Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance. oncoEnrichR differs from general gene set analysis frameworks through the integration of an extensive set of prior knowledge specifically relevant for cancer, including ranked gene-tumor type associations, literature-supported proto-oncogene and tumor suppressor gene annotations, target druggability data, regulatory interactions, synthetic lethality predictions, as well as prognostic associations, gene aberrations and co-expression patterns across tumor types. The software produces a structured and user-friendly analysis report as its main output, where versions of all underlying data resources are explicitly logged, the latter being a critical component for reproducible science. We demonstrate the usefulness of oncoEnrichR through interrogation of two candidate lists from proteomic and CRISPR screens. oncoEnrichR is freely available as a web-based service hosted by the Galaxy platform ( https://oncotools.elixir.no ), and can also be accessed as a stand-alone R package ( https://github.com/sigven/oncoEnrichR ).     

T-cell receptor tau delta +/CD3+4-8-T- cell acute lymphoblastic leukemias: a distinct subgroup of leukemias in children. A report of five cases.

In a 10-year study of T-cell acute lymphoblastic leukemias (T-ALL) in children, we have identified five cases expressing the T-cell receptor tau delta (TCR tau delta). The incidence (26%) of TCR tau delta+T-cell leukemias in our material was high. Clinically, the TCR tau delta+ leukemias represented a distinct subgroup of T-cell leukemias. Mean age at onset of disease, 1.8 years, was remarkably low for mature T-cell leukemias. White blood cell counts were high, lymph node enlargements were discrete, and no mediastinal tumors were seen. Four of five TCR tau delta+ leukemias carried rearrangements of the C tau 2 gene, and transcribed the T-early alpha genetic element.     

The Membrane Glycoprotein IIb/IIIa Complex Mediates Deposition of Thrombin-stimulated Blood Platelets on Polystyrene Plastic Under Static Conditions

A major challenge in the use of artificial materials for implant devices, artificial organs, and extra-corporeal circulation systems, is the adhesion of platelets and the subsequent formation of platelet aggregates on the non-biological surface. The mechanism of platelet attachment to artificial surfaces is not completely understood. Using an enzyme immunoassay, we examined platelet deposition to the polystyrene plastic of microtiter plate wells under static conditions. Following thrombin stimulation, platelets adhered to the wells. This adhesion process was suppressible by the use of different substances known to interfere with the function of the platelet surface glycoprotein IIb/IIIa complex (GPIIb/IIIa). The substances we used were ethylenediaminetetraacetic acid (EDTA), tetrapeptide RGDS (Arg-Gly-Asp-Ser), and a monoclonal antibody directed against the IIIa moiety of the GPIIb/IIIa complex. Our results indicate that the GPIIb/IIIa complex is the platelet receptor which mediates platelet adhesion to polystyrene plastic under such static conditions. The GPIIb/IIIa complex should consequently be regarded as a multifunctional platelet regulator which, depending on the circumstances, may support platelet adhesion as well as platelet aggregation. By contrast, a monoclonal antibody directed against the platelet surface glycoprotein complex Ib/IX (GPIb/IX) did not under the same static conditions inhibit platelet deposition to the polystyrene plastic. In the microtiter wells, platelet alpha-granular proteins were detected either on the surface of adherent platelets or, when platelet deposition was inhibited by EDTA directly on the polystyrene plastic. In the latter case, fibrinogen and thrombospondin were definitely the dominating proteins. The presence of platelet-derived proteins in the microtiter wells significantly enhanced the adhesion of thrombin-stimulated platelets but not of non-stimulated platelets.     

Chlamydia pneumoniae DNA in peripheral blood mononuclear cells in dialysis patients,renal transplant recipients and healthy controls

While nitric oxide (NO) is implicated as an important mediator of hypotension in sepsis and endotoxemia, its role as a mediator of tissue injury in shock is controversial. During porcine endotoxemia (lipopolysaccharide (LPS) 1.7 &#119 g·kg -1 ·h -1 i.v. for 6 h), we compared circulatory and morphological changes in the liver induced by two different NO synthase inhibitors (N G -nitro-L-arginine methyl ester, L-NAME, 25 mg·kg- 1 i.v., and aminoethyl-isothiourea, AE-ITU, 10 mg·kg- 1 i.v.), both given after 3 h. LPS induced time-dependent tissue reactions with edema, sinusoidal dilation, packing of red cells and leukocyte infiltration, progressing to endothelial cell and hepatocyte damage, formation of thrombi, and at 6 h widespread necrosis. These changes were similar in all pigs receiving LPS, regardless of treatment with NOS inhibitors. LPS caused significant increases in aspartate aminotransferase (AST), alkaline phosphatase (ALP) and alpha glutathione S-transferase ( &#102 -GST). L-NAME caused further increases in AST, ALP and &#102 -GST, while AE-ITU prevented the late increase in ALP and &#102 -GST observed in the other LPS groups. LPS reduced liver blood flow by ~ 40%. L-NAME further reduced flow by ~ 50%, while AE-ITU restored liver blood flow to baseline values. Conclusion: L-NAME in endotoxemia had detrimental effects on liver circulation, while AE-ITU improved liver blood flow and attenuated the late increase in liver enzymes. Liver morphology was unaffected within the 3-h observation time after NOS inhibition.     

