Genetic changes in the evolution of multidrug resistance for cultured human ovarian cancer cells

The multidrug resistant (MDR) phenotype is often attributed to the activity of ATP-binding cassette (ABC) transporters such as P-glycoprotein (ABCB1). Previous work has suggested that modulation of MDR may not necessarily be a single gene trait. To identify factors that contribute to the emergence of MDR, we undertook integrative genomics analysis of the ovarian carcinoma cell line SKOV3 and a series of MDR derivatives of this line (SKVCRs). As resistance increased, comparative analysis of gene expression showed conspicuous activation of a network of genes in addition to ABCB1. Functional annotation and pathway analysis revealed that many of these genes were associated with the extracellular matrix and had previously been implicated in tumor invasion and cell proliferation. Further investigation by whole genome tiling-path array CGH suggested that changes in gene dosage were key to the activation of several of these overexpressed genes. Remarkably, alignment of whole genome profiles for SKVCR lines revealed the emergence and decline of specific segmental DNA alterations. The most prominent alteration was a novel amplicon residing at 16p13 that encompassed the ABC transporter genes ABCC1 and ABCC6. Loss of this amplicon in highly resistant SKVCR lines coincided with the emergence of a different amplicon at 7q21.12, which harbors ABCB1. Integrative analysis suggests that multiple genes are activated during escalation of drug resistance, including a succession of ABC transporter genes and genes that may act synergistically with ABCB1. These results suggest that evolution of the MDR phenotype is a dynamic, multi-genic process in the genomes of cancer cells.

Public databases and software for the pathway analysis of cancer genomes

The study of pathway disruption is key to understanding cancer biology. Advances in high throughput technologies have led to the rapid accumulation of genomic data. The explosion in available data has generated opportunities for investigation of concerted changes that disrupt biological functions, this in turns created a need for computational tools for pathway analysis. In this review, we discuss approaches to the analysis of genomic data and describe the publicly available resources for studying biological pathways.

Effect of active smoking on the human bronchial epithelium transcriptome

Background

Lung cancer is the most common cause of cancer-related deaths. Tobacco smoke exposure is the strongest aetiological factor associated with lung cancer. In this study, using serial analysis of gene expression (SAGE), we comprehensively examined the effect of active smoking by comparing the transcriptomes of clinical specimens obtained from current, former and never smokers, and identified genes showing both reversible and irreversible expression changes upon smoking cessation.

Results

Twenty-four SAGE profiles of the bronchial epithelium of eight current, twelve former and four never smokers were generated and analyzed. In total, 3,111,471 SAGE tags representing over 110 thousand potentially unique transcripts were generated, comprising the largest human SAGE study to date. We identified 1,733 constitutively expressed genes in current, former and never smoker transcriptomes. We have also identified both reversible and irreversible gene expression changes upon cessation of smoking; reversible changes were frequently associated with either xenobiotic metabolism, nucleotide metabolism or mucus secretion. Increased expression of TFF3, CABYR, and ENTPD8 were found to be reversible upon smoking cessation. Expression of GSK3B, which regulates COX2 expression, was irreversibly decreased. MUC5AC expression was only partially reversed. Validation of select genes was performed using quantitative RT-PCR on a secondary cohort of nine current smokers, seven former smokers and six never smokers.

Conclusion

Expression levels of some of the genes related to tobacco smoking return to levels similar to never smokers upon cessation of smoking, while expression of others appears to be permanently altered despite prolonged smoking cessation. These irreversible changes may account for the persistent lung cancer risk despite smoking cessation.

Comprehensive serial analysis of gene expression of the cervical transcriptome

Background

More than half of the approximately 500,000 women diagnosed with cervical cancer worldwide each year will die from this disease. Investigation of genes expressed in precancer lesions compared to those expressed in normal cervical epithelium will yield insight into the early stages of disease. As such, establishing a baseline from which to compare to, is critical in elucidating the abnormal biology of disease. In this study we examine the normal cervical tissue transcriptome and investigate the similarities and differences in relation to CIN III by Long-SAGE (L-SAGE).

Results

We have sequenced 691,390 tags from four L-SAGE libraries increasing the existing gene expression data on cervical tissue by 20 fold. One-hundred and eighteen unique tags were highly expressed in normal cervical tissue and 107 of them mapped to unique genes, most belong to the ribosomal, calcium-binding and keratinizing gene families. We assessed these genes for aberrant expression in CIN III and five genes showed altered expression. In addition, we have identified twelve unique HPV 16 SAGE tags in the CIN III libraries absent in the normal libraries.

