Design of VA CoronavirUs Research and Efficacy Studies-1 (VA CURES-1): A double-blind, randomized placebo-controlled trial of COVID-19 convalescent plasma in hospitalized patients with early respiratory compromise

BACKGROUND

Effective therapeutics for severe acute respiratory syndrome CoronaVirus-2 (SARS-CoV-2) infection are evolving. Under Emergency Use Authorization, COVID-19 convalescent plasma (CCP) was widely used in individuals hospitalized for COVID-19, but few randomized controlled trials supported its efficacy to limit respiratory failure or death.

METHODS

VA CoronavirUs Research and Efficacy Studies-1 (VA CURES-1) was a double-blind, multi-site, placebo-controlled, randomized clinical trial evaluating the efficacy and safety of CCP with conventional therapy in hospitalized Veterans with SARS-CoV-2 infection and early respiratory compromise (requirement for oxygen). Participants (planned sample size 702) were randomized 1:1 to receive CCP with high titer neutralizing activity or 0.9% saline, stratified by site and age (≥65 versus <65 years old). Participants were followed daily during initial hospitalization and at Days 15, 22 and 28.

OUTCOMES

The composite primary outcome was acute hypoxemic respiratory failure or all-cause death by Day 28. Secondary outcomes by day 28 included time-to-recovery, clinical severity, mortality, rehospitalization for COVID-19, and adverse events. Serial respiratory and blood samples were collected for safety, virologic and immunologic analyses and future studies. Key variables in predicting the success of CURES-1 were: (1) enrollment early in the course of severe infection; (2) use of plasma with high neutralizing activity; (3) reliance on unambiguous, clinically meaningful outcomes. CURES-1 was terminated for futility due to perceived inability to enroll in the lull between the Alpha and Delta waves of the SARS CoV-2 epidemic.

CONCLUSIONS

VA CURES-1 was a large multi-site trial designed to provide conclusive information about the efficacy of CCP in well-characterized patients at risk for progression of COVID-19. It utilized a rigorous study design with relevant initial timing, quality of product and outcomes.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04539275.

A statistical quality assessment method for longitudinal observations in electronic health record data with an application to the VA million veteran program

Background

To describe an automated method for assessment of the plausibility of continuous variables collected in the electronic health record (EHR) data for real world evidence research use.

Methods

The most widely used approach in quality assessment (QA) for continuous variables is to detect the implausible numbers using prespecified thresholds. In augmentation to the thresholding method, we developed a score-based method that leverages the longitudinal characteristics of EHR data for detection of the observations inconsistent with the history of a patient. The method was applied to the height and weight data in the EHR from the Million Veteran Program Data from the Veteran’s Healthcare Administration (VHA). A validation study was also conducted.

Results

The receiver operating characteristic (ROC) metrics of the developed method outperforms the widely used thresholding method. It is also demonstrated that different quality assessment methods have a non-ignorable impact on the body mass index (BMI) classification calculated from height and weight data in the VHA’s database.

Conclusions

The score-based method enables automated and scaled detection of the problematic data points in health care big data while allowing the investigators to select the high-quality data based on their need. Leveraging the longitudinal characteristics in EHR will significantly improve the QA performance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12911-021-01643-2.

Treatment Preferences for Chronic Low Back Pain: Views of Veterans and Their Providers

Purpose

This study was conducted to characterize chronic low back pain (cLBP) and to identify treatment histories and preferences for cLBP management among Veterans and primary care providers within the Veterans Affairs (VA) healthcare system.

Participants and Methods

Veterans with cLBP from five geographically diverse VA medical centers were identified using International Classification of Diseases (ICD) 9 and 10 codes from VA administrative data as were primary care providers at these same sites. From these data, Veterans (200/per site) and providers (160/per site) were selected and mailed surveys. Open-ended interview data were collected from a subset of Veterans and providers.

Results

In total, 235 Veterans and 67 providers returned completed surveys. More than 80% of the Veteran respondents had daily back pain for more than 1 year. Most Veterans had tried several treatments for their pain with medications and physical therapy being the most commonly used. Veterans and providers had similar attitudes towards many cLBP treatments with the exception of psychological therapies that were more favored by providers. Open-ended interview data showed that Veterans and providers emphasized the need for multi-component approaches to treatment.

