC) though most patients progress. There are limited data regarding molecular predictors of progression. In particular, there is controversy regarding the role of CDKN2A loss-of-function (LOF) in ICB resistance. We analyzed 139 consecutive patients with advanced NSCLC who underwent NGS prior to ICB initiation to explore the association of CDKN2A LOF with clinical outcomes. 73% were PD-L1 positive (≥ 1%). 48% exhibited high TMB (≥ 10 mutations/megabase). CDKN2A LOF was present in 26% of patients and was associated with inferior PFS (multivariate hazard ratio [MVA-HR] 1.66, 95% CI 1.02-2.63, p = 0.041) and OS (MVA-HR 2.08, 95% CI 1.21-3.49, p = 0.0087) when compared to wild-type (WT) patients. These findings held in patients with high TMB (median OS, LOF vs. WT 10.5 vs. 22.3 months; p = 0.069) and PD-L1 ≥ 50% (median OS, LOF vs. WT 11.1 vs. 24.2 months; p = 0.020), as well as in an independent dataset. CDKN2A LOF vs. WT tumors were twice as likely to experience disease progression following ICB (46% vs. 21%; p = 0.021). CDKN2A LOF negatively impacts clinical outcomes in advanced NSCLC treated with ICB, even in high PD-L1 and high TMB tumors. This novel finding should be prospectively validated and presents a potential therapeutic target.

Measurable residual disease monitoring for patients with acute myeloid leukemia following hematopoietic cell transplantation using error corrected hybrid capture next generation sequencing.

Improved systems for detection of measurable residual disease (MRD) in acute myeloid leukemia (AML) are urgently needed, however attempts to utilize broad-scale next-generation sequencing (NGS) panels to perform multi-gene surveillance in AML post-induction have been stymied by persistent premalignant mutation-bearing clones. We hypothesized that this technology may be more suitable for evaluation of fully engrafted patients following hematopoietic cell transplantation (HCT). To address this question, we developed a hybrid-capture NGS panel utilizing unique molecular identifiers (UMIs) to detect variants at 0.1% VAF or below across 22 genes frequently mutated in myeloid disorders and applied it to a retrospective sample set of blood and bone marrow DNA samples previously evaluated as negative for disease via standard-of-care short tandem repeat (STR)-based engraftment testing and hematopathology analysis in our laboratory. Of 30 patients who demonstrated trackable mutations in the 22 genes at eventual relapse by standard NGS analysis, we were able to definitively detect relapse-associated mutations in 18/30 (60%) at previously disease-negative timepoints collected 20-100 days prior to relapse date. MRD was detected in both bone marrow (15/28, 53.6%) and peripheral blood samples (9/18, 50%), while showing excellent technical specificity in our sample set. We also confirmed the disappearance of all MRD signal with increasing time prior to relapse (>100 days), indicating true clinical specificity, even using genes commonly associated with clonal hematopoiesis of indeterminate potential (CHIP). This study highlights the efficacy of a highly sensitive, NGS panel-based approach to early detection of relapse in AML and supports the clinical validity of extending MRD analysis across many genes in the post-transplant setting.

Quantitative next-generation sequencing-based analysis indicates progressive accumulation of microsatellite instability between atypical hyperplasia/endometrial intraepithelial neoplasia and paired endometrioid endometrial carcinoma.

