An R package for simulation experiments evaluating clinical trial designs

This paper presents an open-source application for evaluating competing clinical trial (CT) designs using simulations. The S4 system of classes and methods is utilized. Using object-oriented programming provides extensibility through careful, clear interface specification; using R, an open-source widely-used statistical language, makes the application extendible by the people who design CTs: biostatisticians. Four key classes define the specifications of the population models, CT designs, outcome models and evaluation criteria. Five key methods define the interfaces for generating patient baseline characteristics, stopping rule, assigning treatment, generating patient outcomes and calculating the criteria. Documentation of their connections with the user input screens, with the central simulation loop, and with each other faciliates the extensibility. New subclasses and instances of existing classes meeting these interfaces can integrate immediately into the application. To illustrate the application, we evaluate the effect of patient pharmacokinetic heterogeneity on the performance of a common Phase I "3+3" design.

A clinical and genetic study of the Say/Barber/Biesecker/Young-Simpson type of Ohdo syndrome

We report a series of eight patients with the Say/Barber/Biesecker/Young-Simpson (SBBYS) type of Ohdo syndrome, which is the largest cohort described to date. We expand on the type, frequency and severity of the clinical characteristics in this condition; comment on the natural history of Ohdo syndrome and further refine previously published diagnostic criteria. Cytogenetic investigations and microarray CGH analysis undertaken in this cohort of patients failed to identify a chromosomal aetiology. It remains possible that this rare condition is heterogeneous and therefore caution must be undertaken during counselling until the underlying genetic mechanism(s) is (are) identified.

The Radiation Injury Severity Classification system: an early injury assessment tool for the frontline health-care provider

Our goal was to adapt current diagnostic methods for radiation overexposure patients into a practical system that can be implemented rapidly and reliably by responders unfamiliar with the effects of radiation. Our Radiation Injury Severity Classification (RISC) system uses clinical and haematological parameters from the prodromal phase of the acute radiation syndrome (ARS) to classify acute radiation injury for purposes of managing treatment disposition. Data from well-documented ARS cases were used to test the RISC system. Three-day summaries were generated for each case. These were individually reviewed by the three physicians most involved with the development of the system to establish both a consensus case score (CCS) and disposition category ranges. 30 volunteer raters from varying health disciplines using the RISC system then each independently rated a random selection of 12 cases for injury severity in a self-trained field-simulation exercise. The CCS identified discrete cut-off ranges for the three disposition categories in both manageable and mass casualty events. The group of raters, after a modest period of self-training, achieved overall levels of pairwise agreement with the CCS category of 0.944 for manageable events and 0.947 for mass casualty situations. In conclusion, an early assessment of the severity of the ARS injury is required for an appropriate disposition determination. The RISC system should produce reasonably accurate and reliable assessments of radiation injury severity within 6-12 hours post exposure despite the probable absence of physical dosimetric data.

Assessment of the hip reduction angle for predicting osteoarthritis of the hip in the Labrador Retriever

Hip palpation has been used to provide semiquantitative information regarding passive joint laxity and susceptibility to hip dysplasia. The purpose of this study was to: (1) evaluate the intra- and inter-examiner repeatability of the hip reduction angle measured at 4 months of age by three examiners using manual goniometry and an electromagnetic tracking system; (2) compare the hip reduction angle measured with manual goniometry to the hip reduction angle measured with the electromagnetic tracking system; and (3) evaluate the hip reduction angle, distraction index and Ortolani manoeuvre at 4 months of age as predictors of the development of hip osteoarthritis at 12 months of age in 11 Labrador Retriever dogs. Intra- and inter-examiner repeatability was demonstrated for both the manual and electromagnetic goniometric measurement of the hip reduction angle (coefficient of variation < 4.3% and < 6.1%; and P = 0.163 and P = 0.836 respectively). The hip reduction angle measured by manual goniometry was moderately correlated to the hip reduction angle measured by the electromagnetic tracking system (r = 0.603, P < 0.0000). The hip reduction angle measured by manual and electromagnetic goniometry was a poor predictor of osteoarthritis at 12 months of age (r = 0.231, P < 0.062, and r = 0.321, P < 0.01). The distraction index was moderately correlated with the development of osteoarthritis by 12 months of age (r = 0.493, P < 0.0000). The Ortolani sign was sensitive (100%) but not specific (41%) for the development of osteoarthritis at 12 months of age. The hip reduction angle did not further quantify the Ortolani manoeuvre as a predictor of osteoarthritis in Labrador Retrievers.

