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.

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.

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.

Sequential and Comparative Evaluation of Pain Treatment Effectiveness Response (SCEPTER), a pragmatic trial for conservative chronic low back pain treatment.

BACKGROUND: Chronic low back pain (cLBP) is a common and highly disabling problem world-wide. Although many treatment options exist, it is unclear how to best sequence the multitude of care options to provide the greatest benefit to patients. METHODS: The Sequential and Comparative Evaluation of Pain Treatment Effectiveness Response (SCEPTER) trial uses a pragmatic, randomized, stepped design. Enrollment targets 2529 participants from 20 Veterans Affairs (VA) medical centers. Participants with chronic low back pain will first be randomized to one of three options: 1) an internet-based self-management program (Pain EASE); 2) a tailored physical therapy program (Enhanced PT); or 3) continued care with active monitoring (CCAM), a form of usual care. Participants not achieving a 30% or 2-point reduction on the study's primary outcome (Brief Pain Inventory Pain Interference (BPI-PI) subscale), 3 months after beginning treatment may undergo re-randomization in a second step to cognitive behavioral therapy for chronic pain, spinal manipulation therapy, or yoga. Secondary outcomes include pain intensity, back pain-related disability, depression, and others. Participants will be assessed every three months until 12 months after initiating their final trial therapy. Companion economic and implementation analyses are also planned. RESULTS: The SCEPTER trial is currently recruiting and enrolling participants. CONCLUSIONS: Trial results will inform treatment decisions for the stepped management of chronic low back pain - a common and disabling condition. Additional analyses will help tailor treatment selection to individual patient characteristics, promote efficient resource use, and identify implementation barriers of interventions. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT04142177.

Pregnancy-induced chromatin remodeling in the breast of postmenopausal women.

Early pregnancy and multiparity are known to reduce the risk of women to develop breast cancer at menopause. Based on the knowledge that the differentiation of the breast induced by the hormones of pregnancy plays a major role in this protection, this work was performed with the purpose of identifying what differentiation-associated molecular changes persist in the breast until menopause. Core needle biopsies (CNB) obtained from the breast of 42 nulliparous (NP) and 71 parous (P) postmenopausal women were analyzed in morphology, immunocytochemistry and gene expression. Whereas in the NP breast, nuclei of epithelial cells were large and euchromatic, in the P breast they were small and hyperchromatic, showing strong methylation of histone 3 at lysine 9 and 27. Transcriptomic analysis performed using Affymetrix HG_U133 oligonucleotide arrays revealed that in CNB of the P breast, there were 267 upregulated probesets that comprised genes controlling chromatin organization, transcription regulation, splicing machinery, mRNA processing and noncoding elements including XIST. We concluded that the differentiation process induced by pregnancy is centered in chromatin remodeling and in the mRNA processing reactome, both of which emerge as important regulatory pathways. These are indicative of a safeguard step that maintains the fidelity of the transcription process, becoming the ultimate mechanism mediating the protection of the breast conferred by full-term pregnancy.

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.

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.

Quantitative magnetic resonance imaging evidence of synovial proliferation is associated with radiographic severity of knee osteoarthritis.

