Judith A. Welsh

Mutations of p53 and ras genes in radon-associated lung cancer from uranium miners

Radon increases the risk of lung cancer in smoking and non-smoking underground miners. To investigate the mutational spectrum associated with exposure to high levels of radon, we sequenced exons 5-9 of the p53 tumour suppressor gene and codons 12-13 of the Ki-ras protooncogene in 19 lung cancers from uranium miners exposed to radon and tobacco smoke. Mutations were not found in Ki-ras, but 9 p53 mutations, including 2 deletions, were found in 7 patients by direct DNA sequencing after polymerase chain reaction amplification of DNA from formalin-fixed, paraffin-embedded tissue. In tumours from 5 patients, the mutation produced an aminoacid change and an increased nuclear content of p53 protein. The tumours with either a stop codon or frame-shift deletion in the p53 gene were negative by immunohistochemistry. None of the mutations were G:C to T:A transversions in the coding strand of the p53 gene, which are the most frequent base substitutions associated with tobacco smoking, and none were found at the hotspot codons described in lung cancer. The observed differences from the usual lung cancer mutational spectrum may reflect the genotoxic effects of radon.

Circulating micro-RNA expression profiles in early stage nonsmall cell lung cancer.

Circulating micro‐RNA (miR) profiles have been proposed as promising diagnostic and prognostic biomarkers for cancer, including lung cancer. We have developed methods to accurately and reproducibly measure micro‐RNA levels in serum and plasma. Here, we study paired serum and plasma samples from 220 patients with early stage nonsmall cell lung cancer (NSCLC) and 220 matched controls. We use qRT‐PCR to measure the circulating levels of 30 different miRs that have previously been reported to be differently expressed in lung cancer tissue. Duplicate RNA extractions were performed for 10% of all samples, and micro‐RNA measurements were highly correlated among those duplicates. This demonstrates high reproducibility of our assay. The expressions of miR‐146b, miR‐221, let‐7a, miR‐155, miR‐17‐5p, miR‐27a and miR‐106a were significantly reduced in the serum of NSCLC cases, while miR‐29c was significantly increased. No significant differences were observed in plasma of patients compared with controls. Overall, expression levels in serum did not correlate well with levels in plasma. In secondary analyses, reduced plasma expression of let‐7b was modestly associated with worse cancer‐specific mortality in all patients, and reduced serum expression of miR‐223 was modestly associated with cancer‐specific mortality in stage IA/B patients. MiR profiles also showed considerable differences comparing African American and European Americans. In summary, we found significant differences in miR expression when comparing cases and controls and find evidence that expression of let‐7b is associated with prognosis in NSCLC.

Common Genetic Variation in TP53 Is Associated with Lung Cancer Risk and Prognosis in African Americans and Somatic Mutations in Lung Tumors

Lung cancer is primarily caused by tobacco smoking, but susceptibility is likely modified by common genetic variation. In response to many forms of cellular stress, including DNA damage, the p53 protein functions to induce cell cycle arrest, DNA repair, senescence, or apoptosis. We hypothesized that common TP53 haplotypes modulate pathways of lung carcinogenesis and lung cancer susceptibility or prognosis. To investigate our hypothesis, 14 polymorphisms in TP53, including haplotype tagging and coding single nucleotide polymorphisms, were genotyped in two studies from the greater Baltimore, Maryland area. One study is a case-control study and the second is a case-only study for which TP53 mutational spectra data are available. African Americans with Pro-T-A-G-G haplotypes of the combined TP53 polymorphisms TP53_01 (rs1042522), TP53_65 (rs9895829), TP53_66 (rs2909430), TP53_16 (rs1625895), and TP53_11 (rs12951053) had both an increased risk for lung cancer (odds ratio, 2.32; 95% confidence interval, 1.18-4.57) and a worsened lung cancer prognosis (hazards ratio, 2.38; 95% confidence interval, 1.38-4.10) compared with those with Arg-T-A-G-T haplotypes. No associations of TP53 polymorphisms with lung cancer were observed in Caucasians. In the case-only study, several polymorphisms in TP53 and TP53 haplotypes, overlapping regions of TP53 associated with risk and prognosis in African Americans, were associated with increased odds of somatic TP53 mutation in lung tumors in Caucasians. In conclusion, common genetic variation in TP53 could modulate lung cancer pathways, as suggested by the association with lung cancer in African Americans and somatic TP53 mutation frequency in lung tumors. (Cancer Epidemiol Biomarkers Prev 2007;16(2):214–22)

Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs.