Randomized trial of toremifene to reduce high grade prostatic intraepithelial neoplasia (HGPIN) prior to radical prostatectomy (RP)

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Background HGPIN may be a precursor lesion for prostate cancer (PCA). The selective estrogen-receptor modulator toremifene (TOR) has shown chemopreventive activity in preclinical models of PCA. The effect of TOR on HGPIN was studied in men with PCA prior to RP. Methods Men with biopsy-proven PCA, scheduled for RP were randomized (2:1) either to TOR 40 mg po qd for 3 to 6 weeks prior to RP or to no therapy. The primary endpoint was the proportion of HGPIN in the RP specimen. Planned sample sizes were 35 and 17 per arm respectively, providing 93% power if treatment increased the proportion of patients with no RP HGPIN from 15% to 35% and decreased the mean log nonzero HGPIN values from 1 to ¼ standard deviation. Expression of bcl2, ki67, and CD31 were determined on biopsy (BX), and RP tissues, separately for normal adjacent to tumor (NAT), HGPIN, and PCA tissues. Serum hormone levels and toxicity were also assessed. Results The treatment arm accrued 31 patients, the control arm 13 patients. RP HGPIN ranged from 0.5% to 12%. There was no difference in HGPIN means between treatment (3.8%) and control (3.3%) (P=0.77 one-sided Wilcoxon) HGPIN at baseline predicted HGPIN at RP (Spearman correlation=0.64, P=0.0005) but 66% of patients had no detected HGPIN at baseline. Bcl2, ki67, and CD31 were mutually positively correlated in all 3 tissues, in both BX and RP specimens. In both BX and RP specimens, bcl2 was highest by far in HGPIN, and lowest in PCA. Ki67 was lowest in NAT, elevated in HGPIN and highest in PCA. CD31 showed no differences. In treated patients but not in controls, dihydrotestosterone, testosterone, androstenedion, and estradiol increased significantly between baseline, day 14 and final. TOR was well tolerated. Conclusions These data do not support an effect of TOR on HGPIN over 3 to 6 weeks at 40 mg po qd.

No significant financial relationships to disclose.

Tag-mass: specific molecular imaging of transcriptome and proteome by mass spectrometry based on photocleavable tag

MALDI tissue imaging of tissues has become a promising technique for tracking biomarkers while determining their location and structural characterization. We have now developed specific targeting probes (oligonucleotides, antibodies), named Tag-Mass. This approach is based on probes modified with a photocleavable linker coupled with a tag cleaved and detected using mass spectrometry. Tag-Mass development is the key for a rapid, sensitive, and accurate approach to correlate levels of expression of different mRNA or proteins in diseases.

MALDI-MS direct tissue analysis of proteins: Improving signal sensitivity using organic treatments

Direct tissue analysis using MALDI-MS allows the generation of profiles while maintaining the integrity of the tissue, displaying cellular localizations and avoiding tedious extraction and purification steps. However, lower spectral quality can result from direct tissue analysis due to variations in section thickness, the nature of the tissue, and the limited access to peptides/proteins due to high lipid content. To improve signal sensitivity, we have developed a tissue-washing procedure using organic solvents traditionally used for lipid extraction, i.e., CHCl3, hexane, toluene, acetone, and xylene. The increased detection for peptides/proteins (m/z 5000-30,000) is close to 40% with chloroform or xylene, and 25% with hexane, while also improving sample reproducibility for each solvent used in the present study. This strategy improved matrix cocrystallization with tissue peptides/proteins and more importantly with cytoplasmic proteins without delocalization. The extracted lipids were characterized by nanoESI-QqTOF/MS/MS using the precursor ion mode, lithium adducts, or both and were identified as phospholipids including phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and lysophosphatidylinositol, confirming membrane lipid extraction from the tissues.

