CD47-Dependent Regulation of Immune Checkpoint Gene Expression and MYCN mRNA Splicing in Murine CD8 and Jurkat T Cells

Elevated expression of CD47 in some cancers is associated with poor survival related to its function as an innate immune checkpoint when expressed on tumor cells. In contrast, elevated CD47 expression in cutaneous melanomas is associated with improved survival. Previous studies implicated protective functions of CD47 expressed by immune cells in the melanoma tumor microenvironment. RNA sequencing analysis of responses induced by CD3 and CD28 engagement on wild type and CD47-deficient Jurkat T lymphoblast cells identified additional regulators of T cell function that were also CD47-dependent in mouse CD8 T cells. MYCN mRNA expression was upregulated in CD47-deficient cells but downregulated in CD47-deficient cells following activation. CD47 also regulated alternative splicing that produces two N-MYC isoforms. The CD47 ligand thrombospondin-1 inhibited expression of these MYCN mRNA isoforms, as well as induction of the oncogenic decoy MYCN opposite strand (MYCNOS) RNA during T cell activation. Analysis of mRNA expression data for melanomas in The Cancer Genome Atlas identified a significant coexpression of MYCN with CD47 and known regulators of CD8 T cell function. Thrombospondin-1 inhibited the induction of TIGIT, CD40LG, and MCL1 mRNAs following T cell activation in vitro. Increased mRNA expression of these T cell transcripts and MYCN in melanomas was associated with improved overall survival.

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

Genome-wide transcriptional sequencing identifies novel mutations in metabolic genes in human hepatocellular carcinoma

We report on next-generation transcriptome sequencing results of three human hepatocellular carcinoma tumor/tumor-adjacent pairs. This analysis robustly examined ∼12,000 genes for both expression differences and molecular alterations. We observed 4,513 and 1,182 genes demonstrating 2-fold or greater increase or decrease in expression relative to their normal, respectively. Network analysis of expression data identified the Aurora B signaling, FOXM1 transcription factor network and Wnt signaling pathways pairs being altered in HCC. We validated as differential gene expression findings in a large data set containing of 434 liver normal/tumor sample pairs. In addition to known driver mutations in TP53 and CTNNB1, our mutation analysis identified non-synonymous mutations in genes implicated in metabolic diseases, i.e. diabetes and obesity: IRS1, HMGCS1, ATP8B1, PRMT6 and CLU, suggesting a common molecular etiology for HCC of alternative pathogenic origin.

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia

Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor outcome (Ph-like ALL). The genetic alterations that activate kinase signaling in Ph-like ALL are poorly understood. We performed transcriptome and whole genome sequencing on 15 cases of Ph-like ALL and identified rearrangements involving ABL1, JAK2, PDGFRB, CRLF2, and EPOR, activating mutations of IL7R and FLT3, and deletion of SH2B3, which encodes the JAK2-negative regulator LNK. Importantly, several of these alterations induce transformation that is attenuated with tyrosine kinase inhibitors, suggesting the treatment outcome of these patients may be improved with targeted therapy.

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

SUMMARY

Bambino is a variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. The variant detector takes advantage of SAM-specific annotations, and produces detailed output suitable for genotyping and identification of somatic mutations. The assembly viewer can display reads in the context of either a user-provided or automatically generated reference sequence, retrieve genome annotation features from a UCSC genome annotation database, display histograms of non-reference allele frequencies, and predict protein-coding changes caused by SNPs.

AVAILABILITY

Bambino is written in platform-independent Java and available from https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html, along with documentation and example data. Bambino may be launched online via Java Web Start or downloaded and run locally.

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma

Primary liver cancer is the third most common cause of cancer-related death worldwide, with a rising incidence in Western countries. Little is known about the genetic etiology of this disease. To identify genetic factors associated with hepatocellular carcinoma (HCC) and liver cirrhosis (LC), we conducted a comprehensive, genome-wide variation analysis in a population of unrelated Asian individuals. Copy number variation (CNV) and single nucleotide polymorphisms (SNPs) were assayed in peripheral blood with the high-density Affymetrix SNP6.0 microarray platform. We used a two-stage discovery and replication design to control for overfitting and to validate observed results. We identified a strong association with CNV at the T-cell receptor gamma and alpha loci (P < 1 × 10(-15)) in HCC cases when contrasted with controls. This variation appears to be somatic in origin, reflecting differences between T-cell receptor processing in lymphocytes from individuals with liver disease and healthy individuals that is not attributable to chronic hepatitis virus infection. Analysis of constitutional variation identified three susceptibility loci including the class II MHC complex, whose protein products present antigen to T-cell receptors and mediate immune surveillance. Statistical analysis of biologic networks identified variation in the "antigen presentation and processing" pathway as being highly significantly associated with HCC (P = 1 × 10(-11)). SNP analysis identified two variants whose allele frequencies differ significantly between HCC and LC. One of these (P = 1.74 × 10(-12)) lies in the PTEN homolog TPTE2.