Significance Bloom syndrome is a rare human genetic disease characterized by proportional dwarfism, immunodeficiency, and an elevated risk of many different cancer types. We used RNA expression profiling to identify networks of mRNAs and microRNAs that are differentially expressed in cells from Bloom syndrome patients and associated with cell proliferation, survival, and molecular pathways promoting cancer. Altered mRNA expression was in some cases strongly correlated with the presence of G4 motifs, which may form G-quadruplex targets that are bound by BLM. Further analysis of the genetic networks we identified may elucidate mechanisms responsible for Bloom syndrome disease pathogenesis and ways to ameliorate or prevent disease in affected individuals. Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathological features of Bloom syndrome, we analyzed mRNA and microRNA (miRNA) expression in fibroblasts from individuals with Bloom syndrome and in BLM-depleted control fibroblasts. We identified mRNA and miRNA expression differences in Bloom syndrome patient and BLM-depleted cells. Differentially expressed mRNAs are connected with cell proliferation, survival, and molecular mechanisms of cancer, and differentially expressed miRNAs target genes involved in cancer and in immune function. These and additional altered functions or pathways may contribute to the proportional dwarfism, elevated cancer risk, immune dysfunction, and other features observed in Bloom syndrome individuals. BLM binds to G-quadruplex (G4) DNA, and G4 motifs were enriched at transcription start sites (TSS) and especially within first introns (false discovery rate ≤ 0.001) of differentially expressed mRNAs in Bloom syndrome compared with normal cells, suggesting that G-quadruplex structures formed at these motifs are physiologic targets for BLM. These results identify a network of mRNAs and miRNAs that may drive the pathogenesis of Bloom syndrome.

MDM2 SNP309 and SNP354 Are Not Associated with Lung Cancer Risk

A single nucleotide polymorphism (SNP) in the MDM2 promoter (a T to G exchange at nucleotide 309) has been found to be associated with tumor formation. Publication of this null report is important because an association between MDM2 SNP309 and lung cancer was previously reported in two independent studies. Our findings suggest that MDM2 SNP309 is not a strong factor in lung carcinogenesis. In addition, this is the first MDM2 SNP309 report on a population consisting of Caucasians in the United States and African-Americans. A strength of the study design is that the controls consist of both population and hospital controls. (Cancer Epidemiol Biomarkers Prev 2006;15(8):1559–61)

An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers.

Introduction: Up to 30% stage I lung cancer patients suffer recurrence within 5 years of curative surgery. We sought to improve existing protein-coding gene and microRNA expression prognostic classifiers by incorporating epigenetic biomarkers. Methods: Genome-wide screening of DNA methylation and pyrosequencing analysis of HOXA9 promoter methylation were performed in two independently collected cohorts of stage I lung adenocarcinoma. The prognostic value of HOXA9 promoter methylation alone and in combination with mRNA and miRNA biomarkers was assessed by Cox regression and Kaplan–Meier survival analysis in both cohorts. Results: Promoters of genes marked by polycomb in embryonic stem cells were methylated de novo in tumors and identified patients with poor prognosis. The HOXA9 locus was methylated de novo in stage I tumors (p < 0.0005). High HOXA9 promoter methylation was associated with worse cancer-specific survival (hazard ratio [HR], 2.6; p = 0.02) and recurrence-free survival (HR, 3.0; p = 0.01), and identified high-risk patients in stratified analysis of stages IA and IB. Four protein-coding gene (XPO1, BRCA1, HIF1&agr;, and DLC1), miR-21 expression, and HOXA9 promoter methylation were each independently associated with outcome (HR, 2.8; p = 0.002; HR, 2.3; p = 0.01; and HR, 2.4; p = 0.005, respectively), and when combined, identified high-risk, therapy naive, stage I patients (HR, 10.2; p = 3 × 10−5). All associations were confirmed in two independently collected cohorts. Conclusion: A prognostic classifier comprising three types of genomic and epigenomic data may help guide the postoperative management of stage I lung cancer patients at high risk of recurrence.

