1,3-Butadiene metabolite 1,2,3,4 diepoxybutane induces DNA adducts and micronuclei but not t(9;22) translocations in human cells.

Epidemiological studies of 1,3-butadiene (BD) exposures have reported a possible association with chronic myelogenous leukemia (CML), which is defined by the presence of the t(9;22) translocation (Philadelphia chromosome) creating an oncogenic BCR-ABL fusion gene. Butadiene diepoxide (DEB), the most mutagenic of three epoxides resulting from BD, forms DNA-DNA crosslink adducts that can lead to DNA double-strand breaks (DSBs). Thus, a study was designed to determine if (±)-DEB exposure of HL60 cells, a promyelocytic leukemia cell line lacking the Philadelphia chromosome, can produce t(9;22) translocations. In HL60 cells exposed for 3 h to 0-10 µM DEB, overlapping dose-response curves suggested a direct relationship between 1,4-bis-(guan-7-yl)-2,3-butanediol crosslink adduct formation (R = 0.977, P = 0.03) and cytotoxicity (R = 0.961, P = 0.002). Experiments to define the relationships between cytotoxicity and the induction of micronuclei (MN), a dosimeter of DNA DSBs, showed that 24 h exposures of HL60 cells to 0-5.0 µM DEB caused significant positive correlations between the concentration and (i) the degree of cytotoxicity (R = 0.998, p = 0.002) and (ii) the frequency of MN (R = 0.984, p = 0.016) at 48 h post exposure. To determine the relative induction of MN and t(9;22) translocations following exposures to DEB, or x-rays as a positive control for formation of t(9;22) translocations, HL60 cells were exposed for 24 h to 0, 1, 2.5, or 5 µM DEB or to 0, 2.0, 3.5, or 5.0 Gy x-rays, or treatments demonstrated to yield 0, 20%, 50%, or 80% cytotoxicity. Treatments between 0 and 3.5 Gy x-rays caused significant dose-related increases in both MN (p < 0.001) and t(9;22) translocations (p = 0.01), whereas DEB exposures causing similar cytotoxicity levels did not increase translocations over background. These data indicate that, while DEB induces DNA DSBs required for formation of MN and translocations, acute DEB exposures of HL60 cells did not produce the Philadelphia chromosome obligatory for CML.

Molecular analysis of glycosylphosphatidylinositol anchor deficient aerolysin resistant isolates in gulf war i veterans exposed to depleted uranium.

During the First Gulf War (1991) over 100 servicemen sustained depleted uranium (DU) exposure through wound contamination, inhalation, and shrapnel. The Department of Veterans Affairs has a surveillance program for these Veterans which has included genotoxicity assays. The frequencies of glycosylphosphatidylinositol anchor (GPIa) negative (aerolysin resistant) cells determined by cloning assays for these Veterans are reported in Albertini RJ et al. (2019: Environ Mol Mutagen). Molecular analyses of the GPIa biosynthesis class A (PIGA) gene was performed on 862 aerolysin-resistant T-lymphocyte recovered isolates. The frequencies of different types of PIGA mutations were compared between high and low DU exposure groups. Additional molecular studies were performed on mutants that produced no PIGA mRNA or with deletions of all or part of the PIGA gene to determine deletion size and breakpoint sequence. One mutant appeared to be the result of a chromothriptic event. A significant percentage (>30%) of the aerolysin resistant isolates, which varied by sample year and Veteran, had wild-type PIGA cDNA (no mutation). As described in Albertini RJ et al. (2019: Environ Mol Mutagen), TCR gene rearrangement analysis of these isolates indicated most arose from multiple T-cell progenitors (hence the inability to find a mutation). It is likely that these isolates were the result of failure of complete selection against nonmutant cells in the cloning assays. Real-time studies of GPIa resistant isolates with no PIGA mutation but with a single TCR gene rearrangement found one clone with a PIGV deletion and several others with decreased levels of GPIa pathway gene mRNAs implying mutation in other GPIa pathway genes. Environ. Mol. Mutagen. 60:470-493, 2019. © 2019 Wiley Periodicals, Inc.

Longitudinal study of t-cell somatic mutations conferring glycosylphosphatidylinositol-anchor deficiency in gulf war I veterans exposed to depleted uranium.

