Calyceal diverticula: Clinical, radiological and histopathological findings of an uncommon entity with presumed congenital origin.

Calyceal diverticula (CD) are relatively uncommon urologic conditions that generally follow an asymptomatic course and rarely require medical intervention. CD are thought to have a congenital origin due to abnormalities during the process of ureteral bud formation. Clinically and radiologically, they can mimic multiple neoplastic and non-neoplastic renal processes, with potentially relevant differences in the management of these patients. Symptoms are usually associated with the presence of stones, obstruction to the drainage of the diverticulum, large size, or secondary infection. In chronic cases, surgery might become necessary, creating an opportunity to examine the histopathological characteristics of this condition. Although these are benign in the majority of patients, some rare instances of malignancy arising from the CD have been reported. In this series, we addressed the clinical, radiological, and histopathological findings of CD.

The DNA sequence and biological annotation of human chromosome 1.

The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

Pembrolizumab plus azacitidine in patients with chemotherapy refractory metastatic colorectal cancer: a single-arm phase 2 trial and correlative biomarker analysis.

BACKGROUND: DNA mismatch repair proficient (pMMR) metastatic colorectal cancer (mCRC) is not responsive to pembrolizumab monotherapy. DNA methyltransferase inhibitors can promote antitumor immune responses. This clinical trial investigated whether concurrent treatment with azacitidine enhances the antitumor activity of pembrolizumab in mCRC. METHODS: We conducted a phase 2 single-arm trial evaluating activity and tolerability of pembrolizumab plus azacitidine in patients with chemotherapy-refractory mCRC (NCT02260440). Patients received pembrolizumab 200 mg IV on day 1 and azacitidine 100 mg SQ on days 1-5, every 3 weeks. A low fixed dose of azacitidine was chosen in order to reduce the possibility of a direct cytotoxic effect of the drug, since the main focus of this study was to investigate its potential immunomodulatory effect. The primary endpoint of this study was overall response rate (ORR) using RECIST v1.1., and secondary endpoints were progression-free survival (PFS) and overall survival (OS). Tumor tissue was collected pre- and on-treatment for correlative studies. RESULTS: Thirty chemotherapy-refractory patients received a median of three cycles of therapy. One patient achieved partial response (PR), and one patient had stable disease (SD) as best confirmed response. The ORR was 3%, median PFS was 1.9 months, and median OS was 6.3 months. The combination regimen was well-tolerated, and 96% of treatment-related adverse events (TRAEs) were grade 1/2. This trial was terminated prior to the accrual target of 40 patients due to lack of clinical efficacy. DNA methylation on-treatment as compared to pre-treatment decreased genome wide in 10 of 15 patients with paired biopsies and was significantly lower in gene promoter regions after treatment. These promoter demethylated genes represented a higher proportion of upregulated genes, including several immune gene sets, endogenous retroviral elements, and cancer-testis antigens. CD8+ TIL density trended higher on-treatment compared to pre-treatment. Higher CD8+ TIL density at baseline was associated with greater likelihood of benefit from treatment. On-treatment tumor demethylation correlated with the increases in tumor CD8+ TIL density. CONCLUSIONS: The combination of pembrolizumab and azacitidine is safe and tolerable with modest clinical activity in the treatment for chemotherapy-refractory mCRC. Correlative studies suggest that tumor DNA demethylation and immunomodulation occurs. An association between tumor DNA demethylation and tumor-immune modulation suggests immune modulation and may result from treatment with azacitidine. Trial registration ClinicalTrials.gov, NCT02260440. Registered 9 October 2014, https://clinicaltrials.gov/ct2/show/NCT02260440 .

Cytomorphology of Erdheim-Chester disease presenting as a retroperitoneal soft tissue lesion.

Erdheim-Chester disease (ECD) is a rare, multisystem disorder of macrophages. Patients manifest with histiocytic infiltrates that lead to xanthogranulomatous lesions in multiple organ systems. The cytologic features of this disorder are not well characterized. As a result, the cytologic diagnosis of ECD can be very challenging. The aim of this report is to describe the cytomorphology of ECD in a patient presenting with a retroperitoneal soft tissue lesion. A 54-year-old woman with proptosis and diabetes insipidus was found on imaging studies to have multiple intracranial lesions, sclerosis of both femurs and a retroperitoneal soft tissue mass. Fine needle aspiration (FNA) and a concomitant core biopsy of this abnormal retroperitoneal soft tissue revealed foamy, epithelioid and multinucleated histiocytes associated with fibrosis. The histiocytes were immunoreactive for CD68, CD163, Factor XIIIa and fascin, and negative for S100, confirming the diagnosis of ECD. ECD requires a morphologic diagnosis that fits with the appropriate clinical context. This case describes the cytomorphologic features of ECD and highlights the role of cytology in helping reach a diagnosis of this rare disorder.