Conclusion

Among Veterans, cLBP is typically of sustained duration, is relatively severe, and also interferes significantly with normal functioning. Veterans are experienced with respect to treatments and had similar attitudes towards many cLBP treatments as their providers, especially tailored approaches.

Increasing the Frequency of Night Float Teaching with a Daily Management System: Where Medical Education Meets Quality Improvement

Daytime resident rotations have a well-established system for incorporating didactic teaching into clinical rotations. However, how to create and sustain a parallel system of didactics for night rotations is less established. We aimed to use Lean methodology to increase the frequency of didactic teaching at night and improve house staff perception of the educational value of night float. Our educational intervention was comprised of the implementation of a daily management system (DMS) with a visual dashboard to track whether evening report was held and a repository of prepared lectures. With this intervention, the rate of evening report tripled from 18 to 55%, demonstrating that a daily management system can be successfully used to improve performance of an educational outcome by increasing attending and resident engagement on night float.

Use of a Hands Free, Instantaneous, Closed-Loop Communication Device Improves Perception of Communication and Workflow Integration in an Academic Teaching Hospital: A Pilot Study

Efficient and effective communication between providers is critical to quality patient care within a hospital system. Hands free communication devices (HFCD) allow instantaneous, closed-loop communication between physicians and other members of a multidisciplinary team, providing a communication advantage over traditional pager systems. HFCD have been shown to decrease emergency room interruptions, improve nursing communication, improve speed of information flow, and eliminate health care waste. We evaluated the integration of an HFCD with an existing alphanumeric paging system on an acute inpatient medicine service. We conducted a prospective, observational, survey-based study over twenty-four weeks in an academic tertiary care center with attending physicians and residents. Our intervention involved the implementation of an HFCD alongside the existing paging system. Fifty-six pre and post surveys evaluated the perception of improvement in communication and the integration of the HFCD into existing workflow. We saw significant improvements in the ability of an HFCD to help physicians communicate thoughts clearly, communicate thoughts effectively, reach team members, reach ancillary staff, and stay informed about patients. Physicians also reported better workflow integration during admissions, rounds, discharge, and teaching sessions. Qualitative data from post surveys demonstrated that the greatest strengths of the HFCD included the ability to reach colleagues and staff quickly, provide instant access to individuals of the care team, and improve overall communication. Integration of an instantaneous, hands free, closed loop communication system alongside the existing pager system can provide improvements in the perceptions of communication and workflow integration in an academic medicine service. Future studies are needed to correlate these subjective findings with objective measures of quality and safety.

Atypical ezrin localization as a marker of locally advanced breast cancer

Locally advanced breast cancer (LABC) was initially characterized as a large primary tumor (≥5 cm), associated with or without skin or chest-wall involvement, fixed axillary lymph nodes, or disease spread to the ipsilateral internal mammary or supraclavicular nodes. Since 2002, LABC has been reclassified to include smaller stage IIB tumors (2 to <5 cm) with lymph node involvement, or stages IIIA-IIIB (≥5 cm) with or without nodal involvement. Despite the rather common presentation of LABC, it remains a poorly understood and highly variable clinical presentation of breast cancer that is a challenge to treatment. Here, we characterized a panel of breast tumors of known stage, grade, and key clinical-pathological parameters for the expression of the protein ezrin, which is involved in promoting signaling of the PI3K-Akt-mTOR pathway in response to extracellular and tumor micro-environmental signals, and is involved in breast cancer invasion and metastasis. We show that ezrin, which resides primarily in the apical membrane in normal breast epithelium, relocalizes primarily to the cytoplasm in >80 % of traditional (T3) invasive ductal LABC tumors (≥5 cm). Cytoplasmic ezrin is very strongly associated with a single characteristic in breast cancer-large tumor size. In contrast, in large non-malignant fibroadenomas, ezrin staining was similar to that of normal breast epithelium. Small (T1, 1 cm) invasive ductal carcinomas displayed largely apical membrane and perinuclear ezrin localization with weak cytoplasmic staining. Cytoplasmic ezrin localization was also associated with positive lymph node status, but no other clinical-pathological features, including hormone receptor status, histological or nuclear grade of tumor cell. The cytoplasmic relocalization of ezrin may therefore represent a novel marker for large malignant tumor size, reflecting the unique biology of LABC.