Three-fold reduction in the prevalence of tuberculosis over 25 years in Indonesia

BACKGROUND

Tuberculosis (TB) remains the principal cause of death from a curable infectious disease. Indonesia is estimated to have the third highest case load worldwide, but TB prevalence has not been measured for 25 years.

METHODS

In 2004, 20000 households were selected in all 30 provinces. All adults (aged >/=15 years) in every household were screened for symptoms of pulmonary tuberculosis (PTB). Among those with symptoms, TB was diagnosed by sputum smear microscopy and sputum culture.

RESULTS

Eighty adults were positive on at least two sputum smears (104 per 100000 population, 95%CI 66-142). Prevalence was lower in Central Indonesia (Java-Bali, 59/100000) than in the Western (Sumatra, 160/100000) or Eastern regions (189/100000), but the estimated 225000 prevalent cases were distributed evenly among the three regions. The national per capita prevalence in 2004 was lower than in 1979-1982 by a factor of three (3.1, 95%CI 1.2-4.9), and the total number of cases was lower by a factor of two.

CONCLUSIONS

Although the 2004 national survey may have underestimated the prevalence of smear-positive TB in Indonesia, there is strong evidence that it fell markedly between 1979-1982 and 2004.

Direct analysis and MALDI imaging of formalin-fixed, paraffin-embedded tissue sections

Formalin fixation, generally followed by paraffin embedding, is the standard and well-established processing method employed by pathologist. This treatment conserves and stabilizes biopsy samples for years. Analysis of FFPE tissues from biopsy libraries has been, so far, a challenge for proteomics biomarker studies. Herein, we present two methods for the direct analysis of formalin-fixed, paraffin-embedded (FFPE) tissues by MALDI-MS. The first is based on the use of a reactive matrix, 2,4-dinitrophenylhydrazine, useful for FFPE tissues stored less than 1 year. The second approach is applicable for all FFPE tissues regardless of conservation time. The strategy is based on in situ enzymatic digestion of the tissue section after paraffin removal. In situ digestion can be performed on a specific area of the tissue as well as on a very small area (microdigestion). Combining automated microdigestion of a predefined tissue array with either in situ extraction prior to classical nanoLC/MS-MS analysis or automated microspotting of MALDI matrix according to the same array allows the identification of both proteins by nanoLC-nanoESI and MALDI imaging. When adjacent tissue sections are used, it is, thus, possible to correlate protein identification and molecular imaging. These combined approaches, along with FFPE tissue analysis provide access to massive amounts of archived samples in the clinical pathology setting.

Functional characterization of a novel insulin receptor mutation contributing to Rabson-Mendenhall syndrome

OBJECTIVE/PATIENTS

Rabson-Mendenhall syndrome (RMS) is a rare, recessively inherited disorder of extreme insulin resistance due to mutations in the insulin receptor gene. We have identified a pair of siblings with RMS attributable to compound heterozygosity for two insulin receptor mutations, one previously unreported, and have characterized the novel receptor mutation functionally.

MEASUREMENTS

Insulin receptor sequencing was performed to identify the mutations. Expression levels of the mature receptor were determined in lymphoblastoid cells from the affected subjects. Further studies of immortalized cell lines transfected with mutant and wild type (WT) receptors were undertaken to characterize the effects of the novel mutation on [(125)I]-labelled insulin binding, proreceptor processing and insulin-stimulated receptor autophosphorylation.

RESULTS

Sequencing of the insulin proreceptor coding sequence revealed both siblings to be compound heterozygotes for the missense mutations Arg209His and Gly359Ser in the mature insulin receptor. The former mutation has been described in homozygous form in Donohue syndrome, while the latter is novel. Insulin receptor expression in lymphoblastoid cell lines was present at only 10-30% of that in control cells; studies of immortalized cells transfected with mutant and WT receptors confirmed the reduced expression of the mutant. The degree of impairment of insulin binding and insulin-stimulated receptor autophosphorylation were commensurate with the decrease in expression of the mature receptor.