Conclusion

Establishing a baseline of gene expression in normal cervical tissue is key for identifying changes in cancer. We demonstrate the utility of this baseline data by identifying genes with aberrant expression in CIN III when compared to normal tissue.

Whole-genome analysis and HLA genotyping of enteropathy-type T-cell lymphoma reveals 2 distinct lymphoma subtypes

BACKGROUND & AIMS

Enteropathy-type T-cell lymphoma (ETL) is an aggressive extranodal T-cell non-Hodgkin lymphoma assumed to arise in the setting of celiac disease.

METHODS

To precisely define the genetic alterations underlying the pathogenesis of ETL, 30 ETL samples were profiled for genetic copy number alterations using high-resolution whole-genome tiling path array comparative genomic hybridization. To investigate the potential association of genetic alterations in ETL with celiac disease, HLA-DQB1 genotyping was performed.

RESULTS

By array comparative genomic hybridization, 13 novel recurrent minimal regions of chromosomal alteration were identified on multiple chromosome arms. ETL is characterized by frequent complex gains of 9q31.3-qter (70% of cases), or by an almost mutually exclusive 2.5-megabase loss of 16q12.1 (23% of cases). Two distinct groups of ETL could be delineated morphologically and genetically: type 1 ETL is characterized by nonmonomorphic cytomorphology, CD56 negativity, and chromosomal gains of 1q and 5q. Type 1 ETL also appears to be linked pathogenetically to celiac disease, sharing genetic alterations and HLA-DQB1 genotype patterns with (refractory) celiac disease. Type 2 ETL shows monomorphic small- to medium-sized tumor cell morphology, frequently shows CD56 expression, MYC oncogene locus gain, and rare gains of chromosomes 1q and 5q. In contrast to type 1 ETL, type 2 ETL shows a HLA-DQB1 genotype pattern more resembling that of the normal Caucasian population.

CONCLUSIONS

Contrary to current clinical classification, ETL comprises 2 morphologically, clinically, and genetically distinct lymphoma entities. In addition, type 2 ETL may not be associated with celiac disease.

Computational methods for the analysis of array comparative genomic hybridization

Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.

SIGMA: a system for integrative genomic microarray analysis of cancer genomes

BACKGROUND

The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes.

RESULTS

We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types.

CONCLUSION

In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA) of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression

A description of the transcriptome of human bronchial epithelium should provide a basis for studying lung diseases, including cancer. We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based on a vast dataset of nearly two million sequence tags from 21 serial analysis of gene expression (SAGE) libraries from individuals with a history of smoking. Our analysis suggests that the transcriptome of the bronchial epithelium is distinct from that of lung parenchyma and other tissue types. Moreover, our analysis has identified novel bronchial-enriched genes such as MS4A8B, and has demonstrated the use of SAGE for the discovery of novel transcript variants. Significantly, gene expression associated with ciliogenesis is evident in bronchial epithelium, and includes the expression of transcripts specifying axonemal proteins DNAI2, SPAG6, ASP, and FOXJ1 transcription factor. Moreover, expression of potential regulators of ciliogenesis such as MDAC1, NYD-SP29, ARMC3, and ARMC4 were also identified. This study represents a comprehensive delineation of the bronchial and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical genes expressed in the human lung, and constitutes one of the largest human SAGE studies reported to date.

Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

Array comparative genomic hybridization (array CGH) is a method used to detect segmental DNA copy number alterations. Recently, advances in this technology have enabled high-resolution examination for identifying genetic alterations and copy number variations on a genome-wide scale. This review describes the current genomic array platforms and CGH methodologies, highlights their applications for studying cancer genetics, constitutional disease and human variation, and discusses visualization and analytical software programs for computational interpretation of array CGH data.

Differential disruption of cell cycle pathways in small cell and non-small cell lung cancer

Lung cancer is the leading cause of cancer-related mortality in the world, with small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC) comprising the two major cell types. Although these cell types can be distinguished readily at the histological level, knowledge of their underlying molecular differences is very limited. In this study, we compared 14 SCLC cell lines against 27 NSCLC cell lines using an integrated array comparative genomic hybridisation and gene expression profiling approach to identify subtype-specific disruptions. Using stringent criteria, we have identified 159 of the genes that are responsible for the different biology of these cell types. Sorting of these genes by their biological functions revealed the differential disruption of key components involved in cell cycle pathways. Our novel comparative combined genome and transcriptome analysis not only identified differentially altered genes, but also revealed that certain shared pathways are preferentially disrupted at different steps in these cell types. Small cell lung cancer exhibited increased expression of MRP5, activation of Wnt pathway inhibitors, and upregulation of p38 MAPK activating genes, while NSCLC showed downregulation of CDKN2A, and upregulation of MAPK9 and EGFR. This information suggests that cell cycle upregulation in SCLC and NSCLC occurs through drastically different mechanisms, highlighting the need for differential molecular target selection in the treatment of these cancers.

