Implementing multiplexed genotyping of non-small-cell lung cancers into routine clinical practice.

BACKGROUND: Personalizing non-small-cell lung cancer (NSCLC) therapy toward oncogene addicted pathway inhibition is effective. Hence, the ability to determine a more comprehensive genotype for each case is becoming essential to optimal cancer care. METHODS: We developed a multiplexed PCR-based assay (SNaPshot) to simultaneously identify >50 mutations in several key NSCLC genes. SNaPshot and FISH for ALK translocations were integrated into routine practice as Clinical Laboratory Improvement Amendments-certified tests. Here, we present analyses of the first 589 patients referred for genotyping. RESULTS: Pathologic prescreening identified 552 (95%) tumors with sufficient tissue for SNaPshot; 51% had ≥1 mutation identified, most commonly in KRAS (24%), EGFR (13%), PIK3CA (4%) and translocations involving ALK (5%). Unanticipated mutations were observed at lower frequencies in IDH and ß-catenin. We observed several associations between genotypes and clinical characteristics, including increased PIK3CA mutations in squamous cell cancers. Genotyping distinguished multiple primary cancers from metastatic disease and steered 78 (22%) of the 353 patients with advanced disease toward a genotype-directed targeted therapy. CONCLUSIONS: Broad genotyping can be efficiently incorporated into an NSCLC clinic and has great utility in influencing treatment decisions and directing patients toward relevant clinical trials. As more targeted therapies are developed, such multiplexed molecular testing will become a standard part of practice.

BioWeld(®) Tube and surgical glue for experimental sutureless venous microanastomosis.

BACKGROUND: The medial wall of mammalian veins is generally thin and fragile compared with the thick muscle seen in arteries. This makes venous microanastomoses time consuming and challenging. This study aimed to determine the feasibility and effectiveness of using the BioWeld(®) Tube in conjunction with a surgical glue (butyl-2-cyanoacrylate) in performing sutureless venous microanastomoses. METHODS: The feasibility and effectiveness of microvascular anastomoses in a rabbit jugular vein model were investigated in six animals, using the BioWeld(®) Tube in conjunction with butyl-2-cyanoacrylate surgical glue. Patency and tissue repair mechanisms at the anastomotic site were assessed 1 week after the procedure. RESULTS: All anastomoses remained patent at 1 week. Muscle necrosis occurred only in areas where the tissue was subject to the fold-and-bond procedure. CONCLUSION: The study showed the feasibility and short-term effectiveness of the BioWeld(®) Tube in facilitating venous anastomoses.

Recognition by human V gamma 9/V delta 2 T cells of a GroEL homolog on Daudi Burkitt's lymphoma cells.

All human gamma delta T cells coexpressing the products of the variable (V) region T cell receptor (TCR) gene segments V gamma 9 and V delta 2 recognize antigens from mycobacterial extracts and Daudi cells. Exogenous and endogenous ligands on the cell surface, homologous to the groEL heat shock family, induced reactivities that resembled superantigen responses in this major subset of human peripheral blood gamma delta T cells. Stimulation of human V gamma 9/V delta 2 T cells is not restricted by human leukocyte antigens (HLA), including nonpolymorphic beta 2-microglobulin (beta 2M)-associated class Ib molecules. These data may be important for understanding the role of gamma delta T cells in autoimmunity and in responses to microorganisms and tumors.

Regulation of a double-stranded RNA modification activity in human cells.

