Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins

Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations, and large numbers of somatic genomic alterations, associated with a predisposition to cancer. However, it remains difficult to distinguish background, or 'passenger', cancer mutations from causal, or 'driver', mutations in these data sets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. Here we test the hypothesis that genomic variations and tumour viruses may cause cancer through related mechanisms, by systematically examining host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways, such as Notch signalling and apoptosis, that go awry in cancer. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on a par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches increase the specificity of cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate the prioritization of cancer-causing driver genes to advance the understanding of the genetic basis of human cancer.

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.)

A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.

Ultrasound evaluation of blunt abdominal trauma: program implementation, initial experience, and learning curve

OBJECTIVE

Although sonographic screening for blunt abdominal trauma is gaining acceptance, standards for implementation, training, credentialing, and quality control remain to be established.

DESIGN

This prospective study examines a Level I trauma service experience with the de novo establishment of a trauma ultrasound (US) program credentialed through the Department of Surgery under the auspices of Continuous Quality Improvement.

MATERIALS AND METHODS

All trauma surgeons attended a combined didactic and "hands on" 8-hour trauma US course. Abdominal sonography was subsequently performed on patients with potential blunt abdominal trauma followed by a standard diagnostic evaluation, which included computed tomographic scan, diagnostic peritoneal lavage, or observation.

MEASUREMENTS AND MAIN RESULTS

Three hundred patients were studied over a 4-month period. They averaged 35 years of age with an average injury severity score of 12. The time required to perform the US examination averaged less than 3 minutes. Standard diagnostic evaluation included computed tomographic scan (21%), diagnostic peritoneal lavage (45%), and observation (34%). US examinations resulted in 277 true negatives, 17 true positives, two false positives, and four false negatives for a sensitivity of 81.0%, a specificity of 99.3%, and an accuracy of 98.0%. Annualized cost savings with the use of US evaluation versus standard diagnostic evaluation would amount to over $100,000.00.

CONCLUSIONS

This experience with the de novo implementation of a trauma US program suggests that the training and credentialing requirements in this study are sufficient to provide surgeon ultrasonographers with acceptable competence in US diagnosis of blunt abdominal trauma.

Preoperative serum creatinine as a predictor of survival in perforated gastroduodenal ulcer

Factors affecting survival were retrospectively analyzed in 89 patients (50 men) operated upon for perforated peptic ulcer. Mean age was 52 years. Only 18 per cent had no history of significant medical illness; almost 26 per cent were termed immune suppressed from high-dose steroid therapy or the presence of diffuse, metastatic cancer. The estimated interval between perforation and operation was over 24 hours in one-third. Preoperative serum creatinine, determined in 83 patients, ranged from 0.1 to 6.4 mg/dl (mean, 1.5 mg/dl); no patients were dialysis-dependent. At celiotomy, 75 per cent underwent ulcer plication only; the remainder had a definitive acid reduction procedure. Stepwise logistic regression analysis revealed that a normal preoperative serum creatinine (less than 1.5 mg/dl) was the most powerful predictor of survival (P less than 0.00001), followed by absence of immune suppression, and age under 60 years. The interval between perforation and operation, the site of perforation, and the type of operation did not statistically affect survival.