CONCLUSIONS

Loss of function of the novel insulin receptor (INSR) G359S variant is largely accounted for by aberrant proreceptor processing rather than intrinsically impaired signal transduction by the mutant receptor.

An integrated analysis of five double-blind, randomized controlled trials evaluating the safety and efficacy of a hyaluronan product for intra-articular injection in osteoarthritis of the knee

OBJECTIVE

Five double-blind, randomized, saline-controlled trials (RCTs) were included in the United States marketing application for an intra-articular hyaluronan (IA-HA) product for the treatment of osteoarthritis (OA) of the knee. We report an integrated analysis of the primary Case Report Form (CRF) data from these trials.

METHOD

Trials were similar in design, patient population and outcome measures - all included the Lequèsne Algofunctional Index (LI), a validated composite index of pain and function, evaluating treatment over 3 months. Individual patient data were pooled; a repeated measures analysis of covariance was performed in the intent-to-treat (ITT) population. Analyses utilized both fixed and random effects models. Safety data from the five RCTs were summarized.

RESULTS

A total of 1155 patients with radiologically confirmed knee OA were enrolled: 619 received three or five IA-HA injections; 536 received "placebo" saline injections. In the active and control groups, mean ages were 61.8 and 61.4 years; 62.4% and 58.8% were women; baseline total Lequèsne scores 11.03 and 11.30, respectively. Integrated analysis of the pooled data set found a statistically significant reduction (P < 0.001) in total Lequèsne score with hyaluronan (HA) (-2.68) vs placebo (-2.00); estimated difference -0.68 (95% CI: -0.56 to -0.79), effect size 0.20. Additional modeling approaches confirmed robustness of the analyses.

CONCLUSIONS

This integrated analysis demonstrates that multiple design factors influence the results of RCTs assessing efficacy of intra-articular (IA) therapies, and that integrated analyses based on primary data differ from meta-analyses using transformed data.

Furin regulates the intracellular activation and the uptake rate of cell surface-associated MT1-MMP

Invasion-promoting membrane type-1 matrix metalloproteinase (MT1-MMP) functions in cancer cells as an oncogene and as a mediator of proteolytic events on the cell surface. To exert its functional activity, MT1-MMP requires proteolytic removal of the prodomain sequence. There are two potential furin cleavage motifs, R(89)-R-P-R-C(93) and R(108)-R-K-R-Y(112), in the prodomain sequence of MT1-MMP. Our data suggest an important role of furin and related proprotein convertases (PCs) in mediating both the activation of MT1-MMP and the levels of functionally active MT1-MMP at the surface of cancer cells. We have determined that the peptide sequence that spans the first cleavage site is susceptible to furin and PC5/6, whereas the second sequence is susceptible to furin and also to PC5/6, PC7 and PACE4. In the structure of the MT1-MMP proenzyme, the R(89)-R-P-R-C(93) site, however, is inaccessible to PCs. Our studies also demonstrated a direct functional link between the activation and the uptake rate of the proenzyme and the enzyme of MT1-MMP. Thus, the uptake rate of the latent MT1-MMP proenzyme noticeably exceeded that of the active enzyme. We conclude that furin and related PCs are the essential components of the specialized cellular machinery that controls the levels of the functionally active, mature, MT1-MMP enzyme on the cell surface to continually support the potency of pericellular proteolysis.

Cooperative partnerships or conflict-of-interest? A national survey of interaction between the pharmaceutical industry and medical organizations

BACKGROUND

There is extensive and varied interaction between the pharmaceutical industry and the medical profession. Most empirical research concerns contact between individual physicians and industry, and reflects North American experience. We sought to clarify the extent and nature of relationships between the pharmaceutical industry and Australian medical organizations.

METHODS

We administered questionnaires to 63 medical organizations concerned with clinical practice, continuing medical education or professional accreditation, or the political representation of medical professionals.