A double-stranded RNA (dsRNA)-specific modification activity from Xenopus oocytes and human cells dsRNA modifier) converts adenosine residues present in dsRNA to inosines. The function of the dsRNA modifier is unknown, although it has been suggested that it may be part of the cellular antiviral response. We investigated the relationship between the activity of the dsRNA modifier, viral infection, and the antiviral response in human cells induced by poly(rI)-poly(rC) [poly(I.C)] treatment. We found, unexpectedly, that treatment of HeLa cells with poly(I.C) or other dsRNA molecules resulted in the dramatic inhibition of the dsRNA modifier. Mixing experiments, reconstruction experiments, and pretreatment of extracts with RNases indicated that inhibition of the dsRNA modifier did not result from the continued presence of a soluble inhibitor such as dsRNA) in the in vitro modification reactions. Treatment of cells with cyclohexamide or dactinomycin simultaneously with the poly(I.C) demonstrated that in vivo inhibition of the dsRNA modifier did not require new transcription or translation. The dsRNA modification activity was also substantially inhibited in cells infected with poliovirus and was slightly inhibited in cells infected with adenovirus. The inhibition of the dsRNA modifier during the antiviral state is thus not consistent with an antiviral function, and instead suggests another cellular function for dsRNA modification.

Regional differences in the incidence and growth of mouse tumors following intradermal or subcutaneous inoculation.

Tumor cells inoculated intradermally or s.c. into more cranial regions of the lateral trunk show strikingly greater tumor growth and development than do similar cells injected more caudally. At low tumor cell doses the incidence anteriorly may be double that found posteriorly and tumors become detectable more rapidly anteriorly; at higher cell doses the anterior:posterior ratio of tumor weight may be 4:1. The effect appears to be independent of the type of tumor used (mastocytoma, sarcoma, teratoma, lymphoma, or adenocarcinoma) and of the strain of mouse host; it does not appear to be influenced by the sex of the host animal, the immunogenicity of the tumor, or the immunological competence of the tumor recipient. The results are discussed both in terms of practical considerations for developing adequate tumor transplantation and treatment protocols and in terms of the biological significance in relation to spontaneous or induced oncogenesis.

Paclitaxel and gemcitabine chemotherapy for advanced transitional-cell carcinoma of the urothelial tract: a phase II trial of the Minnie pearl cancer research network.

PURPOSE: To evaluate the toxicity and efficacy of combination chemotherapy with paclitaxel and gemcitabine in patients with advanced transitional-cell carcinoma of the urothelial tract. PATIENTS AND METHODS: Fifty-four patients with advanced unresectable urothelial carcinoma entered this multi-centered, community-based, phase II trial between May 1997 and December 1999. All patients were treated with paclitaxel 200 mg/m(2) by 1-hour intravenous (IV) infusion on day 1 and gemcitabine 1,000 mg/m(2) IV on days 1, 8, and 15; courses were repeated every 21 days. Patients who had objective response or stable disease continued treatment for six courses. RESULTS: Twenty-nine of 54 patients (54%; 95% confidence interval, 40% to 67%) had major responses to treatment, including 7% complete responses. With a median follow-up of 24 months, 16 patients (30%) remain alive and nine (17%) are progression-free. The median survival for the entire group was 14.4 months; 1- and 2-year actuarial survival rates were 57% and 25%, respectively. Seven (47%) of 15 patients previously treated with platinum-based chemotherapy responded to paclitaxel/gemcitabine. Grade 3/4 toxicity was primarily hematologic, including leukopenia (46%), thrombocytopenia (13%), and anemia (28%). Ten patients (19%) required hospitalization for neutropenia and fever, and one patient had treatment-related septic death. CONCLUSION: The combination of paclitaxel and gemcitabine is active and well tolerated in the first- or second-line treatment of patients with advanced transitional-cell carcinoma of the urothelial tract. Response rate and duration compare favorably with those produced by other active, first-line regimens. This regimen should be further evaluated in phase II and III studies, as well as in patients with compromised renal function.

Phase II trial evaluating triplet chemotherapy using gemcitabine, paclitaxel, and carboplatin in the treatment of patients with advanced non-small cell lung cancer.

