@article{adams_collins_williams_holmes_hess_atkins_scheidemantle_liu_lodge_johnson_et al._2024, title={Myeloid cell MHC I expression drives CD8<SUP>+</SUP> T cell activation in nonalcoholic steatohepatitis}, volume={14}, ISSN={["1664-3224"]}, url={https://doi.org/10.3389/fimmu.2023.1302006}, DOI={10.3389/fimmu.2023.1302006}, abstractNote={Background & aims Activated CD8+ T cells are elevated in Nonalcoholic steatohepatitis (NASH) and are important for driving fibrosis and inflammation. Despite this, mechanisms of CD8+ T cell activation in NASH are largely limited. Specific CD8+ T cell subsets may become activated through metabolic signals or cytokines. However, studies in NASH have not evaluated the impact of antigen presentation or the involvement of specific antigens. Therefore, we determined if activated CD8+ T cells are dependent on MHC class I expression in NASH to regulate fibrosis and inflammation. Methods We used H2Kb and H2Db deficient (MHC I KO), Kb transgenic mice, and myeloid cell Kb deficient mice (LysM Kb KO) to investigate how MHC class I impacts CD8+ T cell function and NASH. Flow cytometry, gene expression, and histology were used to examine hepatic inflammation and fibrosis. The hepatic class I immunopeptidome was evaluated by mass spectrometry. Results In NASH, MHC class I isoform H2Kb was upregulated in myeloid cells. MHC I KO demonstrated protective effects against NASH-induced inflammation and fibrosis. Kb mice exhibited increased fibrosis in the absence of H2Db while LysM Kb KO mice showed protection against fibrosis but not inflammation. H2Kb restricted peptides identified a unique NASH peptide Ncf2 capable of CD8+ T cell activation in vitro. The Ncf2 peptide was not detected during fibrosis resolution. Conclusion These results suggest that activated hepatic CD8+ T cells are dependent on myeloid cell MHC class I expression in diet induced NASH to promote inflammation and fibrosis. Additionally, our studies suggest a role of NADPH oxidase in the production of Ncf2 peptide generation.}, journal={FRONTIERS IN IMMUNOLOGY}, author={Adams, Victoria R. and Collins, Leonard B. and Williams, Taufika Islam and Holmes, Jennifer and Hess, Paul and Atkins, Hannah M. and Scheidemantle, Grace and Liu, Xiaojing and Lodge, Mareca and Johnson, Aaron J. and et al.}, editor={Williams, Taufika Islam and Collins, Leonard B. and Kennedy, ArionEditors}, year={2024}, month={Jan} }
 @article{bai_collins_andre_breitschwerdt_williams_2023, title={A bottom-up proteomics workflow for a system containing multiple organisms}, volume={1}, ISSN={["1097-0231"]}, url={https://doi.org/10.1002/rcm.9431}, DOI={10.1002/rcm.9431}, abstractNote={RATIONALE
Discovery proteomics has been popularized to be essential in the investigators' biological toolbox. Many biological problems involve the interplay of multiple organisms. Herein, a bottom-up proteomics workflow was developed to study a system containing multiple organisms to promote a thorough understanding of how each interacts with the others.


METHODS
A label-free quantification proteomics workflow was developed with nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS). This protocol describes a bottom-up proteomics workflow used to study differential protein expression in the context of fleas (Ctenocephalides felis felis) experimentally infected by the bacterium Bartonella henselae, the etiological agent of Cat Scratch Disease (CSD).


RESULTS
Step-by-step instructions are provided for protein cleanup, total protein measurement, nanoLC-MS/MS data acquisition, and data analysis using Proteome Discoverer software. Comprehensive details are included to promote the adaption of proteomics workflow in other laboratories.


CONCLUSION
A proteomics protocol is detailed for a system containing multiple proteomes from different taxonomic lineages using cat-flea-Barttonella as an example. The operating protocol can be readily applied to other label-free proteomics work involving multiple proteomes from taxonomically distinct organisms.}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Bai, Hongxia and Collins, Leonard B. B. and Andre, Marcos Rogerio and Breitschwerdt, Edward B. B. and Williams, Taufika Islam}, year={2023}, month={Jan} }
 @article{williams_kowalchyk_collins_reading_2023, title={Discovery Proteomics and Absolute Protein Quantification Can Be Performed Simultaneously on an Orbitrap-Based Mass Spectrometer}, volume={3}, ISSN={["2470-1343"]}, url={https://doi.org/10.1021/acsomega.2c07614}, DOI={10.1021/acsomega.2c07614}, abstractNote={Mass spectrometry (MS) has steadily moved into the forefront of quantification-centered protein research. Protein cleavage isotope dilution MS is a proven way for quantifying proteins by using an isotope-labeled analogue of a peptide fragment of the parent protein as an internal standard. Parallel reaction monitoring (PRM) has become the go-to approach for such quantification on an Orbitrap-based instrument as it is assumed that the instrument sensitivity is enhanced. We performed a comparative study on data-dependent acquisition (DDA) and PRM-based workflows to quantify egg yolk protein precursors or vitellogenins (VTGs) Aa, Ab, and C in striped bass (Morone saxatilis). VTG proportions serve as a developmental measure of egg quality, possibly changing with the environment, and have been studied as an indicator of the health of North Carolina stocks. Based on single-factor analysis of variance comparisons of mean VTG amounts across fish from the same sample groupings, our results indicate that there is no statistical difference between MS1-based and MS2-based VTG quantification. We further conclude that DDA is able to deliver both discovery data and absolute quantification data in the same experiment.}, number={13}, journal={ACS OMEGA}, author={Williams, Taufika Islam and Kowalchyk, Cara and Collins, Leonard B. and Reading, Benjamin J.}, year={2023}, month={Mar} }
 @article{mcguigan_tereniak_donley_smith_jeon_zhao_sampaio_pauly_keller_collins_et al._2023, title={Discovery of a Hybrid System for Photocatalytic CO<sub>2</sub> Reduction via Attachment of a Molecular Cobalt-Quaterpyridine Complex to a Crystalline Carbon Nitride}, volume={10}, ISSN={["2574-0962"]}, DOI={10.1021/acsaem.3c01670}, abstractNote={While recent reports have demonstrated the attachment of molecular catalysts to amorphous, graphitic carbon nitrides (g-CN) for light-driven CO2 reduction, approaches to the utilization of crystalline carbon nitrides have remained undiscovered. Herein, a functional hybrid photocatalyst system has been found using a crystalline carbon nitride semiconductor, poly(triazine imide) lithium chloride (PTI-LiCl), with a surface-attached CoCl2(qpy-Ph-COOH) catalyst for CO2 reduction. The molecular catalyst attaches to PTI-LiCl at concentrations from 0.10 to 4.30 wt % and exhibits ∼96% selectivity for CO production in a CO2-saturated, aqueous 0.5 M KHCO3 solution. Optimal loadings were found to be within 0.42–1.04 wt % with rates between 1,400 and 1,550 μmol CO/g·h at an irradiance of 172 mW/cm2 (λ = 390 nm) and apparent quantum yields of ∼2%. This optimized loading is postulated to represent a balance between maximal turnover frequency (TOF; 300+ h–1) and excess catalyst that can limit excited-electron lifetimes, as probed via transient absorption spectroscopy. An increase in the incident irradiance yields a concomitant increase in the TOFs and CO rates only for the higher catalyst loadings, reaching up to 2,149 μmol CO/g·h with a more efficient use of the catalyst surface capacity. The lower catalyst loadings, by comparison, already function at maximal TOFs. Higher surface loadings are also found to help mitigate deactivation of the molecular catalysts during extended catalytic testing (>24 h) owing to the greater net surface capacity for CO2 reduction, thus representing an effective strategy to extend lifetime. The hybrid particles can be deposited onto an FTO substrate to yield ∼60% Faradaic efficiency for photoelectrochemical CO production at −1.2 V vs Ag/AgCl bias. In summary, these results demonstrate the synergistic combination of a crystalline carbon nitride with a molecular catalyst that achieves among the highest known rates in carbon-nitride systems for the light-driven CO2 reduction to CO in aqueous solution with >95% selectivity.}, journal={ACS APPLIED ENERGY MATERIALS}, author={McGuigan, Scott and Tereniak, Stephen J. and Donley, Carrie L. and Smith, Avery and Jeon, Sungho and Zhao, Fengyi and Sampaio, Renato N. and Pauly, Magnus and Keller, Landon and Collins, Leonard and et al.}, year={2023}, month={Oct} }
 @article{durmusoglu_al'abri_li_islam williams_collins_martinez_crook_2023, title={Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach}, volume={22}, ISSN={["1475-2859"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85161032784&partnerID=MN8TOARS}, DOI={10.1186/s12934-023-02117-y}, abstractNote={The probiotic yeast Saccharomyces boulardii (Sb) is a promising chassis to deliver therapeutic proteins to the gut due to Sb's innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineer Sb strains with enhanced levels of protein secretion. In this work, we explored genetic modifications in both cis- (i.e. to the expression cassette of the secreted protein) and trans- (i.e. to the Sb genome) that enhance Sb's ability to secrete proteins, taking a Clostridioides difficile Toxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by sixfold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 and 463 mg/L. Then, guided by prior knowledge of S. cerevisiae's secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficient Sb strain that produces 5045 mg/L secretory NPA, an improvement of > tenfold over wild-type Sb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted.}, number={1}, journal={MICROBIAL CELL FACTORIES}, author={Durmusoglu, Deniz and Al'Abri, Ibrahim and Li, Zidan and Islam Williams, Taufika and Collins, Leonard B. and Martinez, Jose L. and Crook, Nathan}, year={2023}, month={Jun} }
 @article{sripada_elhanafi_collins_williams_linova_woodley_boi_menegatti_2023, title={Pseudo-affinity capture of <i>K. phaffii</i> host cell proteins in flow-through mode: Purification of protein therapeutics and proteomic study}, volume={326}, ISSN={["1873-3794"]}, url={https://doi.org/10.1016/j.seppur.2023.124777}, DOI={10.1016/j.seppur.2023.124777}, abstractNote={K. phaffii is a versatile expression system that is increasingly utilized to produce biological therapeutics – including enzymes, engineered antibodies, and gene-editing tools – that feature multiple subunits and complex post-translational modifications. Two major roadblocks limit the adoption of K. phaffii in industrial biomanufacturing: its proteome, while known, has not been linked to downstream process operations and detailed knowledge is missing on problematic host cell proteins (HCPs) that endanger patient safety or product stability. Furthermore, the purification toolbox has not evolved beyond the capture of monospecific antibodies, and few solutions are available for engineered antibody fragments and other protein therapeutics. To unlock the potential of yeast-based biopharmaceutical manufacturing, this study presents the development and performance validation of a novel adsorbent – PichiaGuard – functionalized with peptide ligands that target the whole spectrum of K. phaffii HCPs and designed for protein purification in flow-through mode. The PichiaGuard adsorbent features high HCP binding capacity (∼25 g per liter of resin) and successfully purified a monoclonal antibody and an ScFv fragment from clarified K. phaffii harvests, affording > 300-fold removal of HCPs and high product yields (70–80%). Notably, PichiaGuard outperformed commercial ion exchange and mixed-mode resins without salt gradients or optimization in removing high-risk HCPs – including aspartic proteases, ribosomal subunits, and other peptidases – thus demonstrating its value in modern biopharmaceutical processing.}, journal={SEPARATION AND PURIFICATION TECHNOLOGY}, author={Sripada, Sobhana A. and Elhanafi, Driss and Collins, Leonard B. and Williams, Taufika I. and Linova, Marina Y. and Woodley, John M. and Boi, Cristiana and Menegatti, Stefano}, year={2023}, month={Dec} }
