Lloyd and McCullough Lab

Lloyd-McCullough lab Jan 2020
Lloyd, McCullough lab members L to R. Vlad Vartanian, Irina Minko, R. Stephen Lloyd,
Amanda McCullough, Sami Moellmer, Dmitri Rozanov, (January 2020)

Research interests

The goal of our combined laboratories is to translate fundamental basic science discoveries focused on cellular DNA damage response pathways into actionable clinical interventions and improved therapeutic response. We specifically are interested in mechanisms of DNA repair and replication that modulate mutagenesis and subsequent carcinogenesis in response to a variety of both natural and man-made toxicant exposures. In addition, we investigate how alterations in DNA repair and tolerance networks affect the initiation and progression of human carcinogenesis and how these fundamental principles and acquired genetic instabilities can be used to leverage tumor-specific therapeutics.

Dr. Amanda McCullough

Amanda McCullough, PhD
Amanda McCullough, PhD

Dr. McCullough earned her PhD in Cellular and Molecular Biology from the University of Vermont. She completed postdoctoral training in the Division of Hematology & Medical Oncology at Oregon Health & Science University and in the Department of Human Biological Chemistry & Genetics at the University of Texas Medical Branch. She is currently an Associate Professor in the Department of Molecular & Medical Genetics and the Oregon Institute of Occupational Health Sciences. Dr. McCullough serves as the co-Director of the Molecular & Medical Genetics Graduate Program.

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Publication history

Dr. R. Stephen Lloyd

R. Stephen Lloyd, PhD
R. Stephen Lloyd, PhD

R. Stephen Lloyd earned his PhD in molecular biology at the University of Texas, MD Anderson Hospital and Tumor Institute in Houston and carried out postdoctoral training at Stanford University. Following employment with a genetic engineering company, he has been a faculty member at three US medical schools, including Vanderbilt University, University of Texas Medical Branch (UTMB) at Galveston, and Oregon Health & Science University (OHSU). During his career in academia, he has served as the Principal Investigator of a National Institute of Environmental Health Sciences (NIEHS) Center (UTMB), the Director of the Center in Environmental Health & Medicine (UTMB), and the Director of the Center for Research in Occupational and Environmental Toxicology (OHSU). Dr. Lloyd has authored 219 peer-reviewed publications and 27 review articles. His laboratory has been recognized by an American Cancer Society Faculty Research Award, a Faculty Research Award from the Graduate School of Biomedical Sciences, UTMB, and an Outstanding Achievement Award in Research at OHSU.

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Publication history

Lab members

Irina Minko, PhD
Irina Minko, PhD

Irina attended the Moscow State University and the Institute of Biochemistry of Russian Academy of Sciences. In 1999, she joined the Lloyd lab at the University of Texas Medical Branch in Galveston, Texas and continued her research when the lab transitioned to OHSU, Portland.  Irina's work has been developed in the following directions: (i) The biochemical and cellular processing of DNA-protein cross-links; (ii) The role of specialized DNA polymerases in the bypass of DNA lesions;  and (iii) The mutagenic consequences of cellular processing of damaged DNA. Currently, the main focus of Irina's research is on repair of DNA-DNA cross-links.

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Dr. Vladimir Vartanian

Vladimir received a PhD degree in Linguistics from the Institute of Linguistics at the Russian Academy of Sciences in Moscow. His interests focused on the psychological and social aspects of language. He became interested in biological research and joined the lab in 2003. He currently studies the role of oxidative stress and was first to observe the metabolic syndrome in NEIL1 deficient mice. In his free time, Vladimir enjoys creating art with an emphasis on drawing and painting.  Selections of his work are available for purchase through Forever Art.