RESULTS

Survey instruments were received from 29 organizations, giving a response rate of 46%. Seventeen of these organizations (59%) had received support from one or more pharmaceutical company in the past financial year. Support was predominantly for annual conferences, with some support for continuing medical education, research, travel and library purchases. The majority of organizations had an academic journal or newsletter, and 10 (34%) accepted revenue from pharmaceutical advertising. Twenty organizations (72%) had policies or guidelines covering their relationship with industry. Few organizations indicated that they would be unable to continue their activities without pharmaceutical industry support.

CONCLUSION

These data indicate a high level of inter-action between the pharmaceutical industry and medical organizations in Australia. While most organizations have policies for guiding their relationship with industry, it is unclear whether these are effective in preventing conflicts of interest and maintaining public trust.

Phase I study of a MUC1 vaccine composed of different doses of MUC1 peptide with SB-AS2 adjuvant in resected and locally advanced pancreatic cancer

MUC1 is a glycoprotein overexpressed in tumors as a hypoglycosylated form. A vaccine composed of a 100-amino acid peptide corresponding to five 20-amino acid long repeats, and SB-AS2 adjuvant, was tested in a phase I study for safety, toxicity, and ability to elicit or boost MUC1-specific immune responses. Patients with resected or locally advanced pancreatic cancer without prior chemotherapy or radiotherapy were eligible. Escalating doses of the peptide (100, 300, 1,000, and 3,000 mug) were admixed with SB-AS2 and administered intramuscularly every 3 weeks for three doses, in cohorts of four patients. Sixteen patients were enrolled. Common adverse effects were grade 1 flu-like symptoms, tenderness, and erythema at the injection site. Delayed-type hypersensitivity (DTH) sites showed few or no T cells prevaccination (Pre V), but increased T-cell infiltration postvaccination (Post V). There was an increase in the percentage of CD8(+) T cells in the peripheral blood Post V. An increase in total MUC1-specific antibody was seen in some patients, and several patients developed IgG antibody. Two of 15 resected pancreatic cancer patients are alive and disease free at follow-up of 32 and 61 months. MUC1 100mer peptide with SB-AS2 adjuvant is a safe vaccine that induces low but detectable mucin-specific humoral and T-cell responses in some patients. No difference was seen between different peptide doses. Further evaluation is warranted to examine the effect on disease-free survival and overall survival, especially in early disease and in the absence of immunosuppressive standard therapy.

Low overexpression of HER-2/neu in advanced colorectal cancer limits the usefulness of trastuzumab (Herceptin) and irinotecan as therapy. A phase II trial

BACKGROUND

To determine the response rate of trastuzumab and irinotecan in HER-2/neu overexpressing advanced colorectal cancer (CRC), determine the frequency of HER-2/neu expression in CRC, and evaluate the pharmacokinetics of trastuzumab in a phase II study.

PATIENTS AND METHODS

Patients were screened for HER-2/neu by immunohistochemistry (DAKO HercepTest). Prior chemotherapy was limited to one regimen. Trastuzumab was administered weekly (loading dose of 4 mg/kg i.v. and 2 mg/kg thereafter). Irinotecan 125 mg/m2, i.v. was administered weekly for 4 weeks with a 2-week rest period.

RESULTS

HER-2/neu overexpression was detected in 11 of 138 (8.0%) of screened tumors (2+ in 5 and 3+ in 6 patients). Nine patients were entered in the study; 6 had received prior chemotherapy. Partial responses were seen in 5 of 7 evaluable patients. Grade 3-4 toxicities in 31 cycles of therapy included diarrhea (19%), nausea (10%), and vomiting (6%). Leukopenia occurred in 6%, and congestive heart failure and acute renal failure (secondary to diarrhea and dehydration) were seen in 3% of cycles. The study was prematurely closed due to low accrual.

CONCLUSIONS

The low overexpression rate of HER-2/neu (8.0%) in advanced CRC limits the potential for further investigation of regimens involving trastuzumab, despite evidence suggestive of activity. Irinotecan did not alter the pharmacokinetic disposition of trastuzumab.