 @article{orr_collins_jima_buchwalter_2023, title={Salinity-induced ionoregulatory changes in the gill proteome of the mayfly, Neocloeon triangulifer}, volume={316}, ISSN={["1873-6424"]}, url={https://doi.org/10.1016/j.envpol.2022.120609}, DOI={10.1016/j.envpol.2022.120609}, abstractNote={Ecologists have observed declines in the biodiversity of sensitive freshwater organisms in response to increasing concentrations of major ions (salinization). Yet, how changing salinities physiologically challenge aquatic organisms, such as mayflies, remains remarkably understudied. Moreover, it is not well understood the degree to which species respond and acclimate to salinity changes. Our lab is developing the Baetid mayfly, N. triangulifer, as a model organism for physiological research. We have previously described acclimatory changes in both ion flux rates and altered mRNA transcript levels in response to chronic exposures to elevated major ion concentrations at the whole animal level. In the present study, we use shotgun proteomics to identify the specific proteins associated with apical ion transport and how their abundance changes in response to chronic salinity exposures in gills. Gills were isolated from the penultimate nymphal stage of N. triangulifer reared under control culture conditions, elevated NaCl (157 mg L-1 Na), elevated CaCl2 (121 mg L-1 Ca), elevated Ca/MgSO4 (735 mg L-1 SO4). These conditions mirrored those from previously published physiological work. We also acutely exposed nymphs to dilute (50% dilution of culture water with deionized water) to explore proteomic changes in the gills in response to dilute conditions. We report 710 unique peptide sequences among treatment groups, including important apical ion transporters such as Ca-ATPase, Na/K ATPase, and V-ATPase. Treatment with elevated NaCl and Ca/MgSO4 appeared to cause more significant differential protein expression (452 and 345, respectively) compared to CaCl2 and dilute groups (134 and 17, respectively). Finally, we demonstrated the breadth of physiological functions in gills by exploring non-transport related pathways found in our dataset, including ATP synthesis, calcium signaling, and oxidative stress response. We discuss our results in the context of freshwater salinization and the challenges of working with non-model species without fully sequenced and annotated genomes.}, journal={ENVIRONMENTAL POLLUTION}, author={Orr, Sarah E. and Collins, Leonard B. and Jima, Dereje D. and Buchwalter, David B.}, year={2023}, month={Jan} }
 @article{durmusoglu_al’abri_williams_collins_martínez_crook_2022, title={Improving Therapeutic Protein Secretion in the Probiotic YeastSaccharomyces boulardiiusing a Multifactorial Engineering Approach}, url={https://doi.org/10.1101/2022.12.30.522352}, DOI={10.1101/2022.12.30.522352}, abstractNote={Abstract The probiotic yeast Saccharomyces boulardii ( Sb ) is a promising chassis to deliver therapeutic proteins to the gut due to Sb ’s innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineer Sb strains with enhanced levels of protein secretion. In this work, we explored genetic modifications in both cis - (i.e., to the expression cassette of the secreted protein) and trans - (i.e., to the Sb genome) that enhance Sb ’s ability to secrete proteins, taking a Clostridioides difficile Toxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by 6-fold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 - 463 mg/L. Then, guided by prior knowledge of S. cerevisiae ’s secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficient Sb strain that produces 5045 mg/L secretory NPA, an improvement of >10-fold over wild-type Sb . Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted.}, journal={bioRxiv}, author={Durmusoglu, Deniz and Al’Abri, Ibrahim and Williams, Taufika Islam and Collins, Leonard B. and Martínez, José L. and Crook, Nathan}, year={2022}, month={Dec} }
 @article{manley_phan_stewart_mosley_xue_cha_bai_lightfoot_rucker_collins_et al._2022, title={Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis}, volume={119}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2210908119}, DOI={10.1073/pnas.2210908119}, abstractNote={Significance As a precursor to the essential vitamin tetrahydrofolate, para-aminobenzoate (pABA) is needed for nucleotide and amino acid synthesis. Chlamydia trachomatis, the causative agent of the sexually transmitted infection, lacks the canonical pabABC biosynthetic pathway and instead utilizes a novel stratagem for pABA synthesis that is catalyzed by the enzyme Chlamydia protein associating with death domains (CADD). Originally assigned as a diiron enzyme, we report high in vitro activity relies on the stoichiometric addition of both Fe and Mn. Furthermore, CADD is shown to activate O2 to self-sacrificially produce pABA from Tyr27. This work addresses the unusual mechanism by which Chlamydiae produce pABA, which is a prime target for the development of therapeutic agents to treat infections.}, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Manley, Olivia M. and Phan, Han N. and Stewart, Allison K. and Mosley, Dontae A. and Xue, Shan and Cha, Lide and Bai, Hongxia and Lightfoot, Veda C. and Rucker, Pierson A. and Collins, Leonard and et al.}, year={2022}, month={Sep} }
 @article{biehl_martins_davis_sze_collins_mora-navarro_fisher_freytes_2022, title={Towards a standardized multi-tissue decellularization protocol for the derivation of extracellular matrix materials}, volume={12}, ISSN={["2047-4849"]}, DOI={10.1039/d2bm01012g}, abstractNote={The goal of tissue decellularization is to efficiently remove unwanted cellular components, such as DNA and cellular debris, while retaining the complex structural and molecular milieu within the extracellular matrix (ECM). Decellularization protocols to date are centered on customized tissue-specific and lab-specific protocols that involve consecutive manual steps which results in variable and protocol-specific ECM material. The differences that result from the inconsistent protocols between decellularized ECMs affect consistency across batches, limit comparisons between results obtained from different laboratories, and could limit the transferability of the material for consistent laboratory or clinical use. The present study is the first proof-of-concept towards the development of a standardized protocol that can be used to derive multiple ECM biomaterials (powders and hydrogels) via a previously established automated system. The automated decellularization method developed by our group was used due to its short decellularization time (4 hours) and its ability to reduce batch-to-batch variability. The ECM obtained using this first iteration of a unified protocol was able to produce ECM hydrogels from skin, lung, muscle, tendons, cartilage, and laryngeal tissues. All hydrogels formed in this study were cytocompatible and showed gelation and rheological properties consistent with previous ECM hydrogels. The ECMs also showed unique proteomic composition. The present study represents the first step towards developing standardized protocols that can be used on multiple tissues in a fast, scalable, and reproducible manner.}, journal={BIOMATERIALS SCIENCE}, author={Biehl, Andreea and Martins, Ana M. Gracioso M. and Davis, Zachary G. G. and Sze, Daphne and Collins, Leonard and Mora-Navarro, Camilo and Fisher, Matthew B. B. and Freytes, Donald O. O.}, year={2022}, month={Dec} }
 @article{andre_neupane_lappin_herrin_smith_williams_collins_bai_jorge_balbuena_et al._2022, title={Using Proteomic Approaches to Unravel the Response of Ctenocephalides felis felis to Blood Feeding and Infection With Bartonella henselae}, volume={12}, ISSN={["2235-2988"]}, url={http://dx.doi.org/10.3389/fcimb.2022.828082}, DOI={10.3389/fcimb.2022.828082}, abstractNote={Among the Ctenocephalides felis felis-borne pathogens, Bartonella henselae, the main aetiological agent of cat scratch disease (CSD), is of increasing comparative biomedical importance. Despite the importance of B. henselae as an emergent pathogen, prevention of the diseases caused by this agent in cats, dogs and humans mostly relies on the use of ectoparasiticides. A vaccine targeting both flea fitness and pathogen competence is an attractive choice requiring the identification of flea proteins/metabolites with a dual effect. Even though recent developments in vector and pathogen -omics have advanced the understanding of the genetic factors and molecular pathways involved at the tick-pathogen interface, leading to discovery of candidate protective antigens, only a few studies have focused on the interaction between fleas and flea-borne pathogens. Taking into account the period of time needed for B. henselae replication in flea digestive tract, the present study investigated flea-differentially abundant proteins (FDAP) in unfed fleas, fleas fed on uninfected cats, and fleas fed on B. henselae-infected cats at 24 hours and 9 days after the beginning of blood feeding. Proteomics approaches were designed and implemented to interrogate differentially expressed proteins, so as to gain a better understanding of proteomic changes associated with the initial B. henselae transmission period (24 hour timepoint) and a subsequent time point 9 days after blood ingestion and flea infection. As a result, serine proteases, ribosomal proteins, proteasome subunit α-type, juvenile hormone epoxide hydrolase 1, vitellogenin C, allantoinase, phosphoenolpyruvate carboxykinase, succinic semialdehyde dehydrogenase, glycinamide ribotide transformylase, secreted salivary acid phosphatase had high abundance in response of C. felis blood feeding and/or infection by B. henselae. In contrast, high abundance of serpin-1, arginine kinase, ribosomal proteins, peritrophin-like protein, and FS-H/FSI antigen family member 3 was strongly associated with unfed cat fleas. Findings from this study provide insights into proteomic response of cat fleas to B. henselae infected and uninfected blood meal, as well as C. felis response to invading B. henselae over an infection time course, thus helping understand the complex interactions between cat fleas and B. henselae at protein levels.}, journal={FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Andre, Marcos Rogerio and Neupane, Pradeep and Lappin, Michael and Herrin, Brian and Smith, Vicki and Williams, Taufika Islam and Collins, Leonard and Bai, Hongxia and Jorge, Gabriel Lemes and Balbuena, Tiago Santana and et al.}, year={2022}, month={Jan} }
 @article{zhou_baumann_mead_skrabal_kieber_avery_shimizu_dewitt_sun_vance_et al._2021, title={PFOS dominates PFAS composition in ambient fine particulate matter (PM2.5) collected across North Carolina nearly 20 years after the end of its US production}, volume={23}, ISSN={["2050-7895"]}, DOI={10.1039/d0em00497a}, abstractNote={Contamination of drinking water by per- and polyfluoroalkyl substances (PFASs) emitted from manufacturing plants, fire-fighting foams, and urban waste streams has received considerable attention due to concerns over toxicity and environmental persistence; however, PFASs in ambient air remain poorly understood, especially in the United States (US). We measured PFAS concentrations in ambient fine particulate matter (PM2.5) at 5 locations across North Carolina over a 1 year period in 2019. Thirty-four PFASs, including perfluoroalkyl carboxylic, perfluoroalkane sulfonic, perfluoroalkyl ether carboxylic and sulfonic acids were analyzed by UHPLC/ESI-MS/MS. Quarterly averaged concentrations ranged from <0.004-14.1 pg m-3. Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) ranged from <0.18 to 14.1 pg m-3, comparable to previous PM2.5 measurements from Canada and Europe (<0.02-3.5 pg m-3). Concentrations above 1 pg m-3 were observed in July-September at Charlotte (14.1 pg m-3, PFOA), Wilmington (4.75 pg m-3, PFOS), and Research Triangle Park (1.37 pg m-3, PFOS). Notably, PM2.5 has a short atmospheric lifetime (<2 weeks), and thus, the presence of PFOS in these samples raises questions about their sources, since PFOS production was phased out in the US ∼20 years ago. This is the first US study to provide insights into ambient PFAS concentrations in PM2.5.}, number={4}, journal={ENVIRONMENTAL SCIENCE-PROCESSES & IMPACTS}, author={Zhou, J. and Baumann, K. and Mead, R. N. and Skrabal, S. A. and Kieber, R. J. and Avery, G. B. and Shimizu, M. and DeWitt, J. C. and Sun, M. and Vance, S. A. and et al.}, year={2021}, month={Apr}, pages={580–587} }