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Dmitri Rozanov, PhD

Dmitri obtained a classical education in molecular biology, which has been supplemented with his post-doctoral training at the Burnham Institute for Medical Research under the guidance of world-class enzymologists and acknowledged experts in molecular and cellular biology. Dmitri published over 40 papers in prestigious peer reviewed journals including J. Biol. Chem. and he was the first author in 18 of these papers. An example of the effective use of his personal and professional characteristics is the work he performed leading to the formulation of his hypothesis and subsequent proof that the inhibition of the activity of membrane type-1 matrix metalloprotease (MT1-MMP), in the manner in which it was used in the recent clinical trials, cannot be an effective cancer therapy. These results provided the basis for the NIH funded X01, 2006, “Screening chemicals to suppress MT1-MMP synthesis in cancer” for which he was the co-PI. He also discovered that MT1-MMP is a key player in the tumor’s defense regardless of its catalytically active or inert state. These findings were the basis for the funded Susan G. Komen grant, 2006-2008, “Role of MT1-MMP in protection of breast cancer cells against host immune attack” for which the applicant was the co-PI. He was also the PI for NIH screening grant, 2006, “Screening for Chemicals that Potentiate TRAIL-Induced Apoptosis of Cancer Cells” and DoD funded Concept award, 2009, “Reengineering New, Potent, and Safe TRAIL for Breast Cancer Therapy”. In 2012, he joined Dr. Spellman lab in OHSU where he worked on the DoD funded project to identify tumor-specific epitopes expressed on the surface of cancer cells. The studies also resulted in the successful application for CEDAR award. Currently, Dmitri is working on DNA mutagenesis and repair pathways in Dr. McCullough lab in OHSU.

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Samantha Maellmer

Sami graduated from Linfield College in 2019, earning her Bachelor of Science in Biology. She hopes to gain valuable laboratory experience through working at OHSU. She plans to transition that experience to later attend graduate school with a focus on genetics and molecular biology or genetic counseling. During Sami’s time at Linfield she played women’s soccer for 4 years, and also was able to study abroad in New Zealand and Australia. In her free time Sami enjoys traveling, reading books, and listening to podcasts.

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Projects

The research within our laboratories is concentrated in three major areas that have as a central theme, the biochemical mechanisms of DNA repair and replication in response to environmental toxicant exposures.  These systems are directly germane to human cancers, metabolic syndrome, and aging.  First, we are interested in understanding the cellular pathways for the tolerance, mutagenesis, and repair of alkylated, ring-fragmented purines (Fapy-dG adducts), DNA interstrand crosslinks, and DNA-protein crosslinks.  These DNA adducts are formed as a consequence of environmental exposure to reactive aldehydes and as a result of endogenous metabolism.  Second, we are investigating the biochemical mechanisms and therapeutic applications of ultraviolet (UV) light-induced DNA damage-specific glycosylases for the prevention of skin cancer and UV-induced immunosuppression.  Third, we are using biochemical, cellular and animal models to investigate repair of oxidatively-induced DNA damage that is initiated by either NEIL1 or OGG1 DNA glycosylases.  Defects in these pathways contribute to lung and liver cancers and the absence of these enzymes can lead to the development of many of the symptoms of metabolic disease. 

The combination of chronic dietary exposure to the fungal toxin, aflatoxin B1 (AFB1), and hepatitis B viral (HBV) infection is associated with a significant increased risk for early onset hepatocellular carcinomas (HCCs) in millions of people living in East Asia, Central and South America, and sub-Saharan Africa. Even though dietary exposures to aflatoxins constitute the second largest global environmental risk factor for cancer development, there are still significant questions concerning the molecular mechanisms driving carcinogenesis. In-depth knowledge of these mechanisms is critical for the identification of genetic risk factors that affect individual susceptibility for people who are HBV infected and AFB1 exposed. In this regard, since AFB1 carcinogenesis is driven by high frequency G to T transversions, the DNA repair pathways that initiate and complete repair of persistent AFB1-induced DNA adducts and base damage from HBV-induced inflammation have strong biological significance. These pathways define the mutagenic burden in the target tissues and ultimately limit cellular progression to cancer. To address these issues, we have demonstrated that knockout of the DNA base excision repair pathway, initiated by the DNA glycosylase NEIL1, is extremely important in the removal of the highly mutagenic AFB1-Fapy-dG adducts. Thus, our data suggest that deficiencies in NEIL1 could contribute to the initiation of HCCs in humans. To maximize relevance to human health, all known variants of NEIL1 are being characterized from regions of the world where aflatoxin ingestion and HBV infection are prevalent. Overall, these studies have direct human health relevance pertaining to understanding a global environmental health problem by identifying genetic risk factors and biochemical pathways previously not recognized as germane to AFB1-induced carcinogenesis.