Fifty Veterans of the first Gulf War in 1991 exposed to depleted uranium (DU) were studied for glycosylphosphatidylinositol-anchor (GPIa) deficient T-cell mutants on three occasions during the years 2009, 2011, and 2013. GPIa deficiency was determined in two ways: cloning assays employing aerolysin selection and cytometry using the FLAER reagent for positive staining of GPIa cell surface proteins. Subsequent molecular analyses of deficient isolates recovered from cloning assays (Nicklas JA et al. [2019]: Environ Mol Mutagen) revealed apparent incomplete selection in some cloning assays, necessitating correction of original data to afford a more realistic estimate of GPIa deficient mutant frequency (MF) values. GPIa deficient variant frequencies (VFs) determined by cytometry were determined in the years 2011 and 2013. A positive but nonsignificant association was observed between MF and VF values determined on the same blood samples during 2013. Exposure to DU had no effect on either GPIa deficient MF or VFs. Environ. Mol. Mutagen. 60:494-504, 2019. © 2019 Wiley Periodicals, Inc.

Towards the Standardized Documentation of E-Cigarette Use in the Electronic Health Record for Population Health Surveillance and Research.

The debate regarding potential negative health effects of electronic nicotine delivery systems (ENDS), which include electronic cigarettes, has received much recent attention. Currently, it is unknown whether ENDS pose a real health risk to users or those passively exposed to their vapor. With the increased use of these devices, the goal of this study was to examine if and how their use is being documented in the electronic health record (EHR) and the associated implications for clinical research. Analysis of five years of progress notes and tobacco use comments revealed that ENDS use is documented at an increasing rate with variable associated information, most often consisting of the status, purpose, and side effects of ENDS use. These results highlight that improved and consistent EHR discrete data entry for ENDS with associated clinical standards for documentation and representation of potential exposures are needed for enabling effective population health surveillance and research.

1,3-Butadiene, CML and the t(9:22) translocation: A reality check.

Epidemiological studies of 1,3-butadiene have suggest that exposures to humans are associated with chronic myeloid leukemia (CML). CML has a well-documented association with ionizing radiation, but reports of associations with chemical exposures have been questioned. Ionizing radiation is capable of inducing the requisite CML-associated t(9:22) translocation (Philadelphia chromosome) in appropriate cells in vitro but, thus far, chemicals have not shown this capacity. We have proposed that 1,3-butadiene metabolites be so tested as a reality check on the epidemiological reports. In order to conduct reliable testing in this regard, it is essential that a positive control for induction be available. We have used ionizing radiation to develop such a control. Results described here demonstrate that this agent does in fact induce pathogenic t(9:22) translocations in a human myeloid cell line in vitro, but does so at low frequencies. Conditions that will be required for studies of 1,3-butadiene are discussed.

Both PIGA and PIGL mutations cause GPI-a deficient isolates in the Tk6 cell line.

Molecular analysis of proaerolysin selected glycosylphosphatidylinositol anchor (GPI-a) deficient isolates in the TK6 cell line was performed. Initial studies found that the expected X-linked PIGA mutations were rare among the spontaneous isolates but did increase modestly after ethyl methane sulfate (EMS) treatment (but to only 50% of isolates). To determine the molecular bases of the remaining GPI-a deficient isolates, real-time analysis for all the 25 autosomal GPI-a pathway genes was performed on the isolates without PIGA mutations, determining that PIGL mRNA was absent for many. Further analysis determined these isolates had several different homozygous deletions of the 5' region of PIGL (17p12-p22) extending 5' (telomeric) through NCOR1 and some into the TTC19 gene (total deletion >250,000 bp). It was determined that the TK6 parent had a hemizygous deletion in 17p12-p22 (275,712 bp) extending from PIGL intron 2 into TTC19 intron 7. Second hit deletions in the other allele in the GPI-a deficient isolates led to the detected homozygous deletions. Several of the deletion breakpoints including the original first hit deletion were sequenced. As strong support for TK6 having a deletion, a number of the isolates without PIGA mutations nor homozygous PIGL deletions had point mutations in the PIGL gene. These studies show that the GPI-a mutation studies using TK6 cell line could be a valuable assay detecting point and deletion mutations in two genes simultaneously.

Mutagenicity monitoring following battlefield exposures: Longitudinal study of HPRT mutations in Gulf War I veterans exposed to depleted uranium.