 @article{isom_page_collins_kapolka_taghon_dohlman_2018, title={Coordinated regulation of intracellular pH by two glucose-sensing pathways in yeast}, volume={293}, ISSN={0021-9258}, url={http://dx.doi.org/10.1074/jbc.ra117.000422}, DOI={10.1074/jbc.ra117.000422}, abstractNote={The yeast Saccharomyces cerevisiae employs multiple pathways to coordinate sugar availability and metabolism. Glucose and other sugars are detected by a G protein–coupled receptor, Gpr1, as well as a pair of transporter-like proteins, Rgt2 and Snf3. When glucose is limiting, however, an ATP-driven proton pump (Pma1) is inactivated, leading to a marked decrease in cytoplasmic pH. Here we determine the relative contribution of the two sugar-sensing pathways to pH regulation. Whereas cytoplasmic pH is strongly dependent on glucose abundance and is regulated by both glucose-sensing pathways, ATP is largely unaffected and therefore cannot account for the changes in Pma1 activity. These data suggest that the pH is a second messenger of the glucose-sensing pathways. We show further that different sugars differ in their ability to control cellular acidification, in the manner of inverse agonists. We conclude that the sugar-sensing pathways act via Pma1 to invoke coordinated changes in cellular pH and metabolism. More broadly, our findings support the emerging view that cellular systems have evolved the use of pH signals as a means of adapting to environmental stresses such as those caused by hypoxia, ischemia, and diabetes.}, number={7}, journal={Journal of Biological Chemistry}, publisher={Elsevier BV}, author={Isom, Daniel G. and Page, Stephani C. and Collins, Leonard B. and Kapolka, Nicholas J. and Taghon, Geoffrey J. and Dohlman, Henrik G.}, year={2018}, month={Feb}, pages={2318–2329} }
 @article{cui_zeng_dos santos_zhang_chen_zhang_rose_budisulistiorini_collins_bodnar_et al._2018, title={Development of a hydrophilic interaction liquid chromatography (HILIC) method for the chemical characterization of water-soluble isoprene epoxydiol (IEPOX)-derived secondary organic aerosol}, volume={20}, ISSN={2050-7887 2050-7895}, url={http://dx.doi.org/10.1039/c8em00308d}, DOI={10.1039/c8em00308d}, abstractNote={Acid-catalyzed multiphase chemistry of isoprene epoxydiols (IEPOX) on sulfate aerosol produces substantial amounts of water-soluble secondary organic aerosol (SOA) constituents, including 2-methyltetrols, methyltetrol sulfates, and oligomers thereof in atmospheric fine particulate matter (PM2.5). These constituents have commonly been measured by gas chromatography interfaced to electron ionization mass spectrometry (GC/EI-MS) with prior derivatization or by reverse-phase liquid chromatography interfaced to electrospray ionization high-resolution mass spectrometry (RPLC/ESI-HR-MS). However, both techniques have limitations in explicitly resolving and quantifying polar SOA constituents due either to thermal degradation or poor separation. With authentic 2-methyltetrol and methyltetrol sulfate standards synthesized in-house, we developed a hydrophilic interaction liquid chromatography (HILIC)/ESI-HR-quadrupole time-of-flight mass spectrometry (QTOFMS) protocol that can chromatographically resolve and accurately measure the major IEPOX-derived SOA constituents in both laboratory-generated SOA and atmospheric PM2.5. 2-Methyltetrols were simultaneously resolved along with 4-6 diastereomers of methyltetrol sulfate, allowing efficient quantification of both major classes of SOA constituents by a single non-thermal analytical method. The sum of 2-methyltetrols and methyltetrol sulfates accounted for approximately 92%, 62%, and 21% of the laboratory-generated β-IEPOX aerosol mass, laboratory-generated δ-IEPOX aerosol mass, and organic aerosol mass in the southeastern U.S., respectively, where the mass concentration of methyltetrol sulfates was 171-271% the mass concentration of methyltetrol. Mass concentrations of methyltetrol sulfates were 0.39 and 2.33 μg m-3 in a PM2.5 sample collected from central Amazonia and the southeastern U.S., respectively. The improved resolution clearly reveals isomeric patterns specific to methyltetrol sulfates from acid-catalyzed multiphase chemistry of β- and δ-IEPOX. We also demonstrate that conventional GC/EI-MS analyses overestimate 2-methyltetrols by up to 188%, resulting (in part) from the thermal degradation of methyltetrol sulfates. Lastly, C5-alkene triols and 3-methyltetrahydrofuran-3,4-diols are found to be largely GC/EI-MS artifacts formed from thermal degradation of 2-methyltetrol sulfates and 3-methyletrol sulfates, respectively, and are not detected with HILIC/ESI-HR-QTOFMS.}, number={11}, journal={Environmental Science: Processes & Impacts}, publisher={Royal Society of Chemistry (RSC)}, author={Cui, Tianqu and Zeng, Zhexi and dos Santos, Erickson O. and Zhang, Zhenfa and Chen, Yuzhi and Zhang, Yue and Rose, Caitlin A. and Budisulistiorini, Sri H. and Collins, Leonard B. and Bodnar, Wanda M. and et al.}, year={2018}, pages={1524–1536} }
 @article{shimomoto_collins_yi_holley_zhang_tian_uchida_wang_hörkkö_willis_et al._2017, title={A purified MAA-based ELISA is a useful tool for determining anti-MAA antibody titer with high sensitivity}, volume={12}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0172172}, DOI={10.1371/journal.pone.0172172}, abstractNote={Atherosclerosis is widely accepted to be a chronic inflammatory disease, and the immunological response to the accumulation of LDL is believed to play a critical role in the development of this disease. 1,4-Dihydropyridine-type MAA-adducted LDL has been implicated in atherosclerosis. Here, we have demonstrated that pure MAA-modified residues can be chemically conjugated to large proteins without by-product contamination. Using this pure antigen, we established a purified MAA-ELISA, with which a marked increase in anti-MAA antibody titer was determined at a very early stage of atherosclerosis in 3-month ApoE-/- mice fed with a normal diet. Our methods of Nε-MAA-L-lysine purification and purified antigen-based ELISA will be easily applicable for biomarker-based detection of early stage atherosclerosis in patients, as well as for the development of an adduct-specific Liquid Chromatography/Mass Spectrometry-based quantification of physiological and pathological levels of MAA.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Shimomoto, Takasumi and Collins, Leonard B. and Yi, Xianwen and Holley, Darcy W. and Zhang, Zhenfa and Tian, Xu and Uchida, Koji and Wang, Chunguang and Hörkkö, Sohvi and Willis, Monte S. and et al.}, editor={Hagemeyer, Christoph EEditor}, year={2017}, month={Feb}, pages={e0172172} }
 @article{gao_mutlu_collins_walker_hartwell_olson_sun_gold_ball_swenberg_2017, title={DNA Product Formation in Female Sprague–Dawley Rats Following Polyhalogenated Aromatic Hydrocarbon (PHAH) Exposure}, volume={30}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/acs.chemrestox.6b00368}, DOI={10.1021/acs.chemrestox.6b00368}, abstractNote={DNA oxidation damage has been regarded as one of the possible mechanisms for the hepatic carcinogenesis of dioxin-like compounds (DLCs). In this study, we evaluated the toxic equivalency factor (TEF) from the standpoint of induced DNA oxidation products and their relationship to toxicity and carcinogenicity. Nine DNA oxidation products were analyzed in the liver of female Sprague–Dawley rats exposed to 2,3,7,8-tetrachlorodibenzo-pdioxin (TCDD) alone or the tertiary mixture of TCDD, 3,3′,4,4′,5-pentachlorobiphenyl (PCB 126), and 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) by gavage for 14, 31, and 53 weeks (5 days/week) by LC–MS/MS: 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dGuo); 1,N6-etheno-2′-deoxyadenosine (1,N6-εdAdo); N2,3-ethenoguanine (N2,3-εG); 7-(2-oxoethly)guanine (7-OEG); 1,N2-etheno-2′-deoxyguanosine (1,N2-εdGuo); malondialdehyde (M1dGuo); acrolein (AcrdGuo); crotonaldehyde (CrdGuo); and 4-hydroxynonenal (HNEdGuo) derived 2′-deoxyguanosine adducts. Exposure to TCDD (100 ng/kg/day) significantly induced 1,N6-εdAdo at 31 and 53 weeks, while no increase of 8-oxo-dGuo was observed. Significant increases were observed for 8-oxo-dGuo and 1,N6-εdAdo at all time points following exposure to the tertiary mixture (TEQ 100 ng/kg/day). Exposure to TCDD for 53 weeks only significantly increased 1,N6-εdAdo, while increases of N2,3-εG and 7-OEG were only found in the highest dose group (100 ng/kg/day). Exposure to the tertiary mixture for 53 weeks had no effect on N2,3-εG in any exposure group (TEQ 0, 22, 46, or 100 ng/kg/day), while significant increases were observed for 1,N6-εdAdo (all dose groups), 8-oxo-dGuo (46 and 100 ng/kg/day), and 7-OEG (100 ng/kg/day). While no significant increase was observed at 53 weeks for 1,N2-εdGuo, M1dGuo, AcrdGuo, or CrdGuo following exposure to TCDD (100 ng/kg/day), all of them were significantly induced in animals exposed to the tertiary mixture (TEQ 100 ng/kg/day). This oxidation DNA product data suggest that the simple TEF methodology cannot be applied to evaluate the diverse patterns of toxic effects induced by DLCs.}, number={3}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Gao, Lina and Mutlu, Esra and Collins, Leonard B. and Walker, Nigel J. and Hartwell, Hadley J. and Olson, James R. and Sun, Wei and Gold, Avram and Ball, Louise M. and Swenberg, James A.}, year={2017}, month={Feb}, pages={794–803} }
 @article{nakamura_shimomoto_collins_holley_zhang_barbee_sharma_tian_kondo_uchida_et al._2017, title={Evidence that endogenous formaldehyde produces immunogenic and atherogenic adduct epitopes}, volume={7}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-017-11289-8}, DOI={10.1038/s41598-017-11289-8}, abstractNote={Abstract Endogenous formaldehyde is abundantly present in our bodies, at around 100 µM under normal conditions. While such high steady state levels of formaldehyde may be derived by enzymatic reactions including oxidative demethylation/deamination and myeloperoxidation, it is unclear whether endogenous formaldehyde can initiate and/or promote diseases in humans. Here, we show that fluorescent malondialdehyde-formaldehyde (M2FA)-lysine adducts are immunogenic without adjuvants in mice. Natural antibody titers against M2FA are elevated in atherosclerosis-prone mice. Staining with an antibody against M2FA demonstrated that M2FA is present in plaque found on the aortic valve of ApoE −/− mice. To mimic inflammation during atherogenesis, human myeloperoxidase was incubated with glycine, H 2 O 2 , malondialdehyde, and a lysine analog in PBS at a physiological temperature, which resulted in M2FA generation. These results strongly suggest that the 1,4-dihydropyridine-type of lysine adducts observed in atherosclerosis lesions are likely produced by endogenous formaldehyde and malondialdehyde with lysine. These highly fluorescent M2FA adducts may play important roles in human inflammatory and degenerative diseases.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Nakamura, Jun and Shimomoto, Takasumi and Collins, Leonard B. and Holley, Darcy W. and Zhang, Zhenfa and Barbee, Jenna M. and Sharma, Vyom and Tian, Xu and Kondo, Tomohiro and Uchida, Koji and et al.}, year={2017}, month={Sep} }