  • McCullough, AK and Lloyd, RS. Mechanisms underlying aflatoxin-associated mutagenesis - Implications in carcinogenesis. DNA Repair (Amst). 2019 Mar: 77: 76-86.
  • Minko IG, Christov PP, Li L, Stone MP, McCullough AK, Lloyd RS. Processing of N5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3. DNA Repair (Amst). 2019 Jan;73:49-54
  • Coskun, CE, Jaruga, P, Vartanian, V, Erdem, O, Egner, PA, Groopman, JD, Lloyd, RS, Dizdaroglu, M. Aflatoxin-guanine DNA Adducts and Oxidatively-induced DNA Damage in Aflatoxin-treated Mice in vivo as Measured by Liquid Chromatography-Tandem Mass Spectrometry with Isotope-dilution. Chem. Res. in Toxicol. 2018 Dec. 11
  • Vartanian V, Minko IG, Chawanthayatham S, Egner PA, Lin YC, Earley LF, Makar R, Eng JR, Camp MT, Li L, Stone MP, Lasarev MR, Groopman JD, Croy RG, Essigmann JM, McCullough AK, Lloyd RS. NEIL1 protects against aflatoxin-induced hepatocellular carcinoma in mice. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4207-4212. PMCID: PMC5402411
  • Lin YC, Owen N, Minko IG, Lange SS, Li L, Stone MP, Wood RD,McCullough AK, Lloyd RS. DNA polymerase limits chromosomal damage and promotes cell survival following aflatoxin exposure. Proc Natl Acad Sci, U S A. 2016 Nov 29;113(48):13774-13779. PMCID: PMC5137696

In collaboration with faculty at Vanderbilt University and the University of Minnesota, we are part of a Program Project grant to understand both the fundamental mechanisms underlying the cytotoxic properties of chemotherapeutic drugs that initially damage DNA through alkylation at N7-dG and how these agents, when used in combination with other chemotherapeutic agents, produce here-to-fore uncharacterized complex DNA lesions. The goal is to leverage these discoveries into new therapeutic trial designs that optimize selective toxicities. Our project seeks to understand the biological pathways and consequences of processing these complex DNA damages arising from secondary decomposition products of alkyl-modified N7-dG adducts. These include abasic (AP) sites which can serve as the structural scaffold from which more complex and highly cytotoxic DNA damage can be formed through covalent conjugation with anthracycline-based chemotherapeutic agents such as doxorubicin.