A total of 70 military Veterans have been monitored for HPRT T-cell mutations in five separate studies at 2-year intervals over an 8-year period. Systemic depleted uranium (DU) levels were measured at the time of each study by determining urinary uranium (uU) excretion. Each HPRT study included 30-40 Veterans, several with retained DU-containing shrapnel. Forty-nine Veterans were evaluated in multiple studies, including 14 who were in all five studies. This permitted a characterization of the HPRT mutation assay over time to assess the effects of age, smoking and non-selected cloning efficiencies, as well as the inter- and intra-individual variability across time points. Molecular analyses identified the HPRT mutation and T-cell receptor (TCR) gene rearrangement in 1,377 mutant isolates. An unexpected finding was that in vivo clones of HPRT mutant T-cells were present in some Veterans, and could persist over several years of the study. The calculated HPRT mutant frequencies (MFs) were repeatedly elevated in replicate studies in three outlier Veterans with elevated urinary uranium excretion levels. However, these three outlier Veterans also harbored large and persistent in vivo HPRT mutant T-cell clones, each of which was represented by a single founder mutation. Correction for in vivo clonality allowed calculation of HPRT T-cell mutation frequencies (MutFs). Despite earlier reports of DU associated increases in HPRT MFs in some Veterans, the results presented here demonstrate that HPRT mutations are not increased by systemic DU exposure. Additional battlefield exposures were also evaluated for associations with HPRT mutations and none were found.

Mutagenicity monitoring following battlefield exposures: Molecular analysis of HPRT mutations in Gulf War I veterans exposed to depleted uranium.

Molecular studies that involved cDNA and genomic DNA sequencing as well as multiplex PCR of the HPRT gene were performed to determine the molecular mutational spectrum for 1,377 HPRT mutant isolates obtained from 61 Veterans of the 1991 Gulf War, most of whom were exposed to depleted uranium (DU). Mutant colonies were isolated from one to four times from each Veteran (in 2003, 2005, 2007, and/or 2009). The relative frequencies of the various types of mutations (point mutations, deletions, insertions, etc.) were compared between high versus low DU exposed groups, (based on their urine U concentration levels), with HPRT mutant frequency (as determined in the companion paper) and with a database of historic controls. The mutational spectrum includes all classes of gene mutations with no significant differences observed in Veterans related to their DU exposures.

Representation of Drug Use in Biomedical Standards, Clinical Text, and Research Measures.

Drug misuse is a prominent cause of morbidity and mortality in the United States. Recent focus on behavioral and social domains in the electronic health record (EHR) has highlighted the need for comprehensive examination of social history information, such as drug use. In this study, representation of drug use was examined in three types of sources: (1) standards from HL7 and openEHR, (2) clinical text from publicly accessible clinical notes and a local EHR, and (3) research measures from the PhenX Toolkit and CDE Browser. In total, 27 elements were identified across the examined sources, revealing a diverse set of values that were found to be associated with drug use type, frequency, method, time frame, and amount. The findings of this study provide insight into the representation of drug use information that may contribute to efforts for standardizing collection and use of these data to support clinical care and research.

Automated Extraction of Substance Use Information from Clinical Texts.

Within clinical discourse, social history (SH) includes important information about substance use (alcohol, drug, and nicotine use) as key risk factors for disease, disability, and mortality. In this study, we developed and evaluated a natural language processing (NLP) system for automated detection of substance use statements and extraction of substance use attributes (e.g., temporal and status) based on Stanford Typed Dependencies. The developed NLP system leveraged linguistic resources and domain knowledge from a multi-site social history study, Propbank and the MiPACQ corpus. The system attained F-scores of 89.8, 84.6 and 89.4 respectively for alcohol, drug, and nicotine use statement detection, as well as average F-scores of 82.1, 90.3, 80.8, 88.7, 96.6, and 74.5 respectively for extraction of attributes. Our results suggest that NLP systems can achieve good performance when augmented with linguistic resources and domain knowledge when applied to a wide breadth of substance use free text clinical notes.

Multi-source development of an integrated model for family health history.