 @article{tian_gold_nakamura_zhang_vila_singleton_collins_aitken_2017, title={Nontarget Analysis Reveals a Bacterial Metabolite of Pyrene Implicated in the Genotoxicity of Contaminated Soil after Bioremediation}, volume={51}, ISSN={0013-936X 1520-5851}, url={http://dx.doi.org/10.1021/acs.est.7b01172}, DOI={10.1021/acs.est.7b01172}, abstractNote={Bioremediation is an accepted technology for cleanup of soil contaminated with polycyclic aromatic hydrocarbons (PAHs), but it can increase the genotoxicity of the soil despite removal of the regulated PAHs. Although polar biotransformation products have been implicated as causative genotoxic agents, no specific product has been identified. We pursued a nontarget analytical approach combining effect-directed analysis (EDA) and metabolite profiling to compare extracts of PAH-contaminated soil from a former manufactured-gas plant site before and after treatment in a laboratory-scale aerobic bioreactor. A compound with the composition C15H8O2 and four methylated homologues were shown to accumulate as a result of bioreactor treatment, and the C15H8O2 compound purified from soil extracts was determined to be genotoxic. Its structure was established by nuclear magnetic resonance and mass spectroscopy as a heretofore unidentified α,β-unsaturated lactone derived from dioxygenation of pyrene at an apical ring, 2H-naphtho[2,1,8-def]chromen-2-one (NCO), which was confirmed by synthesis. The concentration of NCO in the bioreactor was 11 μg g-1 dry soil, corresponding to 13% of the pyrene removed. It also accumulated in aerobically incubated soil from two additional PAH-contaminated sites and was formed from pyrene by two pyrene-degrading bacterial cultures known to be geographically widespread, underscoring its potential environmental significance.}, number={12}, journal={Environmental Science & Technology}, publisher={American Chemical Society (ACS)}, author={Tian, Zhenyu and Gold, Avram and Nakamura, Jun and Zhang, Zhenfa and Vila, Joaquim and Singleton, David R. and Collins, Leonard B. and Aitken, Michael D.}, year={2017}, month={May}, pages={7091–7100} }
 @article{klaus_bastek_damme_collins_frötschl_benda_lutter_ellinger-ziegelbauer_swenberg_dietrich_et al._2017, title={Time-matched analysis of DNA adduct formation and early gene expression as predictive tool for renal carcinogenesis in methylazoxymethanol acetate treated Eker rats}, volume={91}, ISSN={0340-5761 1432-0738}, url={http://dx.doi.org/10.1007/s00204-017-1953-6}, DOI={10.1007/s00204-017-1953-6}, abstractNote={Genotoxic carcinogens pose great hazard to human health. Uncertainty of current risk assessment strategies and long latency periods between first carcinogen exposure and diagnosis of tumors have raised interest in predictive biomarkers. Initial DNA adduct formation is a necessary step for genotoxin induced carcinogenesis. However, as DNA adducts not always translate into tumorigenesis, their predictive value is limited. Here we hypothesize that the combined analysis of pro-mutagenic DNA adducts along with time-matched gene expression changes could serve as a superior prediction tool for genotoxic carcinogenesis. Eker rats, heterozygous for the tuberous sclerosis (Tsc2) tumor suppressor gene and thus highly susceptible towards genotoxic renal carcinogens, were continuously treated with the DNA alkylating carcinogen methylazoxymethanol acetate (MAMAc). Two weeks of MAMAc treatment resulted in a time-dependent increase of O6-methylguanine and N7-methylguanine adducts in the kidney cortex, which was however not reflected by significant expression changes of cyto-protective genes involved in DNA repair, cell cycle arrest or apoptosis. Instead, we found a transcriptional regulation of genes involved in the tumor-related MAPK, FoxO and TGF-beta pathways. Continuous MAMAc treatment for up to 6 months resulted in a mild but significant increase of cancerous lesions. In summary, the combined analysis of DNA adducts and early gene expression changes could serve as a suitable predictive tool for genotoxicant-induced carcinogenesis.}, number={10}, journal={Archives of Toxicology}, publisher={Springer Science and Business Media LLC}, author={Klaus, Valentina and Bastek, Heinke and Damme, Katja and Collins, Leonard B. and Frötschl, Roland and Benda, Norbert and Lutter, Dominik and Ellinger-Ziegelbauer, Heidrun and Swenberg, James A. and Dietrich, Daniel R. and et al.}, year={2017}, month={Mar}, pages={3427–3438} }
 @article{sharma_collins_chen_herr_takeda_sun_swenberg_nakamura_2016, title={Oxidative stress at low levels can induce clustered DNA lesions leading to NHEJ mediated mutations}, volume={7}, ISSN={1949-2553}, url={http://dx.doi.org/10.18632/oncotarget.8298}, DOI={10.18632/oncotarget.8298}, abstractNote={DNA damage and mutations induced by oxidative stress are associated with various different human pathologies including cancer. The facts that most human tumors are characterized by large genome rearrangements and glutathione depletion in mice results in deletions in DNA suggest that reactive oxygen species (ROS) may cause gene and chromosome mutations through DNA double strand breaks (DSBs). However, the generation of DSBs at low levels of ROS is still controversial. In the present study, we show that H2O2 at biologically-relevant levels causes a marked increase in oxidative clustered DNA lesions (OCDLs) with a significant elevation of replication-independent DSBs. Although it is frequently reported that OCDLs are fingerprint of high-energy IR, our results indicate for the first time that H2O2, even at low levels, can also cause OCDLs leading to DSBs specifically in G1 cells. Furthermore, a reverse genetic approach revealed a significant contribution of the non-homologous end joining (NHEJ) pathway in H2O2-induced DNA repair & mutagenesis. This genomic instability induced by low levels of ROS may be involved in spontaneous mutagenesis and the etiology of a wide variety of human diseases like chronic inflammation-related disorders, carcinogenesis, neuro-degeneration and aging.}, number={18}, journal={Oncotarget}, publisher={Impact Journals, LLC}, author={Sharma, Vyom and Collins, Leonard B. and Chen, Ting-huei and Herr, Natalie and Takeda, Shunichi and Sun, Wei and Swenberg, James A. and Nakamura, Jun}, year={2016}, month={Mar}, pages={25377–25390} }
 @article{mutlu_gao_collins_walker_hartwell_olson_sun_gold_ball_swenberg_2016, title={Polychlorinated Biphenyls Induce Oxidative DNA Adducts in Female Sprague–Dawley Rats}, volume={29}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/acs.chemrestox.6b00146}, DOI={10.1021/acs.chemrestox.6b00146}, abstractNote={Polychlorinated biphenyls (PCBs) are organic chemicals that were traditionally produced and widely used in industry as mixtures and are presently formed as byproducts of pigment and dye manufacturing. They are known to persist and bioaccumulate in the environment. Some have been shown to induce liver cancer in rodents. Although the mechanism of the toxicity of PCBs is unknown, it has been shown that they increase oxidative stress, including lipid peroxidation. We hypothesized that oxidative stress-induced DNA damage could be a contributor for PCB carcinogenesis and analyzed several DNA adducts in female Sprague-Dawley rats exposed to 3,3',4,4',5-pentachlorobiphenyl (PCB 126), 2,2',4,4',5,5'-hexachlorobiphenyl (PCB 153), and a binary mixture (PCB 126 + 153) for 14, 31, and 53 wks. Eight adducts were measured to profile oxidative DNA lesions, including 8-oxo-deoxyguanosine (8-oxo-dG), 1,N(6)-ethenodeoxyadenosine (1,N(6)-εdA), N(2),3-ethenoguanine (N(2),3-εG), 1,N(2)-ethenodeoxyguanosine (1,N(2)-εdG), as well as malondialdehyde (M1dG), acrolein (AcrdG), crotonaldehyde (CrdG), and 4-hydroxynonenal-derived dG adducts (HNEdG) by LC-MS/MS analysis. Statistically significant increases were observed for 8-oxo-dG and 1,N(6)-εdA concentrations in hepatic DNA of female rats exposed to the binary mixture (1000 ng/kg/day + 1000 μg/kg/day) but not in rats exposed to PCB 126 (1000 ng/kg/day) or PCB 153 (1000 μg/kg/day) for 14 and 31 wks. However, exposure to PCB 126 (1000 ng/kg/day) for 53 wks significantly increased 8-oxo-dG, 1,N(6)-εdA, AcrdG, and M1dG. Exposure to PCB 153 (1000 μg/kg/day) for 53 wks increased 8-oxo-dG, and 1,N(6)-εdA. Exposure to the binary mixture for 53 wks increased 8-oxo-dG, 1,N(6)-εdA, AcrdG, 1,N(2)-εdG, and N(2),3-εG significantly above control groups. Increased hepatic oxidative DNA adducts following exposure to PCB 126, PCB 153, or the binary mixture shows that an increase in DNA damage may play an important role in hepatic toxicity and carcinogenesis in female Sprague-Dawley rats.}, number={8}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Mutlu, Esra and Gao, Lina and Collins, Leonard B. and Walker, Nigel J. and Hartwell, Hadley J. and Olson, James R. and Sun, Wei and Gold, Avram and Ball, Louise M. and Swenberg, James A.}, year={2016}, month={Jul}, pages={1335–1344} }
 @article{leng_wu_collins_thomas_tellez_jauregui_picchi_zhang_juri_desai_et al._2015, title={Implication of a Chromosome 15q15.2 Locus in Regulating UBR1 and Predisposing Smokers to MGMT Methylation in Lung}, volume={75}, ISSN={0008-5472 1538-7445}, url={http://dx.doi.org/10.1158/0008-5472.can-15-0243}, DOI={10.1158/0008-5472.can-15-0243}, abstractNote={O(6)-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that protects cells from carcinogenic effects of alkylating agents; however, MGMT is silenced by promoter hypermethylation during carcinogenesis. A single-nucleotide polymorphism (SNP) in an enhancer in the MGMT promoter was previously identified to be highly significantly associated with risk for MGMT methylation in lung cancer and sputum from smokers. To further genetic investigations, a genome-wide association and replication study was conducted in two smoker cohorts to identify novel loci for MGMT methylation in sputum that were independent of the MGMT enhancer polymorphism. Two novel trans-acting loci (15q15.2 and 17q24.3) that were identified acted together with the enhancer SNP to empower risk prediction for MGMT methylation. We found that the predisposition to MGMT methylation arising from the 15q15.2 locus involved regulation of the ubiquitin protein ligase E3 component UBR1. UBR1 attenuation reduced turnover of MGMT protein and increased repair of O6-methylguanine in nitrosomethylurea-treated human bronchial epithelial cells, while also reducing MGMT promoter activity and abolishing MGMT induction. Overall, our results substantiate reduced gene transcription as a major mechanism for predisposition to MGMT methylation in the lungs of smokers, and support the importance of UBR1 in regulating MGMT homeostasis and DNA repair of alkylated DNA adducts in cells.}, number={15}, journal={Cancer Research}, publisher={American Association for Cancer Research (AACR)}, author={Leng, Shuguang and Wu, Guodong and Collins, Leonard B. and Thomas, Cynthia L. and Tellez, Carmen S. and Jauregui, Andrew R. and Picchi, Maria A. and Zhang, Xiequn and Juri, Daniel E. and Desai, Dhimant and et al.}, year={2015}, month={Jul}, pages={3108–3117} }
 @article{donohoe_holley_collins_montgomery_whitmore_hillhouse_curry_renner_greenwalt_ryan_et al._2014, title={A Gnotobiotic Mouse Model Demonstrates That Dietary Fiber Protects against Colorectal Tumorigenesis in a Microbiota- and Butyrate-Dependent Manner}, volume={4}, ISSN={2159-8274 2159-8290}, url={http://dx.doi.org/10.1158/2159-8290.cd-14-0501}, DOI={10.1158/2159-8290.cd-14-0501}, abstractNote={UNLABELLED
Whether dietary fiber protects against colorectal cancer is controversial because of conflicting results from human epidemiologic studies. However, these studies and mouse models of colorectal cancer have not controlled the composition of gut microbiota, which ferment fiber into short-chain fatty acids such as butyrate. Butyrate is noteworthy because it has energetic and epigenetic functions in colonocytes and tumor-suppressive properties in colorectal cancer cell lines. We used gnotobiotic mouse models colonized with wild-type or mutant strains of a butyrate-producing bacterium to demonstrate that fiber does have a potent tumor-suppressive effect but in a microbiota- and butyrate-dependent manner. Furthermore, due to the Warburg effect, butyrate was metabolized less in tumors where it accumulated and functioned as a histone deacetylase (HDAC) inhibitor to stimulate histone acetylation and affect apoptosis and cell proliferation. To support the relevance of this mechanism in human cancer, we demonstrate that butyrate and histone-acetylation levels are elevated in colorectal adenocarcinomas compared with normal colonic tissues.