Subtype‐specific micro‐RNA expression signatures in breast cancer progression

Robust markers of invasiveness may help reduce the overtreatment of in situ carcinomas. Breast cancer is a heterogeneous disease and biological mechanisms for carcinogenesis vary between subtypes. Stratification by subtype is therefore necessary to identify relevant and robust signatures of invasive disease. We have identified microRNA (miRNA) alterations during breast cancer progression in two separate datasets and used stratification and external validation to strengthen the findings. We analyzed two separate datasets (METABRIC and AHUS) consisting of a total of 186 normal breast tissue samples, 18 ductal carcinoma in situ (DCIS) and 1,338 invasive breast carcinomas. Validation in a separate dataset and stratification by molecular subtypes based on immunohistochemistry, PAM50 and integrated cluster classifications were performed. We propose subtype‐specific miRNA signatures of invasive carcinoma and a validated signature of DCIS. miRNAs included in the invasive signatures include downregulation of miR‐139‐5p in aggressive subtypes and upregulation of miR‐29c‐5p expression in the luminal subtypes. No miRNAs were differentially expressed in the transition from DCIS to invasive carcinomas on the whole, indicating the need for subtype stratification. A total of 27 miRNAs were included in our proposed DCIS signature. Significant alterations of expression included upregulation of miR‐21‐5p and the miR‐200 family and downregulation of let‐7 family members in DCIS samples. The signatures proposed here can form the basis for studies exploring DCIS samples with increased invasive potential and serum biomarkers for in situ and invasive breast cancer.     

Peritoneal, benign, cystic mesothelioma with free-floating cysts, re-examined by new methods. A case report

A histologically-confirmed, multicystic, benign mesothelioma, with free-floating, thin-walled cysts, in the abdominal cavity of a 27-year-old woman was reported in 1954. After removal of all visible cysts by laparotomy, the patient was healthy and well for 29 years, when she was surgically treated for cholecystitis and gall bladder stones in 1982. The whole peritoneum was found covered with small cysts lined by mesothelial cells. The patient is (April 1987) well, with no complaints. Sections from the old paraffin blocks were studied by means of scanning, transmission electron microscopy and immunohistochemistry. These methods confirmed the histological diagnosis. The authors discuss whether such a lesion really is a benign tumor or should rather be otherwise classified.     

Chromosome 13 alterations in osteosarcoma cell lines derived from a patient with previous retinoblastoma.

Various sublines of cells established from an osteosarcoma that developed in a patient (O.H.) with previous bilateral retinoblastoma were examined for different restriction fragment-length polymorphisms of chromosome 13q, as well as for rearrangements of the retinoblastoma gene using a cDNA probe. The independently established sublines were used to help separate primary and secondary events taking place in tumorigenesis of the osteosarcoma of this patient. Information from the present DNA analysis, taken together with data from cytogenetic and enzymatic studies on chromosome 13 in the cell lines, revealed both common and distinct genetic changes on chromosome 13q. The common changes may indicate the nature of the first and second mutational events in the development of the osteosarcoma. The first, constitutional cancer predisposing mutation seemed to be a base mutation or a small deletion/insertion, and the second event involved a deletion of a larger part of the long arm of chromosome 13. The distinct genetic changes included other deletion and duplication events of chromosome 13q. The existence of multiple sublines with different genetic constitutions provides improved possibilities for gaining insight into the nature of the genetic lesions leading to tumor formation, as these may reflect the clonal variation present in the primary tumor. We also demonstrate the difficulty of inferring from single tumor cell isolates to properties of the primary tumor.     

Attachment,spreading and growthin vitro of highly malignant and low malignant murine fibrosarcoma cells

Highly malignant cell lines and low-malignant cell lines isolated from three different methylcholanthrene-induced murine fibrosarcomas were examined for their ability to attach to plastic dishes and collagen-coated dishes under serumfree conditions and in the presence of serum. Most of the cells from the three highly malignant lines attached and spread under all conditions. By 72h, there was a significant increase in the number of cells indicating that at least some of the cells had undergone division (even in the absence of serum). In contrast, fewer of the cells from the three low-malignant lines attached and spread on the plastic or collagen substrates in the absence of serum or in the presence of 0.1 per cent serum. However, when 15g laminin per dish was added along with the lowmalignant cells, they then attached and spread on the plastic and collagen-coated dishes. Previous studies have indicated that the highly malignant lines express cell surface antigens that cross-react with laminin while the low-malignant cell lines do not. We speculate that the differences between the high- and low-malignant cells in the expression of cell surface laminin-like antigens contribute to the dissimilarities in attachment and spreading capacity. These differences may also contribute to the dissimilarity between these cells in malignant potential.