Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma.

Calibration using constrained smoothing with applications to mass spectrometry data.

Linear regressions are commonly used to calibrate the signal measurements in proteomic analysis by mass spectrometry. However, with or without a monotone (e.g.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers.

A new functional data-based biomarker for monitoring cardiovascular behavior.

Cardiac safety assessment in drug development concerns the ventricular repolarization (represented by electrocardiogram (ECG) T-wave) abnormalities of a cardiac cycle, which are widely believed to be linked with torsades de pointes, a potentially life-threatening arrhythmia. The most often used biomarker for such abnormalities is the prolongation of the QT interval, which relies on the correct annotation of onset of QRS complex and offset of T-wave on ECG. A new biomarker generated from a functional data-based methodology is developed to quantify the T-wave morphology changes from placebo to drug interventions.

Variance component analysis of a multi-site study for the reproducibility of multiple reaction monitoring measurements of peptides in human plasma.

Background: In the Addona et al. paper (Nature Biotechnology 2009), a large-scale multi-site study was performed to quantify Multiple Reaction Monitoring (MRM) measurements of proteins spiked in human plasma. The unlabeled signature peptides derived from the seven target proteins were measured at nine different concentration levels, and their isotopic counterparts were served as the internal standards.

Phase I clinical and pharmacokinetic study of rebeccamycin analog NSC 655649 given daily for five consecutive days.

Purpose: Rebeccamycin analog (NSC 655649) is active against a variety of both solid and nonsolid tumor cell lines. We performed a phase I trial to determine the maximum-tolerated dose (MTD) of rebeccamycin analog when given on a daily x 5 schedule repeated every 3 weeks, characterize the toxicity profile using this schedule, observe patients for antitumor response, and determine the pharmacokinetics of the agent and pharmacodynamic interactions.

Patients And Methods: Thirty assessable patients received a total of 153 cycles according to the following dose escalation schema: 60, 80, 106, 141, and 188 mg/m(2)/d x 5 days.

Oral combination chemotherapy in conjunction with filgrastim (G-CSF) in the treatment of AIDS-related non-Hodgkin's lymphoma: evaluation of the role of G-CSF; quality-of-life analysis and long-term follow-up.

In 1993 we reported the efficacy and toxicity profile of an oral combination regimen administered to 18 patients with AIDS-related lymphoma (NHL-1 study). We observed a 61% response rate; 39% one-year survival rate; nearly two-thirds of patients developed > or = grade 3 leukopenia; and 28% of cycles were associated with febrile neutropenia. These results prompted us to shorten the duration of therapy and to add G-CSF to ameliorate the myelosuppression.

Oral combination chemotherapy in the management of AIDS-related lymphoproliferative malignancies.

An oral combination chemotherapy regimen initially developed for AIDS-related non-Hodgkin's lymphoma includes lomustine (CCNU), etoposide, cyclophosphamide, and procarbazine. This regimen takes advantage of oral administration, the in vitro synergy of these drugs and their first-line efficacy in lymphoma, and the ability of lomustine and procarbazine to cross the blood-brain barrier. This regimen was used to treat 38 patients with AIDS-related non-Hodgkin's lymphoma.

Potentiation of lymphomagenesis by methylnitrosourea in mice transgenic for LMO1 is blocked by O6-alkylguanine DNA-alkyltransferase.

We evaluated induction of lymphomas by the methylating carcinogen, N-methylnitrosourea [MNU], in transgenic mice expressing both LMO1 and the DNA repair gene, MGMT, in the thymus. The goal was to determine whether environmental mutagens shorten the latency or increase the incidence of LMO1 + lymphomas and whether mice transgenic for both LMO1 and MGMT, and thereby able to repair O6-methylguanine DNA adducts induced by MNU, would be protected. Mice heterozygous for LMO1 or MGMT were crossed and offspring treated with MNU at 6 weeks of age.

Pulmonary and cardiovascular consequences of immediate fixation or conservative management of long-bone fractures.

We randomly assigned patients with multiple trauma who had tibial or femoral fractures to one of two groups--one group received immediate fixation of all fractures, and the second group received conservative orthopedic management, consisting of traction or plaster casts. Studies were conducted twice each day for four days following injury. Mean cardiac index was 1.

Reversal of fibronectin and opsonic deficiency in patients. A controlled study.

Plasma fibronectin is an opsonic glycoprotein which augments reticuloendothelial phagocytic clearance of nonbacterial particulates. We evaluated the influence of intravenous infusion of plasma cryoprecipitate on circulating immunoreactive fibronectin and associated opsonic activity at 0.5, 2.

Attenuation of hypoxic pulmonary vasoconstriction by pulsatile flow in dog lungs.

We measured pulmonary arterial pressure in isolated lower lobes of dog lungs perfused in situ at several flows during ventilation with 95% O2-5% CO2 and with 3% O2-5% CO2. Pulsatile perfusion was provided by a piston pump, and steady perfusion was provided by a roller pump. The slope of the pressure-flow curve was 16.