The purpose of this study was to evaluate the combination of gemcitabine, paclitaxel, and carboplatin in patients with advanced non-small cell lung cancer. Previously untreated patients with stage IIIB or IV non-small cell lung cancer were enrolled into this trial. Sixty-nine patients from the phase II portion and eight patients from the phase I portion were treated with gemcitabine 1,000 mg/m2 intravenously on days I and 8, paclitaxel 200 mg/m2 as a 1-hour infusion on day 1, and carboplatin at an area under the curve of 5.0 intravenously on day 1. Treatment courses were repeated every 21 days. The phase II component of the study was completed at 13 community-based practices in the Minnie Pearl Cancer Research Network. Thirty-four of 71 fully evaluable patients had an objective response (48%, two complete and 32 partial responses). Twenty-five patients (35%) were stable and 12 (17%) progressed. The median response duration was 6 months (range, 3 to 14 months) and the median survival was 9.9 months, with 1- and 2-year survival rates of 47% and 21%, respectively. The combination of gemcitabine, paclitaxel, and carboplatin has been shown to be safe and effective; thus, this three-drug regimen will be compared with a standard two-drug regimen, paclitaxel/carboplatin, in a phase III study.

The photocatalytic production of organic-free water for molecular biological and pharmaceutical applications.

The inability of conventional water-purification systems to meet the ultra-high purity needs of molecular biology and biopharmaceuticals reliably was attributed to their almost exclusive utilization of phase-transfer technologies. Water quality may unpredictably degrade when confronted by microorganism blooms or altered feed water characteristics. Photocatalytic point-of-use water-purification systems fed by deionized water were demonstrated to meet the most stringent water-purity needs of the molecular biologist. The reliability of the photocatalytic water-purification technology was attributed to its ability to destroy organic contaminants rather than just effect their phase transfer. Photocatalytically produced water was shown to be free of detectable microorganisms, DNA, endotoxins and RNAses. It is suitable for immunological studies involving tissue and other cell cultures because of its lack of detectable endotoxins. Because DNA was also undetectable, it is suitable for DNA and endotoxin zero-standards as well as pharmaceutical formulation. The photocatalytic water is a reliable substitute for diethyl pyrocarbonate-treated water used in RNA work, compatible with PCR and sufficiently free from other contaminants to be useful for most biochemical and enzymatic assays.

Methylprednisolone interventions in myocardial infarction: a controversial subject.

Myocardial infarction is a dynamic evolutionary process which can progress over a relatively prolonged interval after its onset. The ultimate extent of damage depends on coronary artery anatomy, the balance between myocardial oxygen supply and demand, and metabolic modulators of myocardial injury. The possibility that methylprednisolone, a synthetic anti-inflammatory corticosteroid, may exert a beneficial effect on ischemic myocardium has been studied in both animal models and patients. However, the results of these experimental and clinical investigations have been controversial, in that some have demonstrated efficacy of the drug to limit extension of evolving myocardial infarction, while others have not. The effects of dose regimen and duration of methylprednisolone administration on preservation of myocardium and infarct size remain unclear, especially in clinical studies. The problem resides in the large interindividual variations among patients in degree and distribution of coronary disease, concomitant drugs, the accuracy of techniques for measuring and monitoring changes in myocardial infarct size, and the small numbers of patients involved in the majority of these studies. The absence of clarity will continue to cast doubts over the use of methylprednisolone until its marked beneficial effects can be significantly demonstrated.

Hereditary metabolic diseases (HMDs) in adult practice in Ireland: a preliminary assessment.

BACKGROUND: Hereditary metabolic diseases (HMDs) are almost all rare diseases, many of which, if ascertained are treatable and preventable causes of intellectual and general disability. The improved detection and treatment of HMDs in paediatric practice has resulted in increased survival into adult life. The identification of adult patients with HMDs who may benefit from new emerging treatments is challenging. As for many rare diseases, there are difficulties tracing patients for many of these conditions in current Irish coding systems and lack of established patient Registries. METHODS: In this study, we describe the efforts made to trace Irish adult patients with potentially treatable HMDs using (1) a mailed questionnaire sent to all currently registered adult Medical Specialists practising in Ireland requesting details of all cases seen over the 4-year period 2007-2010, (2) the analysis of HIPE in-patient data during this time and (3) analysis of the database held at NCIMD. CONCLUSIONS: The current systems in place for identification and coding of potentially treatable HMDs are very deficient. This emphasizes the need to prioritize the development of a National HMD Registry.