Atypical hyperplasia/endometrial intraepithelial neoplasia is an accepted precursor to endometrioid-type endometrial carcinoma. Mismatch repair-deficient endometrial carcinomas are also known to be a biologically and clinically distinct subset of tumors. However, the development of microsatellite instability in endometrial carcinogenesis has not yet been evaluated by novel next-generation sequencing-based methods. We examined 17 mismatch repair-deficient endometrioid endometrial carcinomas and their paired atypical hyperplasia/endometrial intraepithelial neoplasia precursors using a next-generation sequencing panel with quantitative microsatellite instability detection at 336 loci. Findings were compared to histological features, polymerase chain reaction-based microsatellite instability testing, immunohistochemical expression of mismatch repair proteins, and tumor mutational burden calculations. All 17 endometrial carcinomas and 8/17 atypical hyperplasia/endometrial intraepithelial neoplasia showed microsatellite instability by next-generation sequencing-based testing. Endometrial carcinoma specimens showed significantly more unstable microsatellite loci than paired atypical hyperplasia/endometrial intraepithelial neoplasia (mean: 40.0% vs 19.9 unstable loci, respectively). Out of nine microsatellite-stable atypical hyperplasia/endometrial intraepithelial neoplasia specimens, four showed mismatch repair loss by immunohistochemistry. All atypical hyperplasia/endometrial intraepithelial neoplasia and endometrial carcinoma specimens with microsatellite instability were also mismatch repair-deficient by immunohistochemistry. Tumor mutational burden was significantly greater in endometrial carcinoma than in paired atypical hyperplasia/endometrial intraepithelial neoplasia specimens, and tumor mutational burden was significantly correlated with percent unstable microsatellite loci. Paired atypical hyperplasia/endometrial intraepithelial neoplasia and endometrial carcinoma specimens show progressive accumulation of unstable microsatellite loci following loss of mismatch repair protein expression. Comprehensive next-generation sequencing-based testing of endometrial carcinomas offers new insights into endometrial carcinogenesis and opportunities for improved tumor surveillance, diagnosis, and management.

Which Objective Parameters Are Associated with a Positive Urine Culture in the Setting of Ureteral Calculi: The Ureteral Calculi Urinary Culture Calculator.

OBJECTIVE: To determine associations between laboratory values and subsequent culture positivity in the acute ureteral calculi patient. Specifically, we aim to develop a predictive model to assist with optimization of patient outcomes and improvement of antimicrobial stewardship. METHODS: Utilizing the electronic medical record system, we conducted a retrospective review of 3888 patients with ureteral calculi. Relevant demographic information, vital signs, and laboratory parameters obtained in the emergency department were tabulated. We applied a combination of analysis of variance and Pearson Fisher's Exact test for the analysis. RESULTS: A total of 3888 patients were included in the analysis of whom 3171 (81.6%) had a negative urine culture and 717 (18.4%) had a positive urine culture. Basic vital signs and laboratory parameters, such as heart rate, temperature, white blood cell (WBC) count, platelet count, and neutrophil differential only varied slightly in the positive and negative culture groups. Urinary nitrite was found to have specificity of 97.2% with a negative predictive value of 83.7%. Urinary leukocyte esterase was found to have a sensitivity of 86.8% and positive predictive value of 46.9%. On microscopy analysis, WBCs per high power field (WBCs/hpf) varied directly with likelihood of a positive urine culture; >150 WBCs/hpf had an 86.1% likelihood of positive urine culture. CONCLUSION: With the data provided from this large cohort analysis, we were able to create the ureteral calculi urinary culture calculator. With this calculator, urologists are better equipped to stratify a patient's risk of having a positive urine culture in the setting of a ureteral calculus.

Epididymal Cysts: Are They Associated With Infertility?

Scrotal sonography is commonly used for evaluation of the infertile male. While epididymal cysts are frequently observed during sonographic assessment, their presence has uncertain import. This study is a retrospective case-control sonographic and chart review comparison of infertile men and fertile volunteers to clarify the possible association of epididymal cysts and infertility. The study included 91 consecutively recruited patients from January 2012 to December 2014. The infertile group consisted patients with male factor infertility who underwent scrotal sonography ( n = 67). The fertile group consisted of men requesting vasectomy who were recruited for study involvement and consented to undergo scrotal sonography ( n = 24). The main outcome measure was infertility. The existence of epididymal cysts on scrotal sonography was the main risk factor. Predictably, the only sonographic findings associated with infertility were small testes (right: t(df = 89) = -2.52; left: t(df = 89) = -2.28, both p = .01) and the presence of a varicocele, χ2(df = 1) = 5.766 with p = .02. The infertile men were also younger and more likely to use alcohol. Of the 91 men studied, 71% demonstrated epididymal cysts (73% of infertile and 67% of fertile men). Epididymal cysts were not be associated with infertility, χ2(df = 1) = 0.362 with p = .55. This occurrence of epididymal cysts is the highest ever reported (71% of all men). While the occurrence of epididymal cysts in this cohort is unexplained, our observation that these cysts are not associated with infertility will be useful for those clinicians counseling patients observed to have these structures.