Combination of protein coding and noncoding gene expression as a robust prognostic classifier in stage I lung adenocarcinoma.

Prognostic tests for patients with early-stage lung cancer may provide needed guidance on postoperative surveillance and therapeutic decisions. We used a novel strategy to develop and validate a prognostic classifier for early-stage lung cancer. Specifically, we focused on 42 genes with roles in lung cancer or cancer prognosis. Expression of these biologically relevant genes and their association with relapse-free survival (RFS) were evaluated using microarray data from 148 patients with stage I lung adenocarcinoma. Seven genes associated with RFS were further examined by quantitative reverse transcription PCR in 291 lung adenocarcinoma tissues from Japan, the United States, and Norway. Only BRCA1, HIF1A, DLC1, and XPO1 were each significantly associated with prognosis in the Japan and US/Norway cohorts. A Cox regression-based classifier was developed using these four genes on the Japan cohort and validated in stage I lung adenocarcinoma from the US/Norway cohort and three publicly available lung adenocarcinoma expression profiling datasets. The results suggest that the classifier is robust across ethnically and geographically diverse populations regardless of the technology used to measure gene expression. We evaluated the combination of the four-gene classifier with miRNA miR-21 (MIR21) expression and found that the combination improved associations with prognosis, which were significant in stratified analyses on stage IA and stage IB patients. Thus, the four coding gene classifier, alone or with miR-21 expression, may provide a clinically useful tool to identify high-risk patients and guide recommendations regarding adjuvant therapy and postoperative surveillance of patients with stage I lung adenocarcinoma.

Antitumor necrosis factor therapy is associated with improved survival in clinical sepsis trials: a meta-analysis.

Objectives:Sepsis is a lethal syndrome annually affecting approximately 900,000 patients in the United States alone. Despite their benefit in rheumatoid disease, selective antitumor necrosis factor agents failed to improve outcome in early sepsis trials in the 1990s. However, data from additional sepsis trials testing these agents are now available. We therefore sought to determine the effect on survival of selective antitumor necrosis factor agents in randomized clinical sepsis trials.. Data Sources:PubMed, Scopus, Embase, and Web of Science. Study Selection:Randomized human sepsis trials of selective antitumor necrosis factor agents reporting survival rates. Data Extraction:Two investigators independently collected relevant data on study characteristics, treatment interventions, and patients from each study. Data Synthesis:Antitumor necrosis factor agents in 15 sepsis trials (n = 8,896 patients) meeting inclusion criteria had similar effects (I2 = 0, p = 0.84) and compared with controls (placebo in 14 trials or a lower dose in one trial) overall decreased the relative risk of death (95% CI) (0.93 [0.88–0.98], p = 0.01). In subgroup analysis, tumor necrosis factor monoclonal antibodies (10 trials, n = 6,818) alone produced a significant survival benefit (0.93 [0.87, 0.99], p = 0.02) (I2 = 0, p = 0.83). Tumor necrosis factor polyclonal antibodies (two trials, n = 151) and low-molecular-weight soluble receptor (two trials, n = 1,786) had similar beneficial effects to antitumor necrosis factor agents overall (0.82 [0.49–1.37], p = 0.45; 0.93 [0.81–1.08], p = 0.33, respectively). The effect of tumor necrosis factor high-molecular-weight soluble receptor (one trial, n = 141) was not significantly different from other agents but was on the side of harm (1.50 [0.86–2.61], p = 0.16). Conclusion:Antitumor necrosis factor agents produced a modest but significant decrease in the risk of dying with sepsis. Prior individual trials failed to demonstrate benefit, likely because they were underpowered. A definitive trial demonstrating the potential benefit of such agents might require 10,000 or more patients with sepsis.