CONCLUSION

Combined analysis of CNV, individual SNPs, and pathways suggest that HCC susceptibility is mediated by germline factors affecting the immune response and differences in T-cell receptor processing.

Systematic analysis of genetic alterations in tumors using Cancer Genome WorkBench (CGWB)

Systematic investigations of genetic changes in tumors are expected to lead to greatly improved understanding of cancer etiology. To meet the analytical challenges presented by such studies, we developed the Cancer Genome WorkBench (http://cgwb.nci.nih.gov), the first computational platform to integrate clinical tumor mutation profiles with the reference human genome. A novel heuristic algorithm, IndelDetector, was developed to automatically identify insertion/deletion (indel) polymorphisms as well as indel somatic mutations with high sensitivity and accuracy. It was incorporated into an automated pipeline that detects genetic alterations and annotates their effects on protein coding and 3D structure. The ability of the system to facilitate identifying genetic alterations is illustrated in three projects with publicly accessible data. Mutagenesis in tumor DNA replication leading to complex genetic changes in the EGFR kinase domain is suggested by a novel deletion-insertion combination observed in paired tumor-normal lung cancer resequencing data. Automated analysis of 152 genes resequenced by the SeattleSNPs group was able to identify 91% of the 1251 indel polymorphisms discovered by SeattleSNPs. In addition, our system discovered 518 novel indels in this data set, 451 of which were found to be valid by manual inspection of sequence traces. Our experience demonstrates that CGWB not only greatly improves the productivity and the accuracy of mutation identification, but also, through its data integration and visualization capabilities, facilitates identification of underlying genetic etiology.

Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach

High-density oligonucleotide arrays have become a popular assay for concurrent measurement of mRNA expression at the genome scale. Much effort has been devoted to the development of statistical analysis tools aimed at reducing experimental noise and normalizing experimental variation in gene expression analysis. However, these investigations do not detect or catalog systematic problems associated with specific oligonucleotide probes. Here, we present an investigation of problematic probes that yield consistent but inaccurate signals across multiple experiments. By evaluating data integrity among gene, probe sequence, and genomic structure we identified a total of 20,696 (10.5%) nonspecific probes that could cross-hybridize to multiple genes and a total of 18,363 (9.3%) probes that miss the target transcript sequences on the Affymetrix GeneChip U95A/Av2 array. The numbers of nonspecific and mistargeted probes on the U133A array are 29,405 (12.1%) and 19,717 (8.0%), respectively. The poor performance of the mistargeted probes was confirmed in two GeneChip experiments, in which these probes showed a 20-30% decrease in detecting present signals compared with normal probes. Comparison of qualitative expression signals obtained from SAGE and EST data with those from GeneChip arrays showed that the consistency of the two platforms is 30% lower in problematic probes than in normal probes. A Web application was developed to apply our results for improving the accuracy of expression analysis.

A high-resolution multistrain haplotype analysis of laboratory mouse genome reveals three distinctive genetic variation patterns

Understanding of the structure and the origin of genetic variation patterns in the laboratory inbred mouse provides insight into the utility of the mouse model for studying human complex diseases and strategies for disease gene mapping. In order to address this issue, we have constructed a multistrain, high-resolution haplotype map for the 99-Mb mouse Chromosome 16 using approximately 70,000 single nucleotide polymorphism (SNP) markers derived from whole-genome shotgun sequencing of five laboratory inbred strains. We discovered that large polymorphic blocks (i.e., regions where only two haplotypes, thus one SNP conformation, are found in the five strains), large monomorphic blocks (i.e., regions where the five strains share the same haplotype), and fragmented blocks (i.e., regions of greater complexity not resembling at all the first two categories) span 50%, 18%, and 32% of the chromosome, respectively. The haplotype map has 98% accuracy in predicting mouse genotypes in two other studies. Its predictions are also confirmed by experimental results obtained from resequencing of 40-kb genomic sequences at 21 distinct genomic loci in 13 laboratory inbred strains and 12 wild-derived strains. We demonstrate that historic recombination, intra-subspecies variations and inter-subspecies variations have all contributed to the formation of the three distinctive genetic signatures. The results suggest that the controlled complexity of the laboratory inbred strains may provide a means for uncovering the biological factors that have shaped genetic variation patterns.