DNA sequence and analysis of human chromosome 9.

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

The DNA sequence and comparative analysis of human chromosome 10.

The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.

The DNA sequence and analysis of human chromosome 6.

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

The DNA sequence and analysis of human chromosome 13.

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Lessons learned from clinical trial queries on small biopsy collections: importance of rapid on-site evaluation.

INTRODUCTION: Small biopsies and cytology specimens have become increasingly important for clinical trials and biomarker testing. Thus, institutions must ensure that adequate lesional material meeting the specifications for a multitude of different protocols is available. This can be achieved using rapid on-site evaluation (ROSE). The aim of the present study was to determine the recent clinical trial biopsy characteristics and study the feedback on these collections at our institution. MATERIALS AND METHODS: Clinical trial biopsies performed at our institution and trial feedback (including "queries") were analyzed from the 2017 to 2019. The query data were reviewed in detail, in addition to any protocol modifications related to biopsy requirements and study protocol changes. RESULTS: A total of 698 biopsy collections were performed for clinical trial purposes for 95 trials, with most requiring biopsies at >1 time point (63.2%), for phase I or II trials (92.6%), and for specific tumor types (67.4%). Only 18 of the trials (18.9%) requiring fresh tissue biopsies provided feedback. The feedback included data from 90 cases (12.9%), of which 27 (30.0%) had queries regarding insufficient (n = 10; 37.0%) or borderline (n = 17; 63.0%) tumor tissue. Only 1 (3.7%) of these had had ROSE by cytology. ROSE was performed in accordance with institutional guidelines (45.3%), as required by the study (1.1%), or because of trial modification (5.3%). CONCLUSIONS: The present investigation has shown the high volume of clinical trial biopsies managed at our academic cancer center. Feedback from the trials was low at 18.9% and frequently involved suboptimal cases without ROSE used at acquisition. This has led to more widespread adoption of ROSE to mitigate insufficient biopsy specimens and repeat procedures. The high volume of clinical trial biopsies and variability in trial needs necessitates a collaborative multidisciplinary network, including cytology services, to facilitate these important biopsies for patients with cancer.

Clinical trial cytology: Use of on-site evaluation of small biopsy and FNA samples for clinical trials and biomarker research studies.

BACKGROUND: After increased requests for biopsies for clinical trials and biomarker research, the University of Pittsburgh Medical Center created a clinical trial research service that partnered pathology, radiology, and medicine to facilitate rapid on-site evaluation (ROSE) of fine-needle aspiration (FNA) and/or core needle biopsy (CNB) samples to confirm the presence of tumor in these studies. METHODS: Clinical trial coordinators organized biopsies for patients needing tumor samples for trials, and informed the cytopathology and radiology team. ROSE was performed to confirm the presence of sufficient tumor in FNA specimens and/or touch preparations of CNB. RESULTS: A total of 79 cases from a total of 14 clinical trials were evaluated with ROSE, 77 of which (97%) were for research only. There were 53 cases (67%) from breast/ovarian cancer studies that were initiated between 2008 and 2009, whereas 26 cases (33%) included a variety of other tumors for studies that were started between 2011 and 2014. The majority required CNB samples (60 cases; 76%), 20% of which used an FNA for needle placement before obtaining CNB material and 56% of which had touch preparations of the CNB evaluated without a preceding FNA. The concordance rate for ROSE with final adequacy of the sample was 96% to 100%. CONCLUSIONS: The study institution has experienced an increase in the number of clinical trial studies requesting ROSE to confirm the presence of tumor in a variety of malignancies. Cytology laboratories can help with patient care by offering ROSE to determine the adequacy of clinical trial material to minimize the submission of unsatisfactory or nonrepresentative material. Developing a clinical research service enhances communication and the processing of novel research specimens for cancer patients. Cancer Cytopathol 2018. © 2018 American Cancer Society.

Gemcitabine/nab-paclitaxel as second-line therapy following FOLFIRINOX in metastatic/advanced pancreatic cancer-retrospective analysis of response.