Single versus multiple primary melanomas: old questions and new answers

BACKGROUND

In patients with multiple primary melanomas (MPM), mean tumor thickness tends to decrease from the first melanoma to the second melanoma, and prognosis may be improved compared with the prognosis for patients who have a single primary melanoma (SPM). In this study, the authors compared the clinicopathologic features of patients with MPM and SPM to better characterize the differences between these 2 groups and to determine whether or not there is an inherent difference in tumor aggression.

METHODS

In total, 788 patients with melanoma who were enrolled prospectively in the Interdisciplinary Melanoma Cooperative Group database from 2002 to 2008 were studied. Patients with SPM and with MPM were compared with regard to clinical and primary melanoma characteristics.

RESULTS

Of 788 patients with melanoma, 61 patients (7.7%) had 2 or more primary melanomas. The incidence of developing a second primary melanoma 1 year and 5 years after initial melanoma diagnosis was 4.1% and 8.7%, respectively, and most of the risk accumulated within the first year. The incidence of MPM was greater in patients aged ≥60 years than in those aged ≤60 years. The absence or presence of mitosis and other tumor characteristics did not differ significantly between patients with SPM and patients with MPM (P = .61).

CONCLUSIONS

No difference was observed in the presence or absence of mitoses, a marker of tumor proliferation, in SPM and MPM. Because it has been demonstrated that the presence of mitosis is a powerful prognostic marker, the current findings suggested that the tumors behave similarly in patients with SPM and patients with MPM. The authors concluded that differences in tumor thickness and prognosis between SPM and MPM more likely are caused by factors other than tumor biology, such as increased surveillance.

Abstract 3672: Defining the genomic signature of the parous breast

Epidemiological data have consistently shown that a pregnancy early in life confer mothers lifetime protection against breast cancer, which is enhanced by subsequent pregnancies. Previous studies have demonstrated that the protection conferred by pregnancy is mediated by the differentiation of the breast, which is expressed as a specific genomic profile detectable in breast cells of postmenopausal parous women that serves as a biomarker indicative of reduced cancer risk. For further confirming these observations we designed a multidisciplinary study for determining whether the pattern of gene expression differed between nulliparous and parous postmenopausal women from an ethnically homogeneous population residing in Norrbotten County, Sweden; the study was approved by the IRB/Ethical Board of the University of Umeå, Sweden. Volunteer women from 50-69 years of age, belonging to one of the following categories based on reproductive history: parous (G≥1/P≥1), nulligravida nullipara (G0/P0) or gravida nullipara (G≥1/P0). The subjects signed an informed consent to participate in the study and donated core needle biopsies (CNB) of breast. CNB were taken from the upper outer quadrant of the breast and divided for 70% ethanol fixation for histopathological analysis and RNA extraction for subsequent genomic analysis. Total RNA was isolated using the Qiagen Allprep RNA/DNA Mini Kit. RNA quantity and quality were determined and the GeneChip Expression 3’-Amplification Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) was used to prepare the cRNA for hybridization; samples were hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays; 71 parous and 42 nulliparous satisfied quality control thresholds based on standard Affymetrix quality control measures. Probesets for which the proportion of Present calls was less than 75% in both samples were filtered out. A variance filter was also applied, removing all probesets whose variance across all samples fell below the first quartile, remaining 18,694 probesets for further analysis using both a p-value of 0.001 from the empirical Bayes moderated t-statistics, and a minimum log2 fold-change of 0.3 threshold as criteria of significance. Two hundred and eight genes were found to be differentially expressed between parous and nulliparous women. Gene ontology and pathway analyses revealed enrichment of biological processes related to regulation of transcription, RNA splicing, cell cycle control, adhesion and differentiation. IGF-like growth factor signaling and somatic stem cell maintenance were significantly downregulated. These results demonstrated that the breast of parous postmenopausal women exhibits a transcriptomic profile that differs from that of nulliparous women, representing a genomic signature induced by full term pregnancy that is indicative of breast differentiation.