Postoperative complication from hemostatic clips

Hemostatic clips were found in a patient's bladder four months after radical retropubic prostatectomy. A calculus, which had formed on one clip, caused acute urinary retention. Inadvertent enclosure of the hemoclips within the bladder intraoperatively and early intraurethral migration of the hemoclips are possible causes of this complication. Although this problem is rarely reported, hemoclips should be used sparingly, if at all, around the vesicourethral anastomosis.

The new ALR long cystoresectoscope system

A new long cystoresectoscope system recently has become available. This instrument has the distinct advantage of allowing cystoscopy and endoscopic surgery of the lower urinary tract in men with an unusually long urethra, or a semirigid or intracorporeal inflatable prosthesis.

Finney flexirod prosthesis

The experience gained from the implantation of 763 Flexirod Prosthesis is described. Special features of this design include a tapered distal tip which provides for better glans stability, a soft hinge which allows for improved penile concealment, and a trimmable tail which, together with preoperative measurement of the penis, allows the surgeon to determine the correct prothesis size well in advance of surgery. The surgical procedure is not difficult, the complication rate is low, device failure is extremely rare, and most patients are restored to a satisfactory sex life.

Urinary tract infection after transrectal needle biopsy of the prostate

After routine cleansing enemas 80 patients were randomized to undergo irrigation of the rectal vault with either povidone-iodine or saline. A transrectal prostatic needle biopsy then was performed. Antimicrobials were not used before biopsy and were only ordered after biopsy if fever developed or a positive urine culture was obtained. Over-all, 41 per cent of the patients had positive urine cultures post-biopsy and 44 per cent had febrile episodes. There was no significant difference between the group receiving the povidone-iodine versus those receiving saline irrigations.

Surgical management of "pus-pot" perineum

Ten cases of disabling "pus-pot" perineum secondary to hidradenitis suppurativa, urethral stricture disease, condyloma acuminatum and anoperineal fistula were treated by wide excision of involved tissues. In 7 men the testicles were transposed to thigh pouches, and in 3 the entire penile skin was excised and replaced with a skin graft.

Lack of value of routine preoperative bone and liver scans in cystectomy candidates

A retrospective review of 341 patients with bladder cancer revealed 58 candidates for cystectomy. These patients were evaluated preoperatively by radionuclide bone and/or liver scans in an attempt to increase the accuracy of clinical staging. In the face of a normal history, physical examination, liver function tests or serum alkaline phosphatase routine preoperative bone and liver scans in cystectomy candidates did not contribute significantly to clinical staging or choice of treatment. Since liver and bone scans add significantly to the cost of the illness their use should not be routine but reserved only for those special cases when they are indicated.

Evaluation of povidone-iodine as vesical irrigant for treatment and prevention of urinary tract infections

This is a preliminary study evaluating diluted solutions of povidone-iodine (PVP-I) as urinary bladder irrigants for the treatment and prevention of urinary tract infection. Diluted povidone-iodine solutions were used as indwelling catheter irrigants and as instillations into the urinary bladder following intermittent catheterization. The diluted PVP-I solutions had no efficacy in either the treatment or prevention of urinary tract infections when used as indwelling urethral or suprapubic catheter irrigants. There was a suggestion of a slight decrease in the incidence of urinary tract infections during the use of PVP-I in the intermittent catheterization group in this uncontrolled study, but the percentage of positive urine cultures was greater than desired. The absence of any unfavorable data has led us to conclude that the diluted PVP-I caused no undesirable side effects in any of the patients treated with this agent, PVP-I bladder irrigation warrants further investigation in special cases such as lower urinary tract fungal infections.

Finney hinged penile implant: experience with 100 cases

The flexirod hinged penile prosthesis was implanted in 100 patients: 21 through a perineal incision and 79 through a dorsal penile incision. Surgery via the dorsal approach is performed more easily and quickly, and produces less postoperative pain. The modified technique and results for the hinged implant are described. The complication rate was 5 per cent (4 per cent once the design of the prosthesis was finalized).