  • Sha Y, Minko IG, Malik CK, Rizzo CJ, Lloyd RS. Error prone replication bypass of the imidazole ring-opened formamidopyrimidine deoxyguanosine adduct. Environ Mol Mutagen 2017; PMCID: PMC5476229 Editors Choice Award
  • Minko IG, Jacobs AC, de Leon AR, Gruppi F, Donley N, Harris TM, Rizzo CJ, McCullough AK, Lloyd RS. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites. Nature Sci Reports 2016; PMCID: PMC4929455
  • Minko IG, Earley LF, Larlee KE, Lin YC, Lloyd RS. Pyrosequencing: applicability for studying DNA damage-induced mutagenesis. Environ Mol Mutagen 2014 PMID: 24962778 PMCID: PMC4197070
  • Vartanian V, Minko IG, Chawanthayatham S, Egner PA, Lin YC, Earley LF, Makar R, Eng JR, Camp MT, Li L, Stone MP, Lasarev MR, Groopman JD, Croy RG, Essigmann JM, McCullough AK, Lloyd RS. NEIL1 protects against aflatoxin-induced hepatocellular carcinoma in mice. Proc Natl Acad Sci, USA 2017 PMCID: PMC5402411
  • In addition, our laboratories have investigated the cellular pathways for the repair of DNA-protein crosslinks that form as a consequence of reactive aldehyde exposure. Exposure to DPC-inducing adducts has been linked with nasopharyngeal cancers and leukemia. We used a comprehensive array of over 300 genes representing all major human DNA damage response pathways to assess cell proliferation following siRNA knockdown and subsequent formaldehyde treatment. Although there were gene-specific differences among the different cell lines, four cellular pathways were determined to mitigate formaldehyde toxicity: homologous recombination, double-strand break repair, ionizing radiation response, and DNA replication. The contributions of the different genetic contexts of the cell lines were examined using exome sequencing and Cancer Cell Line Encyclopedia genomic data. These results provide a foundation for detailed mechanistic analyses of pathway involvement and susceptibilities to environmentally-induced DNA-protein crosslinks.
  • Juarez, E, Chambwe, N, Tang, W, Mitchell, AD, Owen, N, Kumari, A., Monnat, RJ, McCullough, AK. An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity. DNA Repair 2018 Dec; 72:1-9.

The prevalence of human obesity continues to rise, with one-third of all U.S. adults classified as obese, and another one-third overweight. Ramifications of this growing trend are highly correlated with comorbidities in a variety of other major secondary medical conditions including elevated heart disease, stroke, type 2 diabetes, fatty liver disease, chronic inflammation, and certain types of cancer. These medical conditions have enormous financial impacts on healthcare and insurance costs that are associated with the treatment and ongoing care for these individuals. Although this epidemic must be first addressed through education concerning the benefits of exercise, balanced diet, and adequate sleep, there are numerous circumstances in which weight gain is highly anticipated as a result of disease progression or pharmacologic treatment. Treatment of such patient populations represents large financial markets in which prevention of weight gain is a win-win-win situation for the patient, healthcare provider and insurance providers. To meet these challenges, our research has identified a mechanism through which diet- or genetic-induced weight gain can be largely prevented by increasing the DNA repair capacity in mitochondria. We propose to translate our findings into pharmacologically tractable approaches. Our goals are to optimize the structure of drug-like molecules that have been selected for enhanced catalytic activity and increased repair activity in mitochondrial DNA.

  • Komakula SSB, Tumova J, Kumaraswamy D, Burchat N, Vartanian V, Ye H, Dobrzyn A, Lloyd RS, Sampath H. The DNA Repair Protein OGG1 Protects Against Obesity by Altering Mitochondrial Energetics in White Adipose Tissue. Sci Rep. 2018 Oct 5;8(1):14886
  • Vartanian, V, Tumova, J, Dobrzyn, P, Dobrzyn, A, Nakabeppu, Y, Lloyd RS, Sampath, H. 8-oxoguanine DNA glycosylase (OGG1) deficiency elicits coordinated changes in lipid and mitochondrial metabolism in muscle. PLoS ONE 12(7):e0181687 2017 PMCID: PMC5519207
  • Sampath H, Vartanian V, Rollins MR, Sakumi K, Nakabeppu Y, Lloyd RS. 8-Oxoguanine DNA Glycosylase (OGG1) Deficiency Increases Susceptibility to Obesity and Metabolic Dysfunction. PLoS One. 7(12):e51697, 2012. PMID: 23284747 PMCID: 3524114
  • Sampath H, Batra AK, Varatanian V, Carmical JR, Prusak D, King IB, Lowell B, Earley LF, Wood TG, Marks DL, McCullough AK, Lloyd RS. Variable penetrance of metabolic phenotypes and development of high fat diet-induced adiposity in NEIL 1-deficient mice. Am J Physiol Endocrinol Metab 300(4): E724-734, 2011. PMID: 21285402, PMCID: 3074946.
  • Vartanian V, Lowell B, Minko IG, Wood TG, Ceci JD, George S, Ballinger SW, Corless CL, McCullough, AK, Lloyd RS. The metabolic syndrome resulting from a knockout of the NEIL1 DNA glycosylase. Proc Natl Acad Sci U S A. 103(6):1864-9, 2006. PMID: 16446448