Work supported by Avon Foundation Women Breast Cancer Research Program grant 02-2008-034.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3672. doi:10.1158/1538-7445.AM2011-3672

Efficacy and safety of radical resection of primary and recurrent craniopharyngiomas in 86 children

OBJECT

Optimal treatment of primary and recurrent craniopharyngiomas remains controversial. Radical resection and limited resection plus radiation therapy yield similar rates of disease control and overall survival. The data are much less clear for recurrent tumors. The authors report their experience with radical resection of both primary and recurrent craniopharyngiomas in children and compare the outcomes between the 2 groups.

METHODS

A retrospective analysis was performed in 86 children younger than 21 years of age who underwent a total of 103 operations for craniopharyngioma between 1986 and 2008; these were performed by the senior author. The goal was resection with curative intent in all patients. Two patients were lost to follow-up and were excluded from analysis. The mean age at the time of surgery was 9.6 years, and the mean follow-up was 9.0 years.

RESULTS

All 57 children with primary tumors underwent gross-total resection (GTR). A GTR was achieved in significantly fewer children with recurrent tumors (18 [62%] of 29). There were 3 perioperative deaths (3%). Tumor recurred after GTR in 14 (20%) of 71 patients. Overall survival and progression-free survival were significantly better in patients with primary tumors at time of presentation to the authors' institution. There were no significant differences in the neurological, endocrinological, visual, or functional outcomes between patients with primary and those with recurrent tumors. Factors negatively affecting overall survival and progression-free survival include subtotal resection (recurrent tumors only), tumor size >or= 5 cm, or presence of hydrocephalus or a ventriculoperitoneal shunt. Prior radiation therapy and increasing tumor size were both risk factors for incomplete resection at reoperation.

CONCLUSIONS

In the hands of surgeons with experience with craniopharyngiomas, the authors believe that radical resection at presentation offers the best chance of disease control and potential cure with acceptable morbidity. While GTR does not preclude recurrence and is more difficult to achieve in recurrent tumors, especially large and previously irradiated tumors, radical resection is still possible in patients with recurrent craniopharyngiomas with morbidity similar to that of primary tumors.

Evaluation of the melanocortin-1-receptor gene in melanoma predisposition, progression, and recurrence

9018

Background: The melanocortin-1-receptor (MC1R) gene is highly polymorphic in humans. Multiple studies have shown the association between MC1R allelic variants and increased risk of melanoma. Over seventy MC1R single nucleotide polymorphisms (SNPs) have been identified making MC1R a likely target for the development of genetic markers for melanoma predisposition and progression. Alleles described as R and r result in a protein with reduced function compared to wild type, with r alleles having the greatest effect. We sought to investigate the impact of MC1R genotype on risk of developing melanoma and will test for association with disease progression and recurrence in a cohort of melanoma patients enrolled in a prospective study. Methods: Our cohort includes 291 newly diagnosed melanoma patients seen at the New York University Langone Medical Center. The control cohort included 449 subjects. DNA was isolated from leukocytes and analyzed for MC1R SNP status by PCR and direct sequencing. Associations were tested for R-variant R151C and r-variants V60L and V92M. Fisher's Exact test was used to detect significant differences in allele frequency. Odds ratios and confidence intervals were computed for each SNP. Results: Allele frequencies were significantly different in cases and controls for each of the variants (p<0.01). The greatest effect was seen with V60L (Odds Ratio=6.281 95% Confidence Interval 1.77- 22.20). Conclusions: Variants that result in reduced MC1R function increase an individual's risk of developing melanoma. We will continue to test associations with additional variants and determine if these alleles also contribute to risk of disease progression and recurrence. In addition, these variants will be tested for utility as biomarkers for risk assessment of melanoma in a clinical setting.

No significant financial relationships to disclose.