BACKGROUND: Given the tolerability of nPG in first-line therapy, we desired to evaluate the response and toxicity profiles of second-line gemcitabine with nab-paclitaxel (nPG) following FOLFIRINOX. Methods: We retrospectively identified 30 patients who received first-line FOLFIRINOX for unresectable or metastatic pancreatic adenocarcinoma followed by second-line nPG. Response was evaluated by RECIST criteria and carbohydrate antigen 19-9 (CA19-9) change. RESULTS: Median age was 63 years with 77% percent having metastatic disease. Nineteen patients (63%) achieved PR based on CA19-9. Median overall survival (OS) with nPG was 12.4 months (mo) and median progression-free survival (PFS) was 3.7 mo. Median PFS and OS for patients with at least stable CA19-9 were 4.7 and 13.9 mo since initiation of nPG. Patients with an increased CA19-9 level during nPG had a shorter median PFS (1.4 mo) and OS (5.3 mo). A significant PFS difference was demonstrated in patients with at least stable disease as the best RECIST response versus in those with progressive disease (5.4 vs. 1.9 mo, P<0.001). Grade 3/4 adverse events include thrombocytopenia (33%), anemia (23%), nausea (17%), lymphopenia (7%), infectious complications (6%), diarrhea (3%), and neuropathy (3%). CONCLUSIONS: This study demonstrates a clinical benefit of second-line nPG. The study also suggests a possible use of CA19-9 to predict response to therapy.

Percutaneous computed tomography-guided gastric remnant access after laparoscopic Roux-en-Y gastric bypass.

BACKGROUND: The bypassed portion of the stomach is difficult to access and evaluate after Roux-en-Y gastric bypass. Access to the excluded stomach may be needed for nutritional support or decompression owing to acute distension and obstruction. We report our experience with percutaneous, computed tomography (CT)-guided gastrostomy tube placement into the gastric remnant after laparoscopic Roux-en-Y gastric bypass (LRYGB). METHODS: Of 569 consecutive LRYGB procedures performed, 9 patients underwent successful percutaneous, CT-guided gastrostomy placement. One additional patient was referred from another facility. We reviewed the indications, interval from surgery to the intervention, interval to removal, complications, and success or outcome of the procedure in our patient population. RESULTS: Ten patients underwent percutaneous, CT-guided gastric remnant gastrostomy tube placement. The indications included distended gastric remnant in 6, nutritional access in 4, and remnant drainage after leak in 1. Of the 10 patients, 2 had undergone previous gastric operations. The attempt at percutaneous gastrostomy was unsuccessful in 1 additional patient, who subsequently required laparoscopic gastrostomy (success rate 91%). CONCLUSION: In selected patients after LRYGB, CT-guided gastrostomy tube placement is safe and efficient. It may be used to manage complications of LRYGB, serve as a bridge to definitive surgery, or offer a convenient route for enteral nutritional support.

Chloramphenicol in aqueous humor after topical application.

Chloramphenicol 0.5% ophthalmic solution was applied topically to patients at various times before cataract surgery. The aqueous humor was obtained at the time of surgery and analyzed for chloramphenicol content by thin-layer chromatography. Aqueous humor chloramphenicol levels ranged from 3.5mn-g/ml to 6.7mn-g/ml at the initial sampling period one to two hours following topical administration. Chloramphenicol was measurable in samples for up to five hours following administration. The compound measured in the aqueous humor samples was chemically identified as intact chloramphenicol, and no metabolites of chloramphenicol were shown.

Multicenter trial of an intraocular hydrogel lens implant.

Several features suggest that hydrogels may have potential advantages as an intraocular lens material. The IOGEL lens is a single piece hydrogel composed of 38% poly HEMA. Clinical experience with the IOGEL lens in Australia has been published, and the safety and efficacy of the lens is currently being investigated in a multicenter trial in Europe, the U.S.A., Canada, Australia, and Japan. This is the first large-scale study of a hydrogel implant. The IOGEL lens clinical study was initiated in May 1986 in Europe, in September 1986 in the U.S.A., and in November 1986 in Canada and Australia. The enrollment progress in May 1987 showed that 501 cases had been implanted in Europe, Canada, and Australia and 100 cases in the U.S.A. The visual acuity outcome is equivalent to that reported in the literature. Patients in the multinational trial achieved 20/40 or better in 86% of cases and in 96% of cases excluding unrelated pathologies. Although hydrogels have only had limited use in the clinical situation, the results of this study suggest that the IOGEL lens is a viable alternative to polymethylmethacrylate lens implants.

Comparison of SSPL90 selection procedures.

Recommended SSPL90 values were determined at 500, 1000, and 2000 Hz for 16 subjects with mild-to-moderate sensorineural hearing losses using six different selection procedures, including an Upper Limit of Comfortable Listening (ULCL) and threshold-based procedure by Cox (1988), a threshold-based procedure by Seewald and Ross (1988), and loudness discomfort procedures by Berger (1988), McCandless and Lyregaard (1983), and Hawkins et al (1987) and Libby (1985). Statistically significant differences were found among the procedures at 500 and 2000 Hz. Analysis of individual data showed that while some subjects obtained similar recommended SSPL90s across the procedures, others showed dramatically different values.