The limitations of simple gene set enrichment analysis assuming gene independence.

Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods.

Dermoid Cyst in a Multicystic Dysplastic Kidney: A Case Report and Literature Review.

Most multicystic dysplastic kidneys (MCDKs) are discovered prenatally. There is no consensus regarding initial workup and appropriate follow-up. We present a 9-year-old female who was fetally diagnosed with a MCDK and without follow-up returned with an 18-cm multicystic mass. The patient underwent laparoscopic nephrectomy. Final pathology revealed a dermoid cyst arising in a pediatric kidney, which to our knowledge has not been previously described. Patients with MCDK have hypertension as a possible sequela and possible reflux to their functioning kidney. Voiding cystourethrogram seems reasonable initially, and renal ultrasound is ideally noninvasive. Focused clinical awareness of the solitary kidney is important.

En Bloc Retroperitoneoscopic Removal of Horseshoe Kidney for End-stage Renal Disease.

Horseshoe kidney (HSK) is the most common renal fusion anomaly. There have been reports of an association of HSKs with medical renal disease. We report a case of a child with nephrotic-range proteinuria and a HSK. As the patient was on peritoneal dialysis, the entire HSK was removed en bloc via a retroperitoneoscopic approach with early postoperative reinitiation of peritoneal dialysis.

Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver.

Hepatocyte-enriched nuclear factor (HNF)6 and CUX2 are GH and STAT5-regulated homeobox transcription factors. CUX2 shows female-specific expression and contributes to liver sex differences by repressing many male-biased genes and inducing many female-biased genes, whereas HNF6 is expressed at similar levels in male and female liver. In cell-based transfection studies, CUX2 inhibited HNF6 transcriptional regulation of the sex-specific gene promoters CYP2C11 and CYP2C12, blocking HNF6 repression of CYP2C11 and HNF6 activation of CYP2C12. These inhibitory actions of CUX2 can be explained by competition for HNF6 DNA binding, as demonstrated by in vitro EMSA analysis and validated in vivo by global analysis of the HNF6 cistrome. Approximately 40 000 HNF6-binding sites were identified in mouse liver chromatin, including several thousand sites showing significant sex differences in HNF6 binding. These sex-biased HNF6-binding sites showed strong enrichment for correspondingly sex-biased DNase hypersensitive sites and for proximity to genes showing local sex-biased chromatin marks and a corresponding sex-biased expression. Further, approximately 90% of the genome-wide binding sites for CUX2 were also bound by HNF6. These HNF6/CUX2 common binding sites were enriched for genomic regions more accessible in male than in female mouse liver chromatin and showed strongest enrichment for male-biased genes, suggesting CUX2 displacement of HNF6 as a mechanism to explain the observed CUX2 repression of male-biased genes in female liver. HNF6 binding was sex independent at a majority of its binding sites, and HNF6 peaks were frequently associated with cobinding by multiple other liver transcription factors, consistent with HNF6 playing a global regulatory role in both male and female liver.

Sonographic assessment of the effect of vesicoureteral reflux and urinary tract infections on growth of the pediatric solitary kidney.