OBJECTIVE: To integrate data elements from multiple sources for informing comprehensive and standardized collection of family health history (FHH). MATERIALS AND METHODS: Three types of sources were analyzed to identify data elements associated with the collection of FHH. First, clinical notes from multiple resources were annotated for FHH information. Second, questions and responses for family members in patient-facing FHH tools were examined. Lastly, elements defined in FHH-related specifications were extracted for several standards development and related organizations. Data elements identified from the notes, tools, and specifications were subsequently combined and compared. RESULTS: In total, 891 notes from three resources, eight tools, and seven specifications associated with four organizations were analyzed. The resulting Integrated FHH Model consisted of 44 data elements for describing source of information, family members, observations, and general statements about family history. Of these elements, 16 were common to all three source types, 17 were common to two, and 11 were unique. Intra-source comparisons also revealed common and unique elements across the different notes, tools, and specifications. DISCUSSION: Through examination of multiple sources, a representative and complementary set of FHH data elements was identified. Further work is needed to create formal representations of the Integrated FHH Model, standardize values associated with each element, and inform context-specific implementations. CONCLUSIONS: There has been increased emphasis on the importance of FHH for supporting personalized medicine, biomedical research, and population health. Multi-source development of an integrated model could contribute to improving the standardized collection and use of FHH information in disparate systems.

Examining the use, contents, and quality of free-text tobacco use documentation in the Electronic Health Record.

Recent initiatives have emphasized the potential role of Electronic Health Record (EHR) systems for improving tobacco use assessment and cessation. In support of these efforts, the goal of the present study was to examine tobacco use documentation in the EHR with an emphasis on free-text. Three coding schemes were developed and applied to analyze 525 tobacco use entries, including structured fields and a free-text comment field, from the social history module of an EHR system to characterize: (1) potential reasons for using free-text, (2) contents within the free-text, and (3) data quality issues. Free-text was most commonly used due to limitations for describing tobacco use amount (23.2%), frequency (26.9%), and start or quit dates (28.2%) as well as secondhand smoke exposure (17.9%) using a variety of words and phrases. The collective results provide insights for informing system enhancements, user training, natural language processing, and standards for tobacco use documentation.

Automated extraction of family history information from clinical notes.

Despite increased functionality for obtaining family history in a structured format within electronic health record systems, clinical notes often still contain this information. We developed and evaluated an Unstructured Information Management Application (UIMA)-based natural language processing (NLP) module for automated extraction of family history information with functionality for identifying statements, observations (e.g., disease or procedure), relative or side of family with attributes (i.e., vital status, age of diagnosis, certainty, and negation), and predication ("indicator phrases"), the latter of which was used to establish relationships between observations and family member. The family history NLP system demonstrated F-scores of 66.9, 92.4, 82.9, 57.3, 97.7, and 61.9 for detection of family history statements, family member identification, observation identification, negation identification, vital status, and overall extraction of the predications between family members and observations, respectively. While the system performed well for detection of family history statements and predication constituents, further work is needed to improve extraction of certainty and temporal modifications.

Measures of genotoxicity in Gulf war I veterans exposed to depleted uranium.

Exposure to depleted uranium (DU), an alpha-emitting heavy metal, has prompted the inclusion of markers of genotoxicity in the long-term medical surveillance of a cohort of DU-exposed Gulf War veterans followed since 1994. Using urine U (uU) concentration as the measure of U body burden, the cohort has been stratified into low-u (<0.10 µg U/g creatinine) and high-u groups (≥ 0.10 µg U/g creatinine). Surveillance outcomes for this cohort have historically included markers of mutagenicity and clastogenicity, with past results showing generally nonsignificant differences between low- vs. high-U groups. However, mean hypoxanthine-guanine phosphoribosyl transferase (HPRT) mutant frequencies (MFs) have been almost 50% higher in the high-U group. We report here results of a more comprehensive protocol performed in a 2009 evaluation of a subgroup (N = 35) of this cohort. Four biomarkers of genotoxicity [micronuclei (MN), chromosome aberrations, and MFs of HPRT and PIGA] were examined. There were no statistically significant differences in any outcome measure when results were compared between the low- vs. high-U groups. However, modeling of the HPRT MF results suggests a possible threshold effect for MFs occurring in the highest U exposed cohort members. Mutational spectral analysis of HPRT mutations is underway to clarify a potential clonal vs. a threshold uU effect to explain this observation. This study provides a comprehensive evaluation of a human population chronically exposed to DU and demonstrates a relatively weak genotoxic effect of the DU exposure. These results may explain the lack of clear epidemiologic evidence for U carcinogenicity in humans. Environ. Mol. Mutagen., 2011. © 2011 Wiley-Liss, Inc.