Bone bruising of the knee

Bone bruising demonstrated by MRI is discussed with histological findings and proposed classifications. The effects of the mechanism of injury on bone bruising at the knee and the natural history of the process are reviewed. The relationship of bone bruising to osteochondral sequelae and to osteoarthritis are considered.

A novel approach in treating recurrent bilateral hepaticojejunostomy biliary strictures post-liver transplantation: Successful use of Simpson's atherectomy device

Biliary complications occur in 6% to 34% of patients who undergo orthotopic liver transplantation. Strictures at the anastomosis site or elsewhere in the biliary tract are common. These strictures are amenable to interventional radiological and surgical procedures; however, retransplantation is sometimes an inevitable outcome. An 8-year-old boy received combined liver and kidney transplants May 31, 1998. Hepatic artery thrombosis was diagnosed postoperative day 1 and treated with revascularization. The choledochojejunostomy was revised twice and resulted in a high hepaticojejunostomy. Significant strictures on both the right and left hepatic ducts at the anastomosis site were unsuccessfully treated by multiple interventional radiological procedures. The option of retransplantation was seriously explored. Simpson's atherectomy device was used in a novel approach February 24, 1999, and strictures on both ducts were successfully treated. At 1-year postprocedure, the patient has normal liver function with no evidence of recurrence of the strictures. Further experience with this novel technique is required to assess its role in treating biliary strictures post liver transplantation.

Inhibited neutrophil apoptosis: proteasome dependent NF-kappaB translocation is required for TRAF-1 synthesis

Neutrophil (PMN) apoptosis regulates local and systemic inflammation during sepsis. Tumor necrosis factor receptor-associated factors (TRAFs) have been implicated as mediators of apoptosis; however, the signaling pathways for their production in stimulated PMN are unclear. We hypothesize that NF-kappaB translocation is necessary for the induction of TRAF-1 in PMNs with prolonged survival. Neutrophils were isolated from the blood of healthy volunteers by Ficoll gradient centrifugation and red blood cell sedimentation. Neutrophil NF-kappaB was inhibited with a proteasome inhibitor, PSI-I. Cells were treated with PSI-I (30 microM) or vehicle (DMSO 0.2%) for 50 min then incubated over an 18-h time course with LPS (10 to 1000 ng/mL), tumor necrosis factor alpha (TNFalpha) (2 to 20 ng/mL) or control media. In vitro apoptosis was quantified by propidium iodide FACS analysis. Total cellular TRAF-1 was detected by Western blot analysis of cell lysates. Steady state TRAF-1 mRNA was detected by RPA. NF-kappaB activity was determined by Western blot analysis for nuclear p65. Means and standard errors were calculated; data were analyzed by ANOVA. Lipopolysaccharide (LPS) and TNFalpha increased PMN nuclear p65 and steady state TRAF-1 mRNA. Apoptosis was inhibited by TNFalpha and LPS at 12 and 18 h (P < 0.01). Incubation of cells in the NF-kappaB inhibitor PSI-I blocked LPS and TNFalpha-induced inhibition of apoptosis (P < 0.05) and the induction of both nuclear p65 and TRAF-1 mRNA. These data demonstrate that inhibition of PMN apoptosis and TRAF-1 induction by LPS and TNFalpha is NF-kappaB dependent.

Acceptance of an ABO-incompatible mismatched (AB(+) to O(+)) liver allograft with the use of daclizumab and mycophenolate mofetil