SIGNIFICANCE
These results, which link diet and microbiota to a tumor-suppressive metabolite, provide insight into conflicting epidemiologic findings and suggest that probiotic/prebiotic strategies can modulate an endogenous HDAC inhibitor for anticancer chemoprevention without the adverse effects associated with synthetic HDAC inhibitors used in chemotherapy.}, number={12}, journal={Cancer Discovery}, publisher={American Association for Cancer Research (AACR)}, author={Donohoe, Dallas R. and Holley, Darcy and Collins, Leonard B. and Montgomery, Stephanie A. and Whitmore, Alan C. and Hillhouse, Andrew and Curry, Kaitlin P. and Renner, Sarah W. and Greenwalt, Alicia and Ryan, Elizabeth P. and et al.}, year={2014}, month={Sep}, pages={1387–1397} }
 @article{yoo_bradford_kosyk_uehara_shymonyak_collins_bodnar_ball_gold_rusyn_2014, title={Comparative Analysis of the Relationship Between Trichloroethylene Metabolism and Tissue-Specific Toxicity Among Inbred Mouse Strains: Kidney Effects}, volume={78}, ISSN={1528-7394 1087-2620}, url={http://dx.doi.org/10.1080/15287394.2015.958418}, DOI={10.1080/15287394.2015.958418}, abstractNote={Trichloroethylene (TCE) is a well-known environmental and occupational toxicant that is classified as carcinogenic to humans based on the epidemiological evidence of an association with higher risk of renal-cell carcinoma. A number of scientific issues critical for assessing human health risks from TCE remain unresolved, such as the amount of kidney-toxic glutathione conjugation metabolites formed, interspecies and interindividual differences, and the mode of action for kidney carcinogenicity. It was postulated that TCE renal metabolite levels are associated with kidney-specific toxicity. Oral dosing with TCE was conducted in subacute (600 mg/kg/d; 5 d; 7 inbred mouse strains) and subchronic (100 or 400 mg/kg/d; 1, 2, or 4 wk; 2 inbred mouse strains) designs. The quantitative relationship was evaluated between strain-, dose, and time-dependent formation of TCE metabolites from cytochrome P-450-mediated oxidation (trichloroacetic acid [TCA], dichloroacetic acid [DCA], and trichloroethanol) and glutathione conjugation [S-(1,2-dichlorovinyl)-L-cysteine and S-(1,2-dichlorovinyl)glutathione], and various kidney toxicity phenotypes. In subacute study, interstrain differences in renal TCE metabolite levels were observed. In addition, data showed that in several strains kidney-specific effects of TCE included induction of peroxisome proliferator-marker genes Cyp4a10 and Acox1, increased cell proliferation, and expression of KIM-1, a marker of tubular damage and regeneration. In subchronic study, peroxisome proliferator-marker gene induction and renal toxicity diminished while cell proliferative response was elevated in a dose-dependent manner in NZW/LacJ but not C57BL/6J mice. Overall, data demonstrated that renal TCE metabolite levels are associated with kidney-specific toxicity and that these effects are strain dependent.}, number={1}, journal={Journal of Toxicology and Environmental Health, Part A}, publisher={Informa UK Limited}, author={Yoo, Hong Sik and Bradford, Blair U. and Kosyk, Oksana and Uehara, Takeki and Shymonyak, Svitlana and Collins, Leonard B. and Bodnar, Wanda M. and Ball, Louise M. and Gold, Avram and Rusyn, Ivan}, year={2014}, month={Nov}, pages={32–49} }
 @article{yoo_bradford_kosyk_shymonyak_uehara_collins_bodnar_ball_gold_rusyn_2014, title={Comparative Analysis of the Relationship Between Trichloroethylene Metabolism and Tissue-Specific Toxicity Among Inbred Mouse Strains: Liver Effects}, volume={78}, ISSN={1528-7394 1087-2620}, url={http://dx.doi.org/10.1080/15287394.2015.958417}, DOI={10.1080/15287394.2015.958417}, abstractNote={Trichloroethylene (TCE) is a widely used organic solvent. Although TCE is classified as carcinogenic to humans, substantial gaps remain in our understanding of interindividual variability in TCE metabolism and toxicity, especially in the liver. A hypothesis was tested that amounts of oxidative metabolites of TCE in mouse liver are associated with hepatic-specific toxicity. Oral dosing with TCE was conducted in subacute (600 mg/kg/d; 5 d; 7 inbred mouse strains) and subchronic (100 or 400 mg/kg/d; 1, 2, or 4 wk; 2 inbred mouse strains) designs. The quantitative relationship was evaluated between strain-, dose-, and time-dependent formation of TCE metabolites from cytochrome P-450-mediated oxidation (trichloroacetic acid [TCA], dichloroacetic acid [DCA], and trichloroethanol) and glutathione conjugation [S-(1,2-dichlorovinyl)-L-cysteine and S-(1,2-dichlorovinyl)glutathione] in serum and liver, and various hepatic toxicity phenotypes. In subacute study, interstrain variability in TCE metabolite amounts was observed in serum and liver. No marked induction of Cyp2e1 protein levels in liver was detected. Serum and hepatic levels of TCA and DCA were correlated with increased transcription of peroxisome proliferator-marker genes Cyp4a10 and Acox1 but not with degree of induction in hepatocellular proliferation. In subchronic study, serum and liver levels of oxidative metabolites gradually decreased over time despite continuous dosing. Hepatic protein levels of CYP2E1, ADH, and ALDH2 were unaffected by treatment with TCE. While the magnitude of induction of peroxisome proliferator-marker genes also declined, hepatocellular proliferation increased. This study offers a unique opportunity to provide a scientific data-driven rationale for some of the major assumptions in human health assessment of TCE.}, number={1}, journal={Journal of Toxicology and Environmental Health, Part A}, publisher={Informa UK Limited}, author={Yoo, Hong Sik and Bradford, Blair U. and Kosyk, Oksana and Shymonyak, Svitlana and Uehara, Takeki and Collins, Leonard B. and Bodnar, Wanda M. and Ball, Louise M. and Gold, Avram and Rusyn, Ivan}, year={2014}, month={Nov}, pages={15–31} }
 @article{shibutani_ito_toda_kanao_collins_shibata_urabe_koseki_masuda_swenberg_et al._2014, title={Guanine- 5-carboxylcytosine base pairs mimic mismatches during DNA replication}, volume={4}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep05220}, DOI={10.1038/srep05220}, abstractNote={Abstract The genetic information encoded in genomes must be faithfully replicated and transmitted to daughter cells. The recent discovery of consecutive DNA conversions by TET family proteins of 5-methylcytosine into 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine (5caC) suggests these modified cytosines act as DNA lesions, which could threaten genome integrity. Here, we have shown that although 5caC pairs with guanine during DNA replication in vitro, G·5caC pairs stimulated DNA polymerase exonuclease activity and were recognized by the mismatch repair (MMR) proteins. Knockdown of thymine DNA glycosylase increased 5caC in genome, affected cell proliferation via MMR, indicating MMR is a novel reader for 5caC. These results suggest the epigenetic modification products of 5caC behave as DNA lesions.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Shibutani, Toshihiro and Ito, Shinsuke and Toda, Mariko and Kanao, Rie and Collins, Leonard B. and Shibata, Marika and Urabe, Miho and Koseki, Haruhiko and Masuda, Yuji and Swenberg, James A. and et al.}, year={2014}, month={Jun} }
 @article{sharma_collins_clement_zhang_nakamura_swenberg_2014, title={Molecular Dosimetry of Endogenous and Exogenous O6-Methyl-dG and N7-Methyl-G Adducts Following Low Dose [D3]-Methylnitrosourea Exposures in Cultured Human Cells}, volume={27}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/tx5000602}, DOI={10.1021/tx5000602}, abstractNote={For DNA-reactive chemicals, a low dose linear assessment of cancer risk is the science policy default. In the present study, we quantitated the endogenous and exogenous N7-methyl-G and O6-methyl-dG adducts in human lymphoblastoid cells exposed to low dose [D3]-methylnitrosourea. Endogenous amounts of both adducts remained nearly constant, while the exogenous adducts showed linear dose-responses. The data show that O6-methyl-dG adducts ≥1.8/108 dG correlated with published studies that demonstrated significant increases of mutations under these conditions. The combined results do not support linear extrapolations to zero when data are available for science-based regulations.}, number={4}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Sharma, Vyom and Collins, Leonard B. and Clement, Jean M. and Zhang, Zhenfa and Nakamura, Jun and Swenberg, James A.}, year={2014}, month={Mar}, pages={480–482} }
 @article{nakamura_mutlu_sharma_collins_bodnar_yu_lai_moeller_lu_swenberg_2014, title={The endogenous exposome}, volume={19}, ISSN={1568-7864}, url={http://dx.doi.org/10.1016/j.dnarep.2014.03.031}, DOI={10.1016/j.dnarep.2014.03.031}, abstractNote={The concept of the Exposome is a compilation of diseases and one's lifetime exposure to chemicals, whether the exposure comes from environmental, dietary, or occupational exposures; or endogenous chemicals that are formed from normal metabolism, inflammation, oxidative stress, lipid peroxidation, infections, and other natural metabolic processes such as alteration of the gut microbiome. In this review, we have focused on the endogenous exposome, the DNA damage that arises from the production of endogenous electrophilic molecules in our cells. It provides quantitative data on endogenous DNA damage and its relationship to mutagenesis, with emphasis on when exogenous chemical exposures that produce identical DNA adducts to those arising from normal metabolism cause significant increases in total identical DNA adducts. We have utilized stable isotope labeled chemical exposures of animals and cells, so that accurate relationships between endogenous and exogenous exposures can be determined. Advances in mass spectrometry have vastly increased both the sensitivity and accuracy of such studies. Furthermore, we have clear evidence of which sources of exposure drive low dose biology that results in mutations and disease. These data provide much needed information to impact quantitative risk assessments, in the hope of moving towards the use of science, rather than default assumptions.}, journal={DNA Repair}, publisher={Elsevier BV}, author={Nakamura, Jun and Mutlu, Esra and Sharma, Vyom and Collins, Leonard and Bodnar, Wanda and Yu, Rui and Lai, Yongquan and Moeller, Benjamin and Lu, Kun and Swenberg, James}, year={2014}, month={Jul}, pages={3–13} }