Developing genetic markers for melanoma risk assessment

9046

Background: Risk assessment for melanoma is currently based on phenotype, family and exposure history. This approach is subject to recall bias and excludes at-risk groups such as those with darker skin pigmentation. Poorly stratified risk pools also result in unnecessary dermatologist visits and biopsies for those at lower risk. Use of genetic markers may improve risk assessment; however few susceptibility markers have been developed to date. There have been a number of reports of association between melanoma and genetic markers though few have been replicated or validated. In addition, these studies frequently utilized specific coding region variants as markers and failed to test the entire gene. We have therefore assembled a case-control cohort in which to search for potential biomarkers for melanoma risk by interrogating genes using recently developed tools for genetic analysis. A pilot study was performed to test the utility of our cohort. Methods: A cohort of 326 individuals diagnosed with melanoma and treated at the New York University Langone Medical Center and 400 controls obtained from the New York Cancer project was assembled. Candidate genes were selected based on involvement in determining melanoma predisposition factors (skin pigmentation and DNA repair capability) and previous studies showing association. Three genes, ERCC1, ERCC4 (DNA repair) and MATP (skin pigmentation) were selected. Tag Single Nucleotide Polymorphisms (tSNPs) were selected using Haploview (Hapmap.org) and DNA genotyped (Sequenom Inc, San Diego, CA). Odds ratios and confidence intervals were computed for each SNP. Results: An association was found between SNP rs11615 at the ERCC1 locus and melanoma (Odds ratio = 1.718, 95% Confidence interval: 1.259 - 2.343 for TT vs TC/CC). Conclusions: A tSNP approach is thus useful in identifying associations in our melanoma case-control cohort. Sequence variation at the ERCC1 locus contributes to melanoma risk and the gene will now be screened for clinically useful susceptibility biomarkers. Additional DNA repair and pigmentation genes will also be interrogated using this approach. Genes found to be associated with melanoma will be screened by high- density SNP analysis to identify the most appropriate biomarker/s for use in risk assessment.

No significant financial relationships to disclose.

Clinical relevance of miRNA expression in metastatic melanoma

9006

Background: We recently reported the identification of a specific miRNA cluster frequently overexpressed in melanoma which enhances the metastatic behavior (Segura et al., 2009. PNAS. In press). In this study, we aim to define the clinical relevance of miRNA expression, in particular whether miRNAs can serve as prognostic biomarkers for melanoma patients. Methods: Total RNA was extracted from formalin-fixed paraffin embedded (FFPE) tissue samples from 61 metastatic melanoma specimens (25 lymph node, 16 soft tissue/skin, 13 brain and 7 visceral) accrued by the NYU Interdisciplinary Melanoma Cooperative Group (IMCG). RNA was hybridized into miRNA arrays (miRdicatorTM, Rosetta Genomics, Inc) containing probes for more than 600 miRNA sequences, including all the human miRNAs in the 9.0 version of miRBase. The Significance Analysis of Microarrays (SAM) was used to identify miRNAs significantly associated with survival, and the False Discovery Rate (FDR) approach was used to adjust for multiple comparisons. Results: We identified a signature of 18 miRNAs, whose up-regulation significantly associates with better prognosis (increased overall survival and post-recurrence survival) using the FDR of 0%. Quantitative RT-PCR on the same tissues has verified the array results in 15 out of 15 miRNAs analyzed. Some of these miRNAs were significantly associated with stage at recurrence, while others significantly correlated with the site of metastasis (i.e. visceral, brain, soft-tissue). Using cross-validation, we selected a miRNA signature consisting of 10 of these significant miRNAs with lowest misclassification error in predicting 1.5-year post-recurrence survival. We are currently validating these findings in a separate cohort of metastatic patients. Furthermore, we are investigating whether these ‘protective' miRNAs can be detected in the corresponding primary lesions and thus, whether they already hold prognostic value at early stages of the disease. Conclusions: Our data suggest a role for miRNAs as melanoma biomarkers, and support the development of miRNA- based monitoring assays. These analyses are also expanding our understanding of the molecular alterations underlying melanoma progression, by revealing miRNAs whose down-regulation associates with a more aggressive biological behavior.