Liver allograft survival rates of 50% to 60% are reported in blood group A, group B, group O (ABO)-incompatible mismatched grafts even when aggressive immunosuppressive protocols, including plasmapheresis, OKT(3), cyclophosphamide, cyclosporine, prostaglandin E(1), and steroids, are used. A 59-year-old woman, blood type O(+), required emergency retransplantation posttransplantation day 2 because of primary nonfunction of the liver allograft. A blood type AB(+) allograft was used. Induction immunosuppressive therapy included tacrolimus, mycophenolate mofetil, OKT(3) (muromonab-CD(3)), steroids, and prostaglandin E(1). In addition, plasmapheresis was performed daily for 9 days. OKT(3) and prostaglandin E(1) were also discontinued postoperative day 9. Biopsy-proven acute cellular rejection was diagnosed postoperative day 12 and was treated with double-dose OKT(3) (10 mg) for another 6 days. On the day OKT(3) was discontinued, daclizumab, 60 mg, was administered intravenously. This dose was repeated every 2 weeks for a total of 5 doses. At 1-year follow-up, the patient is doing very well with normal liver function. We are unaware of previous reports of the use of daclizumab and mycophenolate mofetil as part of an immunosuppressive protocol aimed to induce acceptance of ABO-incompatible mismatched liver allografts. Based on our experience with this case, it seems that mycophenolate mofetil is an adequate replacement for cyclophosphamide. We also believe daclizumab provided adequate protection at a critical time. Further experience with both these drugs is required to establish their role in ABO-incompatible mismatched liver allografts.

Fos in the suprachiasmatic nucleus of house mouse lines that reveal a different phase-delay response to the same light pulse

Increased light intensity of a 5-min light pulse is positively correlated with Fos mRNA and Fos protein levels in the suprachiasmatic nucleus (SCN) of hamsters. These findings suggest that the level of Fos activation is proportional to the light intensity and that the magnitude of the phase-shift response depends on the level of Fos activation. However, to what extent different phase-delay responses to the same light pulse are mediated by differential Fos activation is unknown. To elucidate this, the authors used selected house mouse lines that reveal an almost threefold difference in phase-delay responses in constant darkness (DD) between circadian time (CT) 16 and CT 20 to the same light pulse. The authors measured wheel-running activity and subjected male mice of these lines to a 15-min light pulse at CT 16 after 2 weeks in DD. The behavioral response was measured and 10 to 12 days later the animals were again subjected to the same light pulse at CT 16. One hour after the start of the second light pulse, the animals were sacrificed for Fos immunocytochemistry. Results indicate a significant difference between the lines in the phase-delay response (F2,26 = 5.112, p < 0.017) and the level of Fos activation (F2,26 = 27.15, p < 0.0001) after a 15-min light pulse at CT 16. These findings support the hypothesis that the magnitude of the phase-delay response is proportional to the number of cells in the SCN that exhibit Fos induction after the same 15-min light pulse at CT 16 in DD. It also indicates a possible difference in the input pathways among the lines.

A case controlled study of laparoscopic incisional hernia repair

BACKGROUND

Although the feasibility of laparoscopic incisional herniorrhaphy has been demonstrated, its advantages over the open technique are still unproven.

METHODS

Fourteen consecutive laparoscopic incisional hernia repairs were compared with 14 matched controls of the open repair done by the same surgeon at the same institution. The controls were selected by a medical record technician not connected with the study. The cases were selected to match diagnoses, ASA status, and body weight as closely as possible. The outcome data for operating time, blood loss, hospitalization, resumption of oral intake, and postoperative complications were analyzed for statistically significant differences.

RESULTS

There was no statistical difference between the two groups in the parameters of blood loss, hospital days, or days to oral intake. The laparoscopic operation took 40% longer. Similar complications were seen in both groups. No mortality or early recurrences occurred in either group.

CONCLUSION

Laparoscopic incisional hernia repair of at least moderate complexity had no demonstrable advantage over the open repair in the present study.

Intravascular ultrasonic analysis of plaque characteristics associated with coronary artery remodeling

We sought to determine the patient and plaque characteristics associated with the different forms of arterial remodeling as seen by intravascular ultrasound (IVUS) before coronary intervention. Remodeling in response to plaque accumulation may occur in the form of compensatory enlargement and/or focal vessel contraction. Previous studies report variation in the frequency and form of arterial remodeling. We performed preintervention IVUS imaging on 169 patients. Vessels were categorized as exhibiting compensatory enlargement or focal contraction if the arterial area at the lesion was larger or smaller, respectively, than both proximal and distal reference arterial areas; otherwise the artery was considered not to have undergone significant remodeling. Calcification was assessed and noncalcified plaque density was measured by videodensitometry. Sixty-one of 169 patients (66 narrowings) (46 men and 15 women, age 56+/-11 years) had adequate reference segments. Remodeling occurred in 43 of 66 patients (65%): compensatory enlargement in 27 of 66 (41%) and focal contraction in 16 of 66 (24%). Lesions with focal contraction had significantly smaller arterial area (13.3+/-3.3 vs. 18.1+/-7.0 mm2, p = 0.02) and plaque area (9.5+/-2.8 vs 13.7+/-5.5 mm2, p<0.01). Cross-sectional stenosis was similar (71+/-9% vs. 75+/-10%, p = NS), as was plaque density (p = 0.20), eccentricity, and calcium. Patient age, gender, and lesion location were not related to the form of remodeling. Similarly, history of diabetes, hypercholesterolemia, or hypertension was not predictive. Smoking was the only risk factor associated with focal contraction (p<0.01). Thus, whereas compensatory enlargement appears to be the most common form of coronary artery remodeling, focal contraction occurs more often in smokers.