Laser-assisted end-to-end BioWeld anastomosis in an ovine model.

The BioWeld tube, an albumin-based exovascular stent, has been used for microsurgical anastomoses and compared to conventional sutures. The study presented investigated the potential of the BioWeld tube for vascular anastomosis in larger vessels. Laser-assisted BioWeld anastomoses were compared to conventional-sutured anatomoses of the carotid artery of Merino-x ewes. The BioWeld procedure resulted in 100% survival and 100% patency at 1 and 6 week post-operative periods, with no noticeable foreign body response. Sutured animals showed 100% survival and patency. The ischemic time for BioWeld anastomosis averaged 15 minutes compared with 10 minutes for sutures. This study indicates that the BioWeld tube is an easy to use anastomotic technique with equivalent success rates and comparable anastomotic times.

DNA binding by the bacteriophage SPO1-encoded type II DNA-binding protein, transcription factor 1. Site-specific binding requires 5-hydroxymethyluracil-containing DNA.

The bacteriophage SPO1-encoded Type II DNA-binding protein, transcription factor 1 (TF1), forms complexes with specific sites in SPO1 DNA. We have investigated the binding of TF1 to one of its preferred sites in which the normal 5-hydroxymethyluracil (hmUra) of SPO1 DNA has been replaced by thymine and have also investigated the binding of a bacterial Type II DNA-binding protein (from Bacillus stearothermophilus) to the hmUra- and thymine-containing forms of the same DNA segment. Our results show that TF1 binds selectively to this high affinity binding site only in hmUra-containing DNA and that the bacterial Type II DNA-binding protein interacts nonspecifically with both forms of DNA.

Trans activation by the bovine papillomavirus E2 protein in Saccharomyces cerevisiae.

The papillomavirus E2 protein functions as an enhancer-binding factor to promote transcription in mammalian cells. We found that one copy of the E2 binding site acted as an E2 protein-dependent upstream activating sequence in Saccharomyces cerevisiae. Additional copies of the binding motif further augmented transcription. These results imply that the E2 protein functionally interacts with highly conserved transcriptional elements.

Forward scatter pulse width signals resolve multiple populations of endosomes.

The technique of pulse width analysis, developed to optimize cell size resolution in cell cycle kinetics, has not previously been applied to small particles such as endosomes. Offset is used to subtract a portion of the beam diameter from forward scatter pulse width signals to optimize visualization and discrimination of small particles. We identify multiple endosomal populations by offset pulse width of light scatter parameters. Specifically, linear forward scatter pulse width measurements reveal at least two populations of endosomes in the rat renal cortex, the rat renal papilla, and the luminal endothelium of the toad urinary bladder. Logarithmically amplified forward scatter pulse width measurements display the full dynamic range of these signals, resolving additional populations not manifest with linear amplification. To confirm that the endosomes observed were resolved from optical and electronic noise, we examined physiological function. The endosomes acidified after supplying ATP to the intrinsic membrane H(+)-ATPase present. Further, electron microscopy of sorted endosomal populations from the toad urinary bladder confirmed identity and homogeneity of the fraction. Flow cytometric analysis of endosomal populations by multiparametric techniques including pulse width analysis of structural parameters and pulse height analysis of fluorescence from entrapped fluorophores allows identification, isolation, and quantification of multiple endosomal populations.

DNA binding by the bacteriophage SPO1-encoded type II DNA-binding protein, transcription factor 1. Formation of nested complexes at a selective binding site.