Glomerulonephritis and virus-like particles associated with prostatic cancer

A patient with carcinoma of the prostate and metastases developed the nephrotic syndrome following hormonal therapy. A decrease in the dose of estrogens was associated with decreased proteinuria, but when therapy was increased the nephrotic syndrome became more severe. Renal biopsy performed when proteinuria was present showed subendothelial electron dense deposits, complement by immunofluorescence, and a morphologic pattern of membranoproliferative glomerulonephritis. There was evidence of resorption of the deposits by endothelial cells. Microspherical particles resembling those described in prostatic cancer were found in the glomeruli. On the basis of previous reports it is concluded that circulating tumor antigen-antibody complexes produced glomerulonephritis, the severity of which was related to the amount of soluble antigen released by tumor cell destruction. Apparent phagocytosis of immune complexes by glomerular endothelial cells was believed to account for the reversibility of the nephrotic syndrome. The role of the virus-like particles in the process is as yet unclear.

New technique for percutaneous nephrostomy under ultrasound guidance

The 8F cystocath has been used as a temporary percutaneous nephrostomy. B-mode ultrasonography was used to determine the depth and direction of trocar placement after initial confirmation with a spinal needle. No immediate complications were noted in 10 successful insertions and there was only 1 failure of entry.

Experience with new double J ureteral catheter stent

Experience with a newly designed self-retaining silicone ureteral stent is presented. The stent is supplied in various lengths, has a J or hook molded into each end to prevent migration and has been designed specifically to be passed during an open operation as well as endoscopically. The device is used to provide free drainage to the bladder, reduce or eliminate urine leakage, provide stenting of the ureter and allow for earlier discharge from the hospital of patients without external catheters. In some cases the stent may be used instead of a nephrostomy tube to provide prolonged drainage with less chance of infection. It is removed easily in the outpatient facility by cystoscopy.

New hinged silicone penile implant

A new paired hinged silicone prosthesis is described. The hinge allows the penis to move freely and hang in a dependent position without constrictive clothing and permits satisfactory coitus. A conical tip more nearly conforms to the distal corpus and the proximal end may be trimmed during the operation to fit the individual patient.

Self-retaining loop nephrostomy

A self-retaining loop nephrostomy with an inflated balloon in the renal pelvis to prevent accidental extraction or displacement is described. An additional feature of this tube is a plug that may be positioned to promote maximal irrigation of the kidney with a stone solvent or to allow urine to flow from 1 or both ends of the loop.

Aortic aneurysm with retroperitoneal fibrosis and ureteral obstruction

Arteriosclerotic aneurysms of the abdominal aorta constitute a common clinical entity. Rarely are they associated with retroperitoneal fibrosis and ureteral obstruction requiring ureterolysis. Fifteen such cases have been reported, with resection successful in 5 of 7. A sixteenth case is presented complicated by the presence of a persistent left cardinal vein. It is the third aneurysm resected with such an anomaly, and to our knowledge the first to be associated with retroperitoneal fibrosis and ureteral obstruction. Ureterolysis with resection of the aneurysm was performed. The difficulties presented by these pathologic entities, as well as the anomalous venous pattern, are reviewed. Complete preoperative evaluation, including intravenous pyelogram, retrograde pyelography, aortography, and venacavography, for the definition of anatomic relationships and planning of the surgical approach is stressed.

Embryonal rhabdomyosarcoma of the prostate

Embryonal rhabdomyosarcoma of the prostate is typically a rare mesenchymal tumor of young boys, presenting with obstructive urinary symptoms or an abdominal mass. The origin is probably in undifferentiated mesenchymal cells that persist into adult life. Histologically, the tumor cells resemble normal muscle development in a 7 to 10-week fetus. Treatment is combined radical surgery and chemotherapy, and usually radiotherapy as well. The prognosis is extremely poor in all patients. Our case is added to the few in the literature in which this disease occurred in a man more than 50 years old.

Urethral strictures: treatment with intralesional steroids

A review of steroid management of urethral strictures is presented. The 96 patients were followed for a year or more after urethral injection with triamcinolone. Intralesional steroid may be used in many types of strictures but it is especially useful in those cases with strictures in the distal urethra or the meatus, those occurring after radical prostatectomy and in some cases when 1 or more urethroplasties have been done. Every practicing urologist can benefit from using stricture injection in selected cases.