Long-term clinical results and quality of life after insertion of a self-expanding flexible endourethral prosthesis

OBJECTIVE

To evaluate the safety and efficacy of the Urolume self-expanding flexible endourethral stent, based on a long-term follow-up, and to determine its role amongst the various modalities of treatment available for the relief of bladder outlet obstruction (BOO) arising from benign prostatic hyperplasia (BPH).

PATIENTS AND METHODS

From January 1991 to April 1992, the Urolume wallstent (American Medical Systems, USA) was placed successfully in each of 62 patients (aged 50-89 years) who had significant subjective and objective evidence of BOO. The stent was placed as a daycase procedure under general anaesthesia. Pre-operatively, each patient was assessed fully in an out-patient clinic by symptoms, a flow rate measurement and a rectal examination. Post-operatively, patients were assessed using transrectal ultrasonography, cystoscopy, symptoms and flow rate measurement, and after 5 years, the International Prostate Symptom Score and satisfaction score were obtained.

RESULTS

After 5 years, 27 (39%) patients survived and 10 (14%) died with their Urolume stent intact; 22 (32%) completed the follow-up and five refused or were lost to follow-up. Day and night-time frequencies and flow rates improved continuously. Complete epithelialization occurred in 16 of the 22 patients assessed. Of those in whom the Urolume was removed, 20 are alive and five dead.

CONCLUSION

The effectiveness of the Urolume in improving symptoms and flow rates in patients with BPH was confirmed. However, the high failure rate arose largely from inexperience in selection and deployment. There are no absolute criteria to predict a successful outcome. This study confirms the Urolume as a safe device. Most patients whose symptoms settled in the first year maintained a good flow rate and a significant improvement in symptoms for 5 years; their quality of life at the last follow-up was good.

Malignant mesothelioma of the tunica vaginalis testis diagnosed by aspiration cytology--a case report with review of literature

A case of malignant mesothelioma of the tunica vaginalis testis diagnosed by preoperative cytology of hydrocele fluid is reported. In our view this is only the second case diagnosed by preoperative cytology. The unique feature of this case, the characteristic ultrasound appearance, was recognized and confirmation by aspiration cytology led directly to radical orchiectomy, thus avoiding hydrocelectomy, hemiscrotectomy and possible local recurrence. Aetiopathogenesis and management options of this rare tumour are discussed, with a review of the literature.

Management of major biliary complications after laparoscopic cholecystectomy

OBJECTIVE

A total of 50 major bile duct injuries after laparoscopic cholecystectomy were managed by the Duke University Hepatobiliary Service from 1990-1992. The management of these complex cases is reviewed.

SUMMARY BACKGROUND DATA

Laparoscopic cholecystectomy is the preferred method for removing the gallbladder. Bile duct injury is the most feared complication of the new procedure.

METHODS

Review of videotapes, pathology, and management of the original operations were reviewed retrospectively, and the injuries categorized. Major biliary injury was defined as a recognized disruption of any part of the major extrahepatic biliary system. Biliary leakage was defined as a clinically significant biliary fistula in the absence of major biliary injury, i.e., with an intact extrahepatic biliary system.

RESULTS

Thirty-eight injuries were major biliary ductal injuries and 12 patients had simple biliary leakage. Twenty-four patients had the classic type injury or some variant of the classic injury. A standard treatment approach was developed which consisted of ERCP for diagnosis, preoperative PTC with the placement of stents, CT drainage immediately after the PTC for drainage of biliary ascites, and usually Roux-en-Y hepaticojejunostomy with placement of O-rings for future biliary access if necessary. Major ductal injuries were high in the biliary system involving multiple ducts in 31 of the 38 patients. Re-operation was required in 5 of the 38 patients with particularly complex problems.

CONCLUSIONS

Successful management of bile duct injury after laparoscopic cholecystectomy requires careful understanding of the mechanisms, considerable preoperative assessment by experts, and a multidisciplinary approach.