The interactions of the phage SPO1-encoded Type II DNA-binding protein, transcription factor 1 (TF1), with one of its preferred binding sites in SPO1 DNA have been analyzed in detail. The results suggest that TF1 recognizes a high-affinity "core" binding site and that additional protein moieties can accrue to either side of the occupied core site to form higher order complexes. Close contacts between TF1 and the core binding site as well as some of the steric requirements for recognition of the core site were determined. Comparison of the nucleotide sequences of several preferred binding sites for TF1 reveals a striking lack of precise homology but does show common features.

Bacteriophage T4 regA protein binds to mRNAs and prevents translation initiation.

The bacteriophage T4 regA protein is a translational repressor of a subset of phage mRNAs. We show here that purified regA protein binds specifically to target mRNAs near the initiating AUG and occludes binding of ribosomes. Translational repression by regA protein diminishes expression of many genes whose mRNA sequences around the initiating AUG codons are different. A comparison of nucleotide sequences from several regA-repressed mRNAs suggests that the initiating AUG is an important, but not sufficient, sequence for regA binding.

Heterogeneity of mouse vascular endothelium. In vitro studies of lymphatic, large blood vessel and microvascular endothelial cells.

Microvascular endothelial cell cultures have been established from mouse lung, liver, brain, heart, placenta, kidney, urinary bladder, mammary gland, ovary and epididymal fat pad. In addition, large vessel endothelial cells have been obtained from the mouse aorta and thoracic duct. The heterogeneity of these cells has been shown by flow cytometric determination of angiotensin-converting enzyme, by differential presence of the acetyl low density lipoprotein receptor, by the variable expression of cell surface antigens, and by differential binding of various plant lectins. The endothelial cell lines we have developed provide the means to examine in the mouse, long a key species for biomedical research, a wide range of biological functions and properties of the vascular endothelium.

Expression of organ-specific antigens on capillary endothelial cells.

Our central thesis is that the endothelial cells which line capillaries of various organs are not all alike. Using monoclonal and conventional antibodies we demonstrate that capillary endothelial cells express on their cell surface an array of antigens that manifest organ selectivity. Brain-derived endothelial cells possess brain-associated antigens, ovary-derived endothelial cells share antigenic markers with other ovarian cells, and lung-derived endothelium possesses antigens that are primarily expressed on cells of the lung. Our experiments lead us to suggest that organ-associated determinants on the endothelial cell surface may play a role in the selective adhesion of tumor cells during metastasis, in site-limited vascular pathology, and in the regionally limited release of angiogenesis-induced factors.

Phase I trial of paclitaxel, carboplatin, and topotecan with or without filgrastim (granulocyte-colony stimulating factor) in the treatment of patients with advanced, refractory cancer.

BACKGROUND: Topotecan is a new antineoplastic agent with a broad spectrum of activity. The purpose of this Phase I trial was to define the maximum tolerated dose of topotecan when added to the widely used combination of paclitaxel and carboplatin. METHODS: Patients with advanced cancer that was refractory or resistant to standard treatments were treated with paclitaxel, carboplatin, and topotecan; doses were escalated in sequential cohorts of patients. After definition of the maximum tolerated dose without cytokines, granulocyte-colony stimulating factor (G-CSF) was added and further dose escalation was attempted. RESULTS: The maximum tolerated doses were: paclitaxel, 135 mg/m2, as a 1-hour intravenous (i.v.) infusion on Day 1; carboplatin, area under the curve 5.0, on Day 1; and topotecan, 0.75 mg/m2, i.v. on Days 1, 2, and 3; the regimen was repeated every 21 days. Myelosuppression, particularly thrombocytopenia, was the dose-limiting toxicity with this three-drug combination. Nonhematologic toxicity was uncommon. The addition of G-CSF did not allow substantial dose escalation because thrombocytopenia was uneffected by this agent. Eleven of 25 patients had major responses to this combination, including 8 of 14 patients with previously treated small cell lung carcinoma. CONCLUSIONS: The combination of paclitaxel, carboplatin, and topotecan is feasible, although only relatively low doses of all three drugs can be tolerated due to myelosuppression. This regimen showed a high level of activity in these patients with refractory cancer, and merits further investigation.