[Table: see text]

Use of gene expression profile and mitotic index of metastatic melanoma lesions as an adjunct to TNM staging in predicting patient survival

9014

Background: Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling of metastatic lesions to search for a molecular basis for this observation, and to develop improved methods for predicting patient survival. Methods: We analyzed gene expression profiles of 44 metastatic melanoma specimens collected from 38 patients (median follow-up of 20 months after surgery). We used the False Discovery Rate (FDR) approach to identify genes significantly associated with post-recurrence survival. We then evaluated matching H&E stained tissue samples for the presence of tumor-infiltrating leukocytes (TILs) and mitotic index, (MI). Support vector machines and multi-variable Cox regression analysis was used to examine the relative ability of the pre-validated gene expression predictor, TILs, MI and TNM staging to predict survival. Results: We identified a group of approximately 300 genes associated with survival. Genes associated with immune response (ICOS, CD3d, ZAP70, TRAT1, TARP, GZMK, LCK, CD2, CXCL13, CCL19, CCR7, VCAM1 etc.) or with cell proliferation (PDE4D, CDK2, GREF1, NUSAP1, SPC24 etc.) were highly represented .Prolonged survival was associated with the elevated expression of immune response genes and decreased expression of genes associated with proliferation. Furthermore, any of the three additional parameters (pre-validated gene expression signature, TILs or MI) improved the ability of TNM staging to predict post-recurrence survival; MI was the most significant contributor (HR = 2.65, p = 0.003) followed by the gene expression signature (HR = 2.71, p = 0.05). Conclusions: Gene expression profiling and MI of metastatic lesions can both be utilized to improve upon current staging of metastatic melanoma to predict patient survival. Gene expression signature and analysis of TILs indicate immune surveillance as a mechanism for prolonged survival in these patients.

No significant financial relationships to disclose.

Distribution and evolution of T-cell receptor Vbeta repertoire on peripheral blood lymphocytes of newborn infants of human immunodeficiency virus (HIV)-infected mothers: differential display on CD4 and CD8 T cells and effect of HIV infection

Neonatal human peripheral blood mononuclear cells from 12 human immunodeficiency virus (HIV)-infected and 84 uninfected children were assessed for their distribution of T-cell receptors (TCRs) by flow cytometry employing monoclonal antibodies to 14 Vbeta types. Vbeta 2, 5c, and 13 were the most commonly found on CD4 cells (in that order). There was a bimodal distribution of Vbeta 2, being most common in 48% of individuals but in limiting frequency (<2% of CD4) in 21%. Vbeta 2, 3, 8b, and 13 were most commonly expressed on CD8 cells at similar frequencies. There was little difference in the pattern displayed among the infected compared to that of the uninfected. The variation of the distribution over time was studied in 12 infants (7 infected). Only a single HIV-infected child had a significant difference in the interquartile range; none of the HIV-negative patients showed a significant difference. In conclusion, newborns demonstrate different distributions of TCR Vbeta types on CD4 and CD8 cells. HIV infection produces no change in neonatal TCR and little change over the course of 2 years compared to that seen in the uninfected.

Biologic pathways associated with relapse in childhood acute lymphoblastic leukemia: a Children's Oncology Group study

Outcome for children with childhood acute lymphoblastic leukemia (ALL) who relapse is poor. To gain insight into the mechanisms of relapse, we analyzed gene-expression profiles in 35 matched diagnosis/relapse pairs as well as 60 uniformly treated children at relapse using the Affymetrix platform. Matched-pair analyses revealed significant differences in the expression of genes involved in cell-cycle regulation, DNA repair, and apoptosis between diagnostic and early-relapse samples. Many of these pathways have been implicated in tumorigenesis previously and are attractive targets for intervention strategies. In contrast, no common pattern of changes was observed among late-relapse pairs. Early-relapse samples were more likely to be similar to their respective diagnostic sample while we noted greater divergence in gene-expression patterns among late-relapse pairs. Comparison of expression profiles of early- versus late-relapse samples indicated that early-relapse clones were characterized by overexpression of biologic pathways associated with cell-cycle regulation. These results suggest that early-relapse results from the emergence of a related clone, characterized by the up-regulation of genes mediating cell proliferation. In contrast, late relapse appears to be mediated by diverse pathways.

A Generalized Clustering Problem, with Application to DNA Microarrays

We think of cluster analysis as class discovery. That is, we assume that there is an unknown mapping called clustering structure that assigns a class label to each observation, and the goal of cluster analysis is to estimate this clustering structure, that is, to estimate the number of clusters and cluster assignments. In traditional cluster analysis, it is assumed that such unknown mapping is unique. However, since the observations may cluster in more than one way depending on the variables used, it is natural to permit the existence of more than one clustering structure. This generalized clustering problem of estimating multiple clustering structures is the focus of this paper. We propose an algorithm for finding multiple clustering structures of observations which involves clustering both variables and observations. The number of clustering structures is determined by the number of variable clusters. The dissimilarity measure for clustering variables is based on nearest-neighbor graphs. The observations are clustered using weighted distances with weights determined by the clusters of the variables. The motivating application is to gene expression data.