OBJECTIVE: To evaluate the relationships between both quantitative and semiquantitative assessments of the degree of knee synovitis on 3T magnetic resonance imaging (MRI) and the severity of knee osteoarthritis (OA) on radiography. METHODS: Fifty-eight patients with knee OA underwent nonfluoroscopic fixed-flexion knee radiography. In addition, dynamic contrast-enhanced 3T MRI of the knees was performed, before and after gadolinium administration, to quantify synovial membrane volume (SV) as a measure of synovial proliferation (expressed as the quantitative SV), and semiquantitative measures of synovitis were also applied using both contrast-enhanced and unenhanced images. Two radiologists scored the knee radiographs using the Osteoarthritis Research Society International atlas; interreader agreement was assessed using kappa statistics and concordance correlation coefficients. Multiple linear and logistic regression analyses were used to assess associations among variables, while controlling for the effects of age, body mass index, sex, and meniscal extrusion. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for measures of disease activity. RESULTS: The Kellgren/Lawrence (K/L) grade of radiographic knee OA severity (ß=0.78), the diseased compartment joint space width (dcJSW) (ß=-0.22), and the diseased compartment joint space narrowing (dcJSN) score (ß=0.53) were each significantly associated with the quantitative SV (P=0.0001, P=0.0003, and P=0.0001, respectively). Furthermore, the quantitative SV strongly correlated with the total volume of subchondral bone marrow lesions (BMLs) (ß=0.22, P=0.0003). The K/L grade, dcJSW, and dcJSN score were each significantly associated with the semiquantitative Boston Leeds Osteoarthritis Knee Score (BLOKS) for the extent of infrapatellar synovitis (OR 9.05 [95% CI 1.94, 42.3] for K/L grade; OR 0.75 [95% CI 0.54, 1.03] for dcJSW; and OR 2.22 [95% CI 1.15, 4.31] for dcJSN score) and extent of joint effusion (OR 5.75 [95% CI 1.23, 26.8] for K/L grade; OR 0.70 [95% CI 0.50, 0.98] for dcJSW; and OR 1.96 [95% CI 1.02, 3.74] for dcJSN score). In addition, the semiquantitative synovitis grade on contrast-enhanced MRI was significantly associated with the K/L grade (ß=0.036, P=0.0040) and dcJSN score (ß=0.015, P=0.0266), and also significantly associated with the BLOKS synovitis score. CONCLUSION: Synovitis is a characteristic feature of advancing knee OA and is significantly associated with the K/L grade, JSW, JSN score, and total volume of BMLs on radiographs. Furthermore, BLOKS scoring of synovitis on unenhanced MRI is associated with measurements of synovitis on contrast-enhanced MRI.

Increased interleukin-1ß gene expression in peripheral blood leukocytes is associated with increased pain and predicts risk for progression of symptomatic knee osteoarthritis.

OBJECTIVE: To evaluate whether gene expression profiles could serve as biomarkers of symptomatic knee osteoarthritis (OA) by examining gene expression profiles in peripheral blood leukocytes (PBLs) from patients with OA compared with those from non-OA controls, and to determine whether candidate genomic biomarkers (PBL expression of inflammatory genes) predict an increased risk of disease progression in patients with symptomatic radiographic knee OA. METHODS: Three independent cohorts of patients with knee OA and non-OA control subjects were studied. Two cohorts (a learning cohort and a validation cohort) were recruited at New York University Hospital for Joint Diseases (NYUHJD), and 1 cohort (a validation cohort) was recruited at Duke University Medical Center. PBL gene expression was assessed using Affymetrix microarray and was confirmed by quantitative polymerase chain reaction (qPCR). Radiographic progression at 2 years was assessed in 86 patients. RESULTS: We identified 173 genes that were significantly up-regulated or down-regulated (≥1.5-fold change) in OA PBLs, at a false discovery rate of 5%. Cluster analysis revealed 2 distinct subgroups among the patients with OA: those in whom the expression of interleukin-1ß (IL-1ß) was increased ≥2-fold compared with controls, and those in whom the expression of IL-1ß was comparable with that in controls. Overexpression of IL-1ß in these OA subclasses was validated using qPCR in all 3 cohorts. Patients with the inflammatory "IL-1ß signature" had higher pain scores and decreased function and were at higher risk of radiographic progression of OA. CONCLUSION: PBLs from patients with symptomatic knee OA display a characteristic transcriptome profile. Moreover, increased expression of IL-1ß identifies a subset of patients with OA who have increased pain and are at higher risk of radiographic progression of OA.

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes positively associated with survival were predominantly immune response related (e.g., ICOS, CD3d, ZAP70, TRAT1, TARP, GZMK, LCK, CD2, CXCL13, CCL19, CCR7, VCAM1) while genes negatively associated with survival were cell proliferation related (e.g., PDE4D, CDK2, GREF1, NUSAP1, SPC24). Furthermore, any of the 4 parameters (prevalidated gene expression signature, TILs, CD3, and in particular MI) improved the ability of Tumor, Node, Metastasis (TNM) staging to predict postrecurrence survival; MI was the most significant contributor (HR = 2.13, P = 0.0008). An immune response gene expression signature and presence of TILs and CD3+ cells signify immune surveillance as a mechanism for prolonged survival in these patients and indicate improved patient subcategorization beyond current TNM staging.

Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor.

The highly aggressive character of melanoma makes it an excellent model for probing the mechanisms underlying metastasis, which remains one of the most difficult challenges in treating cancer. We find that miR-182, member of a miRNA cluster in a chromosomal locus (7q31-34) frequently amplified in melanoma, is commonly up-regulated in human melanoma cell lines and tissue samples; this up-regulation correlates with gene copy number in a subset of melanoma cell lines. Moreover, miR-182 ectopic expression stimulates migration of melanoma cells in vitro and their metastatic potential in vivo, whereas miR-182 down-regulation impedes invasion and triggers apoptosis. We further show that miR-182 over-expression promotes migration and survival by directly repressing microphthalmia-associated transcription factor-M and FOXO3, whereas enhanced expression of either microphthalmia-associated transcription factor-M or FOXO3 blocks miR-182's proinvasive effects. In human tissues, expression of miR-182 increases with progression from primary to metastatic melanoma and inversely correlates with FOXO3 and microphthalmia-associated transcription factor levels. Our data provide a mechanism for invasion and survival in melanoma that could prove applicable to metastasis of other cancers and suggest that miRNA silencing may be a worthwhile therapeutic strategy.

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.

Interruptions to Attending Physician Rounds and Their Effect on Resident Education.

BACKGROUND: Daily attending rounds (AR) are a cornerstone of teaching and patient care in academic health centers. Interruptions in health care are common and can cause increased risk of errors, incomplete work, and decreased decision-making accuracy. Interruptions to AR may diminish a trainee's capacity to learn and retain information. OBJECTIVE: We characterized and quantified interruptions that occur during AR. METHODS: We used a mixed-methods design combining a prospective observational study with a qualitative study. AR were observed January to March 2020 to characterize interruptions, followed by semi-structured interviews with the observed physicians to elucidate the effect of interruptions on workflow and the educational value of rounds. RESULTS: There were 378 observed interruptions over the course of 30 AR sessions, averaging 12.6 (range 1-22, median 13) interruptions per rounding session. Bedside nursing staff was the most common source of interruptions (25%) and consultant recommendations was the most common topic of interruption (21%). Most interruptions occurred during patient presentations (76%), and the most common method of interaction was text message (24%). Most team members described negative effects of interruptions, including loss of focus and missing critical clinical information; some also reported that certain interruptions had positive effects on education and clinical care. Interns were more likely to report negative emotional reactions to interruptions. CONCLUSIONS: AR are frequently interrupted for non-urgent topics by a variety of methods and sources. Negative effects included loss of focus, missed information, and increased stress. Proactive communication, particularly between physicians and nurses, was suggested to reduce interruptions.

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.

Gene expression profiles of bronchoalveolar cells in pulmonary TB.

The host response to Mycobacterium tuberculosis includes macrophage activation, inflammation with increased immune effector cells, tissue necrosis, and cavity formation, and fibrosis, distortion, and bronchiectasis. To evaluate the molecular basis of the immune response in the lungs of patients with active pulmonary tuberculosis (TB), we used bronchoalveolar lavage to obtain cells at the site of infection. Affymetrix GeneChip microarrays and cDNA nylon filter microarrays interrogated gene expression in bronchoalveolar lavage (BAL) cells from 11 healthy controls and 17 patients with active pulmonary TB. We found altered gene expression for 69 genes in TB versus normal controls that included cell surface markers, cytokines, chemokines, receptors, transcription factors, and complement components. In addition, TB BAL cell gene expression patterns segregated into 2 groups: one suggestive of a T helper type 1 (Th1) cellular immune response with increased signal transducer and activator of transcription-4 (STAT-4), interferon-gamma (IFN-gamma receptor), and monokine induced by IFN-gamma (MIG) expression with increased IFN-gamma protein levels in BAL fluid; the other group displayed characteristics of Th2 immunity with increased STAT-6, CD81, and IL-10 receptor expression. We were able to demonstrate that a Th2 presentation could change to a Th1 pattern after anti-tuberculous treatment in 1 TB patient studied serially. These gene expression data support the conclusion that pulmonary TB produces a global change in the BAL cell transcriptome with manifestations of either Th1 or Th2 immunity.