INTRODUCTION: Perusal of recent guidelines relating to proper evaluation of infants and children with urinary tract infection (UTI) suggests that the occurrence of vesicoureteral reflux (VUR) may not have the clinical import previously ascribed to this anatomic abnormality. Patients with a solitary kidney uniquely allow investigation of the effects of both vesicoureteral reflux (VUR) and urinary tract infection (UTI) on renal growth unencumbered with the inevitable questions of laterality that confound analysis in patients with two kidneys. Several previous studies with conflicting results have addressed whether vesicoureteral reflux (VUR) impacts ultimate renal size in children with a solitary kidney. Few published studies have considered the occurrence of both urinary tract infection (UTI) and VUR on the degree of compensatory hypertrophy. This is the largest series to date investigating the effect of both UTI and VUR on the degree of compensatory hypertrophy with time. OBJECTIVE: Our objective was to analyze sonographically determined renal growth in patients with a solitary kidney, stratifying for both the occurrence and severity of UTIs and the occurrence and severity of VUR. STUDY DESIGN: We retrospectively reviewed the clinical history (including bladder and bowel dysfunction (BBD)) and radiology reports of 145 patients identified as having either a congenital or acquired solitary kidney in our pediatric urology practice from the prior 10 years. UTIs were tabulated by severity, where possible, and the grade of VUR was recorded based on the initial cystogram. Sonographically determined renal length was tabulated for all ultrasounds obtained throughout the study. Based on a mixed-effects model, we investigated the influence of UTI and VUR on renal growth. RESULTS: Of the 145 patients analyzed, 105 had no VUR and 39 had VUR (16 = Gr I&II, 11 = GIII, 12 = GIV&V). Comparison showed that there was no difference in the occurrence of UTI between those without VUR (27/105 with UTI) and those with VUR (15/39 with UTI; p = 0.14). There was no difference in the occurrence of BBD in patients with VUR (15/39) and those without VUR (36/106, p = 0.62). While neither VUR nor UTI alone affected renal growth in the solitary kidney, the three-way interaction term among age, VUR, and UTI was significant (p = 0.016). The growth of the kidneys in the various patient groups is depicted in the table. From the analysis, a refluxing solitary kidney with UTI showed a significantly lower growth rate than the other groups (p < 0.001). DISCUSSION: This study is limited by the inherent selection bias of retrospective studies. Additionally, the variability of sonographic renal measurement is well recognized. Lastly, our sample size did not allow us to incorporate the severity of the UTIs and the grades of VUR in our final regression model. Nevertheless, the overall patterns suggest that when both VUR and UTI are present, the solitary kidney demonstrates less renal growth with time. Study of larger cohorts of patients with solitary kidneys will be necessary to confirm our observations and discern what, if any, are the consequences of high-grade VUR and upper tract UTI in these patients. CONCLUSION: In the largest series to date we were able to discern no independent effect of either VUR or UTI on sonographically determined renal growth in patients with a solitary kidney. However, UTI and VUR together result in kidneys that are smaller than other solitary kidneys not so affected. Follow-up studies of larger cohorts seem warranted to confirm these findings and discern the clinical import of these smaller kidneys.

Duration of urinary leakage after open non-stented dismembered pyeloplasty in pediatric patients.

OBJECTIVE: We aimed to determine the duration and associated complications of postoperative urinary leakage in pediatric patients undergoing open, non-stented dismembered pyeloplasty for ureteropelvic junction obstruction. METHODS: A retrospective review of 100 patients who underwent an open non-stented dismembered pyeloplasty between 2003 and 2008 was performed. Duration of urinary leakage and postoperative complications were tabulated. Patients were considered to have a dry anastomosis if the Penrose drain was removed within one week of surgery. RESULTS: Duration of leakage ranged from 0 to 27 days. 86% had Penrose drain removal within 7 days of surgery and were considered dry.14 patients demonstrated a persistent urinary leakage (PUL) ranging from 7 to 27 days. Complications of any type were significantly more likely in the group with prolonged drainage (p = .0126). UTI and obstruction were not significantly more likely to occur in patients with PUL (p = .0931 and p = .2616 respectively). Only one patient with PUL required placement of a ureteral stent. CONCLUSION: We demonstrate that stentless dismembered pyeloplasty is feasible with a low rate of urinary drainage beyond one week. The character and quality of the slightly increased complications in those that demonstrated PUL were not great and not bothersome enough to warrant routine stenting.