Agents for the treatment of brain injury. 1. (Aryloxy)alkanoic acids.

Blunt and ischemic injuries of the brain have been shown to result in swelling that is predominantly limited to a single cell type, the astrocyte, within the complex cellular mosiac of cerebral gray matter. Evaluation of various diuretic (aryloxy)acetic acids in vitro using incubating cat brain slices and primary astrocyte cultures identified compounds with marked ability to inhibit brain tissue swelling. Some of the compounds significantly reduced the mortality and morbidity following acceleration/deceleration brain injury in anesthesized cats.

Beneficial effects of an anabolic steroid during cytotoxic chemotherapy for metastatic cancer.

To investigate the effects of concurrent administration of an anabolic steroid upon hematopoiesis and metabolism in patients with cancer who were receiving cytotoxic chemotherapy, a randomized trial was conducted. Thirty-three evaluable patients received intensive multiple-agent chemotherapy: 17 received in addition nandrolone decanoate ("Deca-Durabolin"), 200 mg intramuscularly each week. The nandrolone-treated patients showed significantly better maintenance of hemoglobin concentrations and body weight, and a highly significant reduction in number of blood transfusions.

Perceptions of the coordinating center: as viewed by a site visitor.

The evaluation of a coordinating center by a site visitor requires understanding the nature of the tasks for the particular project being coordinated, appraisal of performance, discovery of the coordinating center's self-assessment, evaluation of the competence within the center and consideration of causes for any inadequacies present. The crux of the evaluation lies in assessing the ways in which major decisions are reached and the abilities to recognize and to utilize the expertise required for reaching sound decisions.

Dental root abnormalities and gingival overgrowth in epileptic patients receiving anticonvulsant therapy.

Forty-six mentally retarded epileptic patients being treated with phenytoin and phenobarbital were studied to determine the root/crown length ratios. Forty-five mentally retarded patients not receiving anticonvulsant drugs provided the controls. Further, because serum phenytoin levels have been related to severity of gingival hyperplasia, efforts were made to determine if the hyperplasia was associated with dental root abnormalities and also whether these abnormalities could be related to epilepsy per se.

Operative procedures: is standardization feasible or necessary?

Standardization of surgical procedures is both feasible and necessary in clinical trials. To the extent that an operation may influence prognosis, identify prognostic factors, or reveal variables upon which additional treatment is contingent, the operation must be defined precisely enough to permit the determinations to be made uniformly and to enable the surgeons to meet the necessary standardization. If uniform procedures are to be applied widely, surgeons who participate in therapeutic trials must meet the standards of clinical scientists and accept special obligations for eduction and self-discipline.

Experimental alveolar bone loss in the monkey evaluated by 125I absorptiometry.

An 125I absorptiometry technique is described which has sufficient precision to detect the alveolar bone loss associated with ligature-related periodontitis in the monkey. Six monkeys had significant drops in alveolar bone mass 14 days after the the application of a silk ligature around the gingival margin of an adjacent tooth. Variation in the magnitude of bone loss was observed.

Results with methyl-CCNU and DTIC in metastatic melanoma.

This report is the result of an Eastern Cooperative Oncology Group (ECOG) study. Four hundred and 15 patients with inoperable metastatic malignant melanoma, excluding those with cutaneous metastases only, were randomized to one of three drug treatments: DTIC alone, methyl-CCNU alone, or the combination DTIC plus methyl-CCNU. Responses were seen in 14% of DTIC patients (19/127), 15% of methyl-CCNU patients (18/119) and 14% of DTIC plus methyl-CCNU patients (18/122).

Lymphoproliferative response during resolution and recurrence of naturally occurring gingivitis.

The lymphocyte blastogenic response in humans to oral bacterial antigens was investigated during resolution and recurrence of naturally occurring gingivitis. The following conclusions were drawn: 1. Actinomyces and Fusobacterium and the host responses they evoke, are associated with gingival inflammation.

Diethylstilbestrol: recommended dosages for different categories of breast cancer patients. Report of the Cooperative Breast Cancer Group.

A total of 523 postmenopausal breast cancer patients with progressive disease were entered in a radomized, double-blind study of four dosages of diethylstibestrol (DES): 1.5, 15, 150, OR 1,500 MG/DAY. Higher dosages produced significantly (p less than .

Combined androgen and antimetabolite therapy of advanced female breast cancer. A report of the cooperative breast cancer group.

A clinical trial of androgen and antimetabolite therapy of advanced female breast cancer was conducted in 110 patients by the Cooperative Breast Cancer Group. An objective regression rate of 20% was achieved in women receiving oral testolactone, 6% in patients given intravenous fluorouracil alone, and 14% when the androgen and antimetabolite were administered together. This randomized trial according to the CBCG protocol did not produce the high regression rate noted previously in a nonrandomized, nonprotocol evaluation of these drugs.