Impact of apolipoprotein E genotypes on vitamin E and memantine treatment outcomes in Alzheimer's disease.

INTRODUCTION: Because apolipoprotein E (APOE) genotypes are known risk factors for Alzheimer's disease (AD), they have been measured in clinical trial participants to determine their effect on treatment outcome. METHODS: We determined APOE genotypes in a subset of subjects (N = 415) who participated in a randomized controlled trial of vitamin E and memantine in 613 veterans with mild-to-moderate AD. RESULTS: Similar to the primary study, substudy participants receiving vitamin E also had slower functional decline than those receiving placebo. Overall, there was no difference in the rate of functional decline between APOE ε4 allele carriers and noncarriers. A significant interaction was observed between treatment and the APOE genotype on AD progression: ε4 carriers declined faster than noncarriers in the vitamin E plus memantine treatment arm. DISCUSSION: APOE genotypes may modulate AD treatment response and should be included in the design of future randomized controlled trials.

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 profiling of normal human bronchial epithelial cells in response to asbestos and benzo(a)pyrene diol epoxide (BPDE).

Asbestos and benzo(a)pyrene diol epoxide (BPDE) are pulmonary carcinogens with synergistic interaction in causing lung cancer. We used Affymetrix microarrays to study gene modulation in vitro using normal human bronchial epithelial cells exposed to chrysotile asbestos and/or BPDE for 4 or 24 h. Linear models were used to compare treated cells to controls at each time point to identify statistically significant up- or downregulation of genes. Profiles of genes regulated by chrysotile were dominated by cytokines, growth factors, and DNA damage. Profiles of genes with BPDE and chrysotile regulation were correlated with proliferation, DNA damage recognition and nucleotide-excision repair, cytokines, and apoptosis. Chemokines, growth-regulated oncogene-alpha (Gro-alpha, CXCL-1), and IL-8, were significantly increased, and these had previously been observed in bronchoalveolar lavage from asbestos workers or in animal models. Interestingly, the Hermansky-Pudlak gene, which is mutated in an autosomal recessive form of pulmonary fibrosis, was downregulated threefold by BPDE at 4 h. This is an interesting example of gene (Hermansky-Pudlak syndrome) and environment (BPDE) interaction. Transcription factors, including activating transcription factor 3 and Cbp/p300-interacting transactivator, were upregulated by chrysotile. Real Time PCR for IL-8, ATF-3, GADD45B, CXC Ligand 1, and CTGF compared to GAPDH validated microarray findings at 24 h. These in vitro findings in NHBE cells model environment-gene interaction for asbestos and BPDE, highlighting effects of inflammation, fibrosis, proliferation, and DNA damage recognition and repair.

Genetic Variation in the IL-6 and HLA-DQB1 Genes Is Associated with Spontaneous Clearance of Hepatitis C Virus Infection.

Background. Millions of people are infected with hepatitis C virus (HCV) worldwide and 30% spontaneously clear the infection. Reasons for HCV clearance without antiviral treatment are not well understood. Methods. Blood was collected for DNA analysis from patients with chronic HCV infection or evidence of spontaneous clearance. To overcome anticipated limitations of small sample size, primary analyses consisted of a candidate gene analysis of 12 preselected genes based on known association with host immunologic response to HCV infection. To further reduce the impact of multiple testing on power, a single likelihood ratio test was conducted for each gene using all associated SNPs assayed on the Illumina Quad 610/660W chip. Step-down permutation methods were used to adjust for multiple testing in all analyses. Results. Ninety-five and 62 patients with HCV chronic infection or spontaneous clearance, respectively, were included for analysis. HLA-DQB1 (p = 1.76⁎10(-5)) and IL-6 (p = 0.0007) genes were significantly associated with spontaneous HCV clearance. IL-28B was not significantly associated with spontaneous clearance (p = 0.17). Conclusion. Our whole-gene analytic strategy identified a previously unreported association of IL-6 with spontaneous clearance of HCV infection. We also confirmed the finding that HLA-DQB1 is associated with spontaneous resolution of HCV infection.