Gene expression studies provide clues to the pathogenesis of uterine leiomyoma: new evidence and a systematic review

BACKGROUND

Uterine leiomyomas are extremely common and a major cause of pelvic pain, bleeding, infertility, and the leading indication for hysterectomy. Familial and epidemiological studies provide compelling evidence that genetic alterations play an important role in leiomyoma development.

METHODS

Using Affymetrix U133A GeneChip we analysed expression profiles of 22,283 genes in paired samples of leiomyoma and adjacent normal myometrium. We compared our results with previously published data on gene expression in uterine leiomyoma and identified the overlapping gene alterations.

RESULTS

We detected 80 genes with average differences of > or = 2-fold and false discovery rates of < 5% (14 overexpressed and 66 underexpressed). A comparative analysis including eight previous gene expression studies revealed eight prominent genes (ADH1, ATF3, CRABP2, CYR61, DPT, GRIA2, IGF2, MEST) identified by at least five different studies, eleven genes (ALDH1, CD24, CTGF, DCX, DUSP1, FOS, GAGEC1, IGFBP6, PTGDS, PTGER3, TYMS) reported by four studies, twelve genes (ABCA, ANXA1, APM2, CCL21, CDKN1A, CRMP1, EMP1, ESR1, FY, MAP3K5, TGFBR2, TIMP3) identified by three studies, and 40 genes reported by two different studies.

CONCLUSIONS

Review of gene expression data revealed concordant changes in genes regulating retinoid synthesis, IGF metabolism, TGF-beta signaling and extracellular matrix formation. Gene expression studies provide clues to the relevant pathways of leiomyoma development.

Renal Masses: Quantitative Analysis of Enhancement with Signal Intensity Measurements versus Qualitative Analysis of Enhancement with Image Subtraction for Diagnosing Malignancy at MR Imaging

PURPOSE

To retrospectively compare quantitative and qualitative methods of assessing magnetic resonance (MR) imaging contrast enhancement as the basis for diagnosing renal malignancy.

MATERIALS AND METHODS

MR imaging was performed by using a gadolinium-enhanced breath-hold fat-suppressed three-dimensional T1-weighted gradient-echo sequence in 71 patients (48 men and 23 women; mean age, 62 years; age range, 26-87 years) with 93 renal lesions for which pathologic correlation was available. For quantitative measurements of enhancement, the relative increase in signal intensity values was measured by one investigator with manually defined regions of interest, and the threshold of an increase of 15% or greater was used to distinguish malignant from benign masses. For qualitative assessment, two investigators independently reviewed the subtracted images of all lesions and subjectively determined whether enhancement was present or absent. The sensitivity, specificity, and positive and negative predictive values for each method were calculated and compared. Mean (+/- standard deviation) and median values of relative enhancement were also calculated for benign and malignant lesions.

RESULTS

At pathologic analysis, 74 (80%) of the 93 lesions were malignant, and 19 (20%)-including seven oncocytomas-were benign. For diagnosing malignancy based on enhancement alone, sensitivity and specificity, respectively, were 95% (70 of 74 lesions) and 53% (10 of 19 lesions) at quantitative analysis and 99% (73 of 74 lesions) and 58% (11 of 19 lesions) at qualitative analysis. All seven oncocytomas were considered to be malignant with both methods. When the oncocytomas were excluded, specificities increased to 83% (10 of 12 lesions) and 92% (11 of 12 lesions) for the quantitative and qualitative evaluations, respectively. Three of the four malignant lesions incorrectly characterized as benign at quantitative assessment were hyperintense on unenhanced MR images; all were diagnosed correctly at qualitative evaluation.

CONCLUSION

Image subtraction enables accurate assessment of renal tumor enhancement, particularly in the setting of masses that are hyperintense on unenhanced MR images.