Our laboratories also focus on mechanisms of DNA repair of oxidatively-induced DNA damage in which we are using biochemical, cellular and animal models to investigate repair that is initiated by either OGG1 or NEIL1 DNA glycosylases. These enzymes are potentially excellent new targets for therapeutic intervention, To augment these studies and to develop novel drug therapeutic strategies, we have developed fluorescence-based high throughput methodologies to screen for inhibitors of DNA glycosylases and polymerases. These small molecule inhibitors will have the capacity to be used therapeutically in conjunction with standard chemotherapeutic regimens.

  • Minko IG, Jacobs AC, de Leon AR, Gruppi F, Donley N, Harris TM, Rizzo CJ, McCullough AK, Lloyd RS. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites. Nature Sci Reports 2016; PMCID: PMC4929455
  • Yamanaka K, Dorjsuren D, Eoff RL, Egli M, Maloney DJ, Jadhav A, Simeonov A, Lloyd RS. A comprehensive strategy to discover inhibitors of the translesion synthesis DNA polymerase . PLoS One. 2012;7(10): e45032. PMCID: PMC3466269.
  • Jacobs AC, Calkins MJ, Jadhav A, Dorjsuren D, Maloney D, Simeonov A, Jaruga P, Dizdaroglu M, McCullough AK, Lloyd RS. Inhibition of DNA glycosylases via small molecule purine analogs. PLoS One. 2013;8(12): e81667. PMCID: PMC3857224.
  • Donley N, Jaruga P, Coskun E, Dizdaroglu M, McCullough AK, Lloyd RS. Small Molecule Inhibitors of 8-Oxoguanine DNA Glycosylase-1 (OGG1) ACS Chemical Biology 2015 Oct 16;10(10):2334-43 PMCID: PMC4894821.

Our laboratories also focus on mechanisms of DNA repair of oxidatively-induced DNA damage in which we are using biochemical, cellular and animal models to investigate repair that is initiated by either OGG1 or NEIL1 DNA glycosylases. These enzymes are potentially excellent new targets for therapeutic intervention, To augment these studies and to develop novel drug therapeutic strategies, we have developed fluorescence-based high throughput methodologies to screen for inhibitors of DNA glycosylases and polymerases. These small molecule inhibitors will have the capacity to be used therapeutically in conjunction with standard chemotherapeutic regimens.

  • Minko IG, Jacobs AC, de Leon AR, Gruppi F, Donley N, Harris TM, Rizzo CJ, McCullough AK, Lloyd RS. Catalysts of DNA Strand Cleavage at Apurinic/Apyrimidinic Sites. Nature Sci Reports 2016; PMCID: PMC4929455
  • Yamanaka K, Dorjsuren D, Eoff RL, Egli M, Maloney DJ, Jadhav A, Simeonov A, Lloyd RS. A comprehensive strategy to discover inhibitors of the translesion synthesis DNA polymerase . PLoS One. 2012;7(10): e45032. PMCID: PMC3466269.
  • Jacobs AC, Calkins MJ, Jadhav A, Dorjsuren D, Maloney D, Simeonov A, Jaruga P, Dizdaroglu M, McCullough AK, Lloyd RS. Inhibition of DNA glycosylases via small molecule purine analogs. PLoS One. 2013;8(12): e81667. PMCID: PMC3857224.
  • Donley N, Jaruga P, Coskun E, Dizdaroglu M, McCullough AK, Lloyd RS. Small Molecule Inhibitors of 8-Oxoguanine DNA Glycosylase-1 (OGG1) ACS Chemical Biology 2015 Oct 16;10(10):2334-43 PMCID: PMC4894821.