 @article{mutlu_jeong_collins_ham_upton_hatch_winsett_evansky_swenberg_2012, title={A New LC-MS/MS Method for the Quantification of Endogenous and Vinyl Chloride-Induced 7-(2-Oxoethyl)Guanine in Sprague–Dawley Rats}, volume={25}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/tx200447w}, DOI={10.1021/tx200447w}, abstractNote={Vinyl chloride (VC) is an industrial chemical that is known to be carcinogenic to animals and humans. VC primarily induces hepatic angiosarcomas following high exposures (≥50 ppm). VC is also found in Superfund sites at ppb concentrations as a result of microbial metabolism of trichloroethylene and perchloroethylene. Here, we report a new sensitive LC-MS/MS method to analyze the major DNA adduct formed by VC, 7-(2-oxoethylguanine) (7-OEG). We used this method to analyze tissue DNA from both adult and weanling rats exposed to 1100 ppm [(13)C(2)]-VC for 5 days. After neutral thermal hydrolysis, 7-OEG was derivatized with O-t-butyl hydroxylamine to an oxime adduct, followed by LC-MS/MS analysis. The limit of detection was 1 fmol, and the limit of quantitation was 1.5 fmol on the column. The use of stable isotope VC allowed us to demonstrate for the first time that endogenous 7-OEG was present in tissue DNA. We hypothesized that endogenous 7-OEG was formed from lipid peroxidation and demonstrated the formation of [(13)C(2)]-7-OEG from the reaction of calf thymus DNA with [(13)C(18)]-ethyl linoleate (EtLa) under peroxidizing conditions. The concentrations of endogenous 7-OEG in liver, lung, kidney, spleen, testis, and brain DNA from adult and weanling rats typically ranged from 1.0 to 10.0 adducts per 10(6) guanine. The exogenous 7-OEG in liver DNA from adult rats exposed to 1100 ppm [(13)C(2)]-VC for 5 days was 104.0 ± 23.0 adducts per 10(6) guanine (n = 4), while concentrations in other tissues ranged from 1.0 to 39.0 adducts per 10(6) guanine (n = 4). Although endogenous concentrations of 7-OEG in tissues in weanling rats were similar to those of adult rats, exogenous [(13)C(2)]-7-OEG concentrations were higher in weanlings, averaging 300 adducts per 10(6) guanine in liver. Studies on the persistence of [(13)C(2)]-7-OEG in adult rats sacrificed 2, 4, and 8 weeks postexposure to [(13)C(2)]-VC demonstrated a half-life of 7-OEG of 4 days in both liver and lung.}, number={2}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Mutlu, Esra and Jeong, Yo-Chan and Collins, Leonard B. and Ham, Amy-Joan L. and Upton, Patricia B. and Hatch, Gary and Winsett, Darrell and Evansky, Paul and Swenberg, James A.}, year={2012}, month={Jan}, pages={391–399} }
 @article{donohoe_collins_wali_bigler_sun_bultman_2012, title={The Warburg Effect Dictates the Mechanism of Butyrate-Mediated Histone Acetylation and Cell Proliferation}, volume={48}, ISSN={1097-2765}, url={http://dx.doi.org/10.1016/j.molcel.2012.08.033}, DOI={10.1016/j.molcel.2012.08.033}, abstractNote={Widespread changes in gene expression drive tumorigenesis, yet our knowledge of how aberrant epigenomic and transcriptome profiles arise in cancer cells is poorly understood. Here, we demonstrate that metabolic transformation plays an important role. Butyrate is the primary energy source of normal colonocytes and is metabolized to acetyl-CoA, which was shown to be important not only for energetics but also for HAT activity. Due to the Warburg effect, cancerous colonocytes rely on glucose as their primary energy source, so butyrate accumulated and functioned as an HDAC inhibitor. Although both mechanisms increased histone acetylation, different target genes were upregulated. Consequently, butyrate stimulated the proliferation of normal colonocytes and cancerous colonocytes when the Warburg effect was prevented from occurring, whereas it inhibited the proliferation of cancerous colonocytes undergoing the Warburg effect. These findings link a common metabolite to epigenetic mechanisms that are differentially utilized by normal and cancerous cells because of their inherent metabolic differences.}, number={4}, journal={Molecular Cell}, publisher={Elsevier BV}, author={Donohoe, Dallas R. and Collins, Leonard B. and Wali, Aminah and Bigler, Rebecca and Sun, Wei and Bultman, Scott J.}, year={2012}, month={Nov}, pages={612–626} }
 @article{king_ramachandran_chaney_collins_swenberg_dekrafft_lin_cicurel_barbier_2011, title={Debio 0507 primarily forms diaminocyclohexane-Pt-d(GpG) and -d(ApG) DNA adducts in HCT116 cells}, volume={69}, ISSN={0344-5704 1432-0843}, url={http://dx.doi.org/10.1007/s00280-011-1744-3}, DOI={10.1007/s00280-011-1744-3}, abstractNote={To characterize the cellular action mechanism of Debio 0507, we compared the major DNA adducts formed by Debio 0507- and oxaliplatin-treated HCT116 human colon carcinoma cells by a combination of inductively coupled plasma mass spectrometry (ICP-MS) and ultraperformance liquid chromatography mass spectrometry (UPLC-MS/MS). HCT116 cells were treated with IC50 doses of Debio 0507 or oxaliplatin for 3 days. Total cellular Pt–DNA adducts were determined by ICP-MS. The DNA was digested, and the major Pt–DNA adducts formed by both drugs were characterized by UPLC/MS/MS essentially as described previously for cisplatin (Baskerville-Abraham et al. in Chem Res Toxicol 22:905–912, 2009). The Pt level/deoxynucleotide was 7.4/104 for DNA from Debio 0507-treated cells and 5.5/104 for oxaliplatin-treated cells following a 3-day treatment at the IC50 for each drug. UPLC-MS/MS in the positive ion mode confirmed the major Pt–DNA adducts formed by both drugs were dach-Pt-d(GpG) (904.2 m/z → 610 m/z and 904.2 m/z → 459 m/z) and dach-Pt-d(ApG) (888.2 m/z → 594 m/z and 888.2 m/z → 459 m/z). These data show that the major DNA adducts formed by Debio 0507 are the dach-Pt-d(GpG) and dach-Pt-d(ApG) adducts and at equitoxic doses Debio 0507 and oxaliplatin form similar levels of dach-Pt-d(GpG) and dach-Pt-d(ApG) adducts. This suggests that the action mechanisms of Debio 0507 and oxaliplatin are similar at a cellular level.}, number={3}, journal={Cancer Chemotherapy and Pharmacology}, publisher={Springer Science and Business Media LLC}, author={King, C. L. and Ramachandran, S. and Chaney, S. G. and Collins, L. and Swenberg, J. A. and deKrafft, K. E. and Lin, W. and Cicurel, L. and Barbier, M.}, year={2011}, month={Oct}, pages={665–677} }
 @inproceedings{mutlu_collins_stout_upton_daye_winsett_hatch_evansky_swenberg_2011, title={Pseudo-SRM Conditions Improve Detection of N 2,3-ethenoguanine in DNA}, author={Mutlu, Esra and Collins, Leonard and Stout, Matthew and Upton, Patricia and Daye, Laura and Winsett, Darrell and Hatch, Gary and Evansky, Paul and Swenberg, James}, year={2011}, month={Jun} }
 @article{ito_shen_dai_wu_collins_swenberg_he_zhang_2011, title={Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine}, volume={333}, ISSN={0036-8075 1095-9203}, url={http://dx.doi.org/10.1126/science.1210597}, DOI={10.1126/science.1210597}, abstractNote={Evidence for a possible route for DNA demethylation in animals is suggested. 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity–dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.}, number={6047}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Ito, Shinsuke and Shen, Li and Dai, Qing and Wu, Susan C. and Collins, Leonard B. and Swenberg, James A. and He, Chuan and Zhang, Yi}, year={2011}, month={Jul}, pages={1300–1303} }
 @article{boysen_collins_liao_luke_pachkowski_watters_swenberg_2010, title={Analysis of 8-oxo-7,8-dihydro-2′-deoxyguanosine by ultra high pressure liquid chromatography–heat assisted electrospray ionization–tandem mass spectrometry}, volume={878}, ISSN={1570-0232}, url={http://dx.doi.org/10.1016/j.jchromb.2009.12.004}, DOI={10.1016/j.jchromb.2009.12.004}, abstractNote={Increased amounts of reactive oxygen species (ROS), generally termed oxidative stress, are frequently hypothesized to be causally associated with many diseases. Analyses of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) in DNA and urine are widely used biomarkers for oxidative stress. Over the years it became clear that analysis of 8-oxo-dG in DNA is challenging due to artifactual formation during sample work up. The present study demonstrates that 8-oxo-dG can be measured reliably and accurately when appropriate precautions are taken. First, the presence of an antioxidant, metal chelator, or free radical trapping agent during sample preparation improves reproducibility. Second, sample enrichment by HPLC fraction collection was used to optimize sensitivity. Third, heat assisted electrospray ionization (HESI) eliminated potential interferences and improved assay performance and sensitivity. Subsequently, the UPLC-HESI-MS/MS method was applied to show the biphasic dose response of 8-oxo-dG in H(2)O(2)-treated HeLa cells. Application of this method to human lymphocyte DNA (n=156) gave a mean+/-SD endogenous amount of 1.57+/-0.88 adducts per 10(6) dG, a value that is in agreement with the suggested amount previously estimated by European Standard Committee on Oxidative DNA Damage (ESCODD) and others. These results suggest that the present method is well suited for application to molecular toxicology and epidemiology studies investigating the role of oxidative stress.}, number={3-4}, journal={Journal of Chromatography B}, publisher={Elsevier BV}, author={Boysen, Gunnar and Collins, Leonard B. and Liao, Shengkai and Luke, April M. and Pachkowski, Brian F. and Watters, Joanne L. and Swenberg, James A.}, year={2010}, month={Feb}, pages={375–380} }
 @article{mutlu_collins_stout_upton_daye_winsett_hatch_evansky_swenberg_2010, title={Development and Application of an LC-MS/MS Method for the Detection of the Vinyl Chloride-Induced DNA Adduct N2,3-Ethenoguanine in Tissues of Adult and Weanling Rats Following Exposure to [13C2]-VC}, volume={23}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/tx1001767}, DOI={10.1021/tx1001767}, abstractNote={In the 1970s, exposure to vinyl chloride (VC) was shown to cause liver angiosarcoma in VC workers. We have developed a new LC-MS/MS method for analyzing the promutagenic DNA adduct N(2),3-ethenoguanine (εG) and have applied this to DNA from tissues of both adult and weanling rats exposed to 1100 ppm [(13)C(2)]-VC for 5 days or 1100 ppm VC for 1 day. This assay utilizes neutral thermal hydrolysis and an HPLC cleanup prior to quantitation by LC-MS/MS. The number of endogenous and exogenous εG adducts in DNA from tissues of adult rats exposed to [(13)C(2)]-VC for 5 days was 4.1 ± 2.8 adducts/10(8) guanine of endogenous and 19.0 ± 4.9 adducts/10(8) guanine of exogenous εG in the liver, 8.4 ± 2.8 adducts/10(8) guanine of endogenous and 7.4 ± 0.5 adducts/10(8) guanine of exogenous εG in the lung, and 5.9 ± 3.3 adducts/10(8) guanine of endogenous and 5.7 ± 2.1 adducts/10(8) guanine of exogenous εG in the kidney (n = 4). Additionally, the data from weanling rats demonstrated higher numbers of exogenous εG, with ∼4-fold higher amounts in the liver DNA of weanlings (75.9 ± 17.9 adducts/10(8) guanine) in comparison to adult rats and ∼2-fold higher amounts in the lung (15.8 ± 3.6 adducts/10(8) guanine) and kidney (12.9 ± 0.4 adducts/10(8) guanine) (n = 8). The use of stable isotope labeled VC permitted accurate estimates of the half-life of εG for the first time by comparing [(13)C(2)]-εG in adult rats with identically exposed animals euthanized 2, 4, or 8 weeks later. The half-life of εG was found to be 150 days in the liver and lung and 75 days in the kidney, suggesting little or no active repair of this promutagenic adduct.}, number={9}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Mutlu, Esra and Collins, Leonard B. and Stout, Matthew D. and Upton, Patricia B. and Daye, Laura R. and Winsett, Darrell and Hatch, Gary and Evansky, Paul and Swenberg, James A.}, year={2010}, month={Aug}, pages={1485–1491} }