Biomedical Data Sharing and Reuse: Attitudes and Practices of Clinical and Scientific Research Staff

Background Significant efforts are underway within the biomedical research community to encourage sharing and reuse of research data in order to enhance research reproducibility and enable scientific discovery. While some technological challenges do exist, many of the barriers to sharing and reuse are social in nature, arising from researchers’ concerns about and attitudes toward sharing their data. In addition, clinical and basic science researchers face their own unique sets of challenges to sharing data within their communities. This study investigates these differences in experiences with and perceptions about sharing data, as well as barriers to sharing among clinical and basic science researchers. Methods Clinical and basic science researchers in the Intramural Research Program at the National Institutes of Health were surveyed about their attitudes toward and experiences with sharing and reusing research data. Of 190 respondents to the survey, the 135 respondents who identified themselves as clinical or basic science researchers were included in this analysis. Odds ratio and Fisher’s exact tests were the primary methods to examine potential relationships between variables. Worst-case scenario sensitivity tests were conducted when necessary. Results and Discussion While most respondents considered data sharing and reuse important to their work, they generally rated their expertise as low. Sharing data directly with other researchers was common, but most respondents did not have experience with uploading data to a repository. A number of significant differences exist between the attitudes and practices of clinical and basic science researchers, including their motivations for sharing, their reasons for not sharing, and the amount of work required to prepare their data. Conclusions Even within the scope of biomedical research, addressing the unique concerns of diverse research communities is important to encouraging researchers to share and reuse data. Efforts at promoting data sharing and reuse should be aimed at solving not only technological problems, but also addressing researchers’ concerns about sharing their data. Given the varied practices of individual researchers and research communities, standardizing data practices like data citation and repository upload could make sharing and reuse easier.

Tidal volume and plateau pressure use for acute lung injury from 2000 to present: a systematic literature review.

Objective:Since publication of the Respiratory Management of Acute Lung Injury and Acute Respiratory Distress Syndrome (ARMA) trial in 2000, use of tidal volume (VT) less than or equal to 6 mL/kg predicted body weight with corresponding plateau airway pressures (PPlat) less than or equal to 30 cm H2O has been advocated for acute lung injury. However, compliance with these recommendations is unknown. We therefore investigated VT (mL/kg predicted body weight) and PPlat (cm H2O) practices reported in studies of acute lung injury since ARMA using a systematic literature review (i.e., not a meta-analysis). Data Sources:PubMed, Scopus, and EMBASE. Study Selection:Randomized controlled trials and nonrandomized studies enrolling patients with acute lung injury from May 2000 to June 2013 and reporting VT. Data Extraction:Whether the study was a randomized controlled trial or a nonrandomized study and performed or not at an Acute Respiratory Distress Syndrome Network center; in randomized controlled trials, the pre- and postrandomization VT (mL/kg predicted body weight) and PPlat (cm H2O) and whether a VT protocol was used postrandomization; in nonrandomized studies, baseline VT and PPlat. Data Synthesis:Twenty-two randomized controlled trials and 71 nonrandomized studies were included. Since 2000 at acute respiratory distress syndrome Network centers, routine VT was similar comparing randomized controlled trials and nonrandomized studies (p = 0.25) and unchanged over time (p = 0.75) with a mean value of 6.81 (95% CI, 6.45, 7.18). At non-acute respiratory distress syndrome Network centers, routine VT was also similar when comparing randomized controlled trials and nonrandomized studies (p = 0.71), but decreased (p = 0.001); the most recent estimate for it was 6.77 (6.22, 7.32). All VT estimates were significantly greater than 6 (p ⩽ 0.02). In randomized controlled trials employing VT protocols, routine VT was reduced in both acute respiratory distress syndrome Network (n = 4) and non-acute respiratory distress syndrome Network (n = 11) trials (p ⩽ 0.01 for both), but even postrandomization was greater than 6 (6.47 [6.29, 6.65] and 6.80 [6.42, 7.17], respectively; p ⩽ 0.0001 for both). In 59 studies providing data, routine PPlat, averaged across acute respiratory distress syndrome Network or non-acute respiratory distress syndrome Network centers, was significantly less than 30 (p ⩽ 0.02). Conclusions:For clinicians treating acute lung injury since 2000, achieving VT less than or equal to 6 mL/kg predicted body weight may not have been as attainable or important as PPlat less than or equal to 30 cm H2O. If so, there may be equipoise to test if VT less than or equal to 6 mL/kg predicted body weight are necessary to improve acute lung injury outcome.