 @article{lu_collins_ru_bermudez_swenberg_2010, title={Distribution of DNA Adducts Caused by Inhaled Formaldehyde Is Consistent with Induction of Nasal Carcinoma but Not Leukemia}, volume={116}, ISSN={1096-6080 1096-0929}, url={http://dx.doi.org/10.1093/toxsci/kfq061}, DOI={10.1093/toxsci/kfq061}, abstractNote={Inhaled formaldehyde is classified as a known human and animal carcinogen, causing nasopharyngeal cancer. Additionally, limited epidemiological evidence for leukemia in humans is available; however, this is inconsistent across studies. Both genotoxicity and cytotoxicity are key events in formaldehyde nasal carcinogenicity in rats, but mechanistic data for leukemia are not well established. Formation of DNA adducts is a key event in initiating carcinogenesis. Formaldehyde can induce DNA monoadducts, DNA-DNA cross-links, and DNA protein cross-links. In this study, highly sensitive liquid chromatography-tandem mass spectrometry-selected reaction monitoringmethods were developed and [(13)CD(2)]-formaldehyde exposures utilized, allowing differentiation of DNA adducts and DNA-DNA cross-links originating from endogenous and inhalation-derived formaldehyde exposure. The results show that exogenous formaldehyde induced N(2)-hydroxymethyl-dG monoadducts and dG-dG cross-links in DNA from rat respiratory nasal mucosa but did not form [(13)CD(2)]-adducts in sites remote to the portal of entry, even when five times more DNA was analyzed. Furthermore, no N(6)-HO(13)CD(2)-dA adducts were detected in nasal DNA. In contrast, high amounts of endogenous formaldehyde dG and dA monoadducts were present in all tissues examined. The number of exogenous N(2)-HO(13)CD(2)-dG in 1- and 5-day nasal DNA samples from rats exposed to 10-ppm [(13)CD(2)]-formaldehyde was 1.28 +/- 0.49 and 2.43 +/- 0.78 adducts/10(7) dG, respectively, while 2.63 +/- 0.73 and 2.84 +/- 1.13 N(2)-HOCH(2)-dG adducts/10(7) dG and 3.95 +/- 0.26 and 3.61 +/- 0.95 N(6)-HOCH(2)-dA endogenous adducts/10(7) dA were present. This study provides strong evidence supporting a genotoxic and cytotoxic mode of action for the carcinogenesis of inhaled formaldehyde in respiratory nasal epithelium but does not support the biological plausibility that inhaled formaldehyde also causes leukemia.}, number={2}, journal={Toxicological Sciences}, publisher={Oxford University Press (OUP)}, author={Lu, Kun and Collins, Leonard B. and Ru, Hongyu and Bermudez, Edilberto and Swenberg, James A.}, year={2010}, month={Feb}, pages={441–451} }
 @article{lu_ye_zhou_collins_chen_gold_ball_swenberg_2010, title={Structural Characterization of Formaldehyde-Induced Cross-Links Between Amino Acids and Deoxynucleosides and Their Oligomers}, volume={132}, ISSN={0002-7863 1520-5126}, url={http://dx.doi.org/10.1021/ja908282f}, DOI={10.1021/ja908282f}, abstractNote={Exposure to formaldehyde results in the formation of DNA-protein cross-links (DPCs) as a primary genotoxic effect. Although DPCs are biologically important and eight amino acids have been reported to form stable adducts with formaldehyde, the structures of these cross-links have not yet been elucidated. We have characterized formaldehyde-induced cross-links of Lys, Cys, His, and Trp with dG, dA, and dC. dT formed no cross-links, nor did Arg, Gln, Tyr, or Asn. Reaction of formaldehyde with Lys and dG gave the highest yield of cross-linked products, followed by reaction with Cys and dG. Yields from the other coupling reactions were lower by a factor of 10 or more. Detailed structural examination by NMR and mass spectrometry established that the cross-links between amino acids and single nucleosides involve a formaldehyde-derived methylene bridge. Lys yielded two additional products with dG in which the linking structure is a 1,N(2)-fused triazino ring. The Lys cross-linked products were unstable at ambient temperature. Reactions between the reactive N(alpha)-Boc-protected amino acids and the trinucleotides d(T(1)B(2)T(3)) where B(2) is the target base G, A, or C and reactions between dG, dA and dC and 8-mer peptides containing a single reactive target residue at position 5 yielded cross-linked products with structures inferred from high resolution mass spectrometry and fragmentation patterns that are consistent with those between N(alpha)-Boc-protected amino acids and single nucleotides rigorously determined by NMR studies. These structures will provide a basis for investigation of the characteristics and properties of DPCs formed in vivo and will be helpful in identifying biomarkers for the evaluation of formaldehyde exposure both at the site of contact and at distant sites.}, number={10}, journal={Journal of the American Chemical Society}, publisher={American Chemical Society (ACS)}, author={Lu, Kun and Ye, Wenjie and Zhou, Li and Collins, Leonard B. and Chen, Xian and Gold, Avram and Ball, Louise M and Swenberg, James A.}, year={2010}, month={Feb}, pages={3388–3399} }
 @article{bordeerat_georgieva_klapper_collins_cross_borchers_swenberg_boysen_2009, title={Accurate quantitation of standard peptides used for quantitative proteomics}, volume={9}, ISSN={1615-9853 1615-9861}, url={http://dx.doi.org/10.1002/pmic.200900043}, DOI={10.1002/pmic.200900043}, abstractNote={MS‐based proteomics has become an indispensable tool in system biology generating a need for accurate and precise quantitation of peptide standards. The presented method utilizes ultra performance LC‐MS/MS (UPLC‐MS/MS) to accurately quantify peptide standards at concentrations of 0.1–10 μM. The ability for accurate quantitation of micro‐molar concentrations has the advantages that quantitation can be performed routinely with high precision and the high sensitivity of the method minimizes the amounts required.}, number={15}, journal={Proteomics}, publisher={Wiley}, author={Bordeerat, Narisa K. and Georgieva, Nadia I. and Klapper, David G. and Collins, Leonard B. and Cross, Tyra J. and Borchers, Christoph H. and Swenberg, James A. and Boysen, Gunnar}, year={2009}, month={Aug}, pages={3939–3944} }
 @article{watters_satia_costa_boysen_collins_morrow_milne_swenberg_2009, title={Comparison of three oxidative stress biomarkers in a sample of healthy adults}, volume={14}, ISSN={1354-750X 1366-5804}, url={http://dx.doi.org/10.3109/13547500903183954}, DOI={10.3109/13547500903183954}, abstractNote={Oxidative stress is a potentially important aetiological factor for many chronic diseases, including cardiovascular disease, neurodegenerative disease and cancer, yet studies often find inconsistent results. The associations between three of the most widely used biomarkers of oxidative stress, i.e. F2-isoprostanes for lipid peroxidation and 8-oxo-7,8-dihydro-2’-deoxyguanosine (8-oxo-dG) and the comet assay with FPG for oxidative DNA damage, were compared in a sample of 135 healthy African-American and white adults. Modest associations were observed between F2-isoprostanes and the comet assay (r = 0.22, p = 0.01), but there were no significant correlations between 8-oxo-dG and the comet assay (r = −0.09) or F2-IsoP (r = −0.04). These results are informative for researchers seeking to compare results pertaining to oxidative stress across studies and/or assessment methods in healthy disease-free populations. The development and use of oxidative stress biomarkers is a promising field; however, additional validation studies are necessary to establish accuracy and comparability across oxidative stress biomarkers.}, number={8}, journal={Biomarkers}, publisher={Informa UK Limited}, author={Watters, Joanne L. and Satia, Jessie A. and Costa, Kerry-Ann da and Boysen, Gunnar and Collins, Leonard B. and Morrow, Jason D. and Milne, Ginger L. and Swenberg, James A.}, year={2009}, month={Dec}, pages={587–595} }
 @article{baskerville-abraham_boysen_troutman_mutlu_collins_dekrafft_lin_king_chaney_swenberg_2009, title={Development of an Ultraperformance Liquid Chromatography/Mass Spectrometry Method To Quantify Cisplatin 1,2 Intrastrand Guanine−Guanine Adducts}, volume={22}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/tx800481j}, DOI={10.1021/tx800481j}, abstractNote={Platinum chemotherapeutic agents have been widely used in the treatment of cancer. Cisplatin was the first of the platinum-based chemotherapeutic agents and therefore has been extensively studied as an antitumor agent since the late 1960s. Because this agent forms several DNA adducts, a highly sensitive and specific quantitative assay is needed to correlate the molecular dose of individual adducts with the effects of treatment. An ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay for quantification of 1,2 guanine-guanine intrastrand cisplatin adducts [CP-d(GpG)], using (15)N(10) CP-d(GpG) as an internal standard, was developed. The internal standard was characterized by MS/MS, and its concentration was validated by inductively coupled plasma mass spectrometry. Samples containing CP-d(GpG) in DNA were purified by enzyme hydrolysis, centrifugal filtration, and HPLC with fraction collection prior to quantification by UPLC-MS/MS in the selective reaction monitoring mode [m/z 412.5-->248.1 for CP-d(GpG); m/z 417.5-->253.1 for [(15)N(10)] CP-d(GpG)]. The recovery of standards was >90%, and quantification was unaffected by increasing concentrations of calf thymus DNA. This method utilizes 25 mug of DNA per injection. The limit of quantification was 3 fmol or 3.7 adducts per 10(8) nucleotides, which approaches the sensitivity of the (32)P postlabeling method for this adduct. These data suggested that this method is suitable for in vitro and in vivo assessment of CP-d(GpG) adducts formed by cisplatin and carboplatin. Subsequently, the method was applied to studies using ovarian carcinoma cell lines and C57/BL6 mice to illustrate that this method is capable of quantifying CP-d(GpG) adducts using biologically relevant systems and doses. The development of biomarkers to determine tissue-specific molecular dosimetry during treatment will lead to a more complete understanding of both therapeutic and adverse effects of cisplatin and carboplatin. This will support the refinement of therapeutic regimes and appropriate individualized treatment protocols.}, number={5}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Baskerville-Abraham, Irene M. and Boysen, Gunnar and Troutman, J. Mitchell and Mutlu, Esra and Collins, Leonard and deKrafft, Kathryn E. and Lin, Wenbin and King, Candice and Chaney, Stephen G. and Swenberg, James A.}, year={2009}, month={Mar}, pages={905–912} }
 @article{kim_collins_boysen_swenberg_gold_ball_bradford_rusyn_2009, title={Liquid chromatography electrospray ionization tandem mass spectrometry analysis method for simultaneous detection of trichloroacetic acid, dichloroacetic acid, S-(1,2-dichlorovinyl)glutathione and S-(1,2-dichlorovinyl)-L-cysteine}, volume={262}, ISSN={0300-483X}, url={http://dx.doi.org/10.1016/j.tox.2009.06.013}, DOI={10.1016/j.tox.2009.06.013}, abstractNote={Trichloroethylene (TCE, CAS 79-01-6) is a widely used industrial chemical, and a common environmental pollutant. TCE is a well-known carcinogen in rodents and is classified as "probably carcinogenic to humans". Several analytical methods have been proposed for detection of TCE metabolites in biological media utilizing derivatization-free techniques; however, none of them is suitable for simultaneous detection of both oxidative metabolites and glutathione conjugates of TCE in small volume biological samples. Here, we report a new combination of methods for assessment of major TCE metabolites: dichloroacetic acid (DCA), trichloroacetic acid (TCA), S-(1,2-dichlorovinyl)-L-cysteine (DCVC), and S-(1,2-dichlorovinyl) glutathione (DCVG). First, DCA and TCA were extracted with ether. Second, the remaining aqueous fraction underwent solid phase extraction for DCVC and DCVG. Then, DCA and TCA were measured by hydrophilic interaction liquid chromatography ion exchange negative electrospray ionization tandem mass spectrometry, while DCVC and DCVG were measured by reverse phase positive electrospray ionization tandem mass spectrometry. This method was applied successfully to measure all 4 TCE metabolites in as little as 50 microl of serum from mice orally exposed to TCE (2100 mg/kg, 2h). Serum concentrations (mean+/-standard deviation) of the TCE metabolites obtained with this method are comparable or equivalent to those previously reported in the literature: DCA, 0.122+/-0.014 nmol/ml (limit of detection: 0.01 nmol/ml); TCA, 256+/-30 nmol/ml (0.4 nmol/ml); DCVG, 0.037+/-0.015 nmol/ml (0.001 nmol/ml); DCVC, 0.0024+/-0.0009 nmol/ml (0.001 nmol/ml). This method opens new opportunities to increase throughput and decrease number of animals required for mechanistic studies on TCE in rodents.}, number={3}, journal={Toxicology}, publisher={Elsevier BV}, author={Kim, Sungkyoon and Collins, Leonard B. and Boysen, Gunnar and Swenberg, James A. and Gold, Avram and Ball, Louise M. and Bradford, Blair U. and Rusyn, Ivan}, year={2009}, month={Aug}, pages={230–238} }
 @article{kim_kim_pollack_collins_rusyn_2009, title={Pharmacokinetic analysis of trichloroethylene metabolism in male B6C3F1 mice: Formation and disposition of trichloroacetic acid, dichloroacetic acid, S-(1,2-dichlorovinyl)glutathione and S-(1,2-dichlorovinyl)-l-cysteine}, volume={238}, ISSN={0041-008X}, url={http://dx.doi.org/10.1016/j.taap.2009.04.019}, DOI={10.1016/j.taap.2009.04.019}, abstractNote={Trichloroethylene (TCE) is a well-known carcinogen in rodents and concerns exist regarding its potential carcinogenicity in humans. Oxidative metabolites of TCE, such as dichloroacetic acid (DCA) and trichloroacetic acid (TCA), are thought to be hepatotoxic and carcinogenic in mice. The reactive products of glutathione conjugation, such as S-(1,2-dichlorovinyl)-L-cysteine (DCVC), and S-(1,2-dichlorovinyl) glutathione (DCVG), are associated with renal toxicity in rats. Recently, we developed a new analytical method for simultaneous assessment of these TCE metabolites in small-volume biological samples. Since important gaps remain in our understanding of the pharmacokinetics of TCE and its metabolites, we studied a time-course of DCA, TCA, DCVG and DCVG formation and elimination after a single oral dose of 2100 mg/kg TCE in male B6C3F1 mice. Based on systemic concentration-time data, we constructed multi-compartment models to explore the kinetic properties of the formation and disposition of TCE metabolites, as well as the source of DCA formation. We conclude that TCE-oxide is the most likely source of DCA. According to the best-fit model, bioavailability of oral TCE was approximately 74%, and the half-life and clearance of each metabolite in the mouse were as follows: DCA: 0.6 h, 0.081 ml/h; TCA: 12 h, 3.80 ml/h; DCVG: 1.4 h, 16.8 ml/h; DCVC: 1.2 h, 176 ml/h. In B6C3F1 mice, oxidative metabolites are formed in much greater quantities (approximately 3600 fold difference) than glutathione-conjugative metabolites. In addition, DCA is produced to a very limited extent relative to TCA, while most of DCVG is converted into DCVC. These pharmacokinetic studies provide insight into the kinetic properties of four key biomarkers of TCE toxicity in the mouse, representing novel information that can be used in risk assessment.}, number={1}, journal={Toxicology and Applied Pharmacology}, publisher={Elsevier BV}, author={Kim, Sungkyoon and Kim, David and Pollack, Gary M. and Collins, Leonard B. and Rusyn, Ivan}, year={2009}, month={Jul}, pages={90–99} }
 @article{esther_jasin_collins_swenberg_boysen_2008, title={A mass spectrometric method to simultaneously measure a biomarker and dilution marker in exhaled breath condensate}, volume={22}, ISSN={0951-4198}, url={http://dx.doi.org/10.1002/rcm.3408}, DOI={10.1002/rcm.3408}, abstractNote={Exhaled breath condensate (EBC) collection is a simple and non-invasive method to sample airway secretions, but analysis is limited by extensive and variable dilution of airway secretions within the condensate. To overcome this limitation, we developed a sensitive and specific liquid chromatography/tandem mass spectrometry (LC/MS/MS) method to simultaneously detect adenyl purines as biomarkers of inflammation and urea as a dilution marker in EBC. Separation prior to mass spectrometry was achieved using a C18 column with methanol and formic acid as the mobile phase, and characteristic precursor to product ion transitions of m/z 268 to 136 (for adenosine), m/z 348 to 136 (for AMP), and m/z 61 to 44 (for urea) were monitored for quantification. To correct for matrix effects, isotopically labeled adenosine, AMP, and urea were used as internal standards. Using these methods, we detected urea and the adenyl purines adenosine and AMP in EBC from seven subjects with cystic fibrosis (CF) and seven healthy controls and found that the AMP/urea ratio was elevated in the CF samples. These results demonstrate that mass spectrometry can be used successfully in EBC analysis to simultaneously detect a biomarker for airway inflammation and control for variable dilution.}, number={5}, journal={Rapid Communications in Mass Spectrometry}, publisher={Wiley}, author={Esther, Charles R., Jr and Jasin, H. Matias and Collins, Leonard B. and Swenberg, James A. and Boysen, Gunnar}, year={2008}, month={Feb}, pages={701–705} }
 @article{lu_boysen_gao_collins_swenberg_2008, title={Formaldehyde-Induced Histone Modifications in Vitro}, volume={21}, ISSN={0893-228X 1520-5010}, url={http://dx.doi.org/10.1021/tx8000576}, DOI={10.1021/tx8000576}, abstractNote={Numerous experiments have demonstrated the genotoxic and mutagenic effects of formaldehyde, including DNA-protein cross-links (DPC). Histone was reported to be involved in the formation of DPC in which the epsilon-amino groups of lysine and exocyclic amino groups of DNA were thought to be cross-linked through multiple step reactions. Using mass spectrometry, the N-terminus of histone and lysine residues located in both the histone N-terminal tail and the globular fold domain were identified as binding sites for formaldehyde in the current study. The observation that only lysine residues without post-translational modification (PTM) can be attacked by formaldehyde indicates that PTM blocks the reaction between lysine and formaldehyde. Additionally, we found that formaldehyde-induced Schiff bases on lysine residues could inhibit the formation of PTM on histone, raising the possibility that formaldehyde might alter epigenetic regulation.}, number={8}, journal={Chemical Research in Toxicology}, publisher={American Chemical Society (ACS)}, author={Lu, Kun and Boysen, Gunnar and Gao, Lina and Collins, Leonard B. and Swenberg, James A.}, year={2008}, month={Jul}, pages={1586–1593} }
 @inproceedings{collins_2005, title={Use of QuEChERS for residue determination in unusual matrices}, author={Collins, L.B.}, year={2005}, month={Apr} }
 @inproceedings{saha_harrison_collins_1998, title={HPLC/UV method for determination of Tepraloxydim major metabolites in soil and sediment}, author={Saha, M. and Harrison, B. and Collins, L.B.}, year={1998}, month={Aug} }
 @article{jones_mickelson_collins_kawagoe_mark wightman_1994, title={Interference by pH and Ca2+ ions during measurements of catecholamine release in slices of rat amygdala with fast-scan cyclic voltammetry}, volume={52}, ISSN={0165-0270}, url={http://dx.doi.org/10.1016/0165-0270(94)90048-5}, DOI={10.1016/0165-0270(94)90048-5}, abstractNote={Fast-scan cyclic voltammetry (FSCV) at carbon-fiber microelectrodes was used to investigate catecholamine release and uptake induced by local electrical stimulation of rat brain slices containing the basolateral amygdaloid nucleus. The amygdala contains less catecholamine than the striatum, and the observed release is proportionately smaller. Stimulus trains of long duration were required to obtain a well-resolved concentration change in the basolateral amygdala. Voltammetric detection of catecholamines under these conditions was complicated by interference from two extracellular ions, H+ and Ca2+. Ion-selective microelectrodes were used in conjunction with carbon-fiber microelectrodes to monitor pH and Ca2+. The magnitude of the pH changes was correlated with stimulation length and followed the pattern of a brief alkaline shift followed by a longer acidic shift. Extracellular Ca2+ concentration decreased during stimulation and returned fairly rapidly to baseline after the stimulation was over. Because it was not possible to account for all of the ionic interferences using information in the voltammograms, other strategies were employed. Exposure of amygdala slices to L-DOPA or DA increased electrically evoked release of catecholamine, but the effect was transient, and uptake rates decreased during continued exposure to these agents. The most successful approach to remove the interferences was to subtract the response obtained after exposure of the slice to the catecholamine depleter, Ro 4-1284. This agent eliminates the catecholamine response but does not appear to alter the ionic changes.}, number={1}, journal={Journal of Neuroscience Methods}, publisher={Elsevier BV}, author={Jones, Sara R. and Mickelson, George E. and Collins, Leonard B. and Kawagoe, Kirk T. and Mark Wightman, R.}, year={1994}, month={Apr}, pages={1–10} }
 @article{garris_collins_jones_wightman_1993, title={Evoked Extracellular Dopamine In Vivo in the Medial Prefrontal Cortex}, volume={61}, ISSN={0022-3042}, url={http://dx.doi.org/10.1111/j.1471-4159.1993.tb02168.x}, DOI={10.1111/j.1471-4159.1993.tb02168.x}, abstractNote={Abstract: The measurement of evoked extracellular dopamine in the medial prefrontal cortex by using fast‐scan cyclic voltammetry with carbon‐fiber microelectrodes was established and release characteristics of mesoprefrontal dopamine neurons were examined in vivo in anesthetized rats. Despite the sparse dopaminergic innervation and the presence of more dense noradrenergic and serotonergic innervations overall in the medial prefrontal cortex, the measurement of extracellular dopamine was achieved by selective recording in dopamine‐rich terminal fields and selective activation of ascending dopamine neurons. This was confirmed by electrochemical, pharmacological, and anatomical evidence. An increased release capacity for mesoprefrontal dopamine neurons was also demonstrated by the slower decay of the evoked dopamine response after inhibition of catecholamine synthesis and the maintenance of the evoked dopamine response at higher levels in the medial prefrontal cortex compared with the striatum during supraphysiological stimulation.}, number={2}, journal={Journal of Neurochemistry}, publisher={Wiley}, author={Garris, Paul A. and Collins, Leonard B. and Jones, Sara R. and Wightman, R. Mark}, year={1993}, month={Aug}, pages={637–647} }