Caroline Thorn

All Publications

• PharmGKB summary: disulfiram pathway. Pharmacogenetics and genomics Gonzalez-Suarez, A. D., Thorn, C. F., Whirl-Carrillo, M., Klein, T. E. 2023

  View details for DOI 10.1097/FPC.0000000000000509

  View details for PubMedID 37728645

• An evidence-based framework for evaluating pharmacogenomics knowledge for personalized medicine. Clinical pharmacology and therapeutics Whirl-Carrillo, M., Huddart, R., Gong, L., Sangkuhl, K., Thorn, C. F., Whaley, R., Klein, T. E. 2021

  Abstract

  Clinical annotations are one of the most popular resources available on the Pharmacogenomics Knowledgebase (PharmGKB). Each clinical annotation summarizes the association between variant-drug pairs, shows relevant findings from the curated literature and is assigned a level of evidence (LOE) to indicate the strength of support for that association. Evidence from the pharmacogenomic literature is curated into PharmGKB as variant annotations, which can be used to create new clinical annotations or added to existing clinical annotations. This means that the same clinical annotation can be worked on by multiple curators over time. As more evidence is curated into PharmGKB, the task of maintaining consistency when assessing all the available evidence and assigning a level of evidence becomes increasingly difficult. To remedy this, a scoring system has been developed to automate LOE assignment to clinical annotations. Variant annotations are scored according to certain attributes including study size, reported p-value and whether the variant annotation supports or fails to find an association. Clinical guidelines or FDA-approved drug labels which give variant-specific prescribing guidance are also scored. The scores of all annotations attached to a clinical annotation are summed together to give a total score for the clinical annotation, which is used to calculate a LOE. Overall, the system increases transparency, consistency and reproducibility in LOE assignment to clinical annotations. In combination with increased standardization of how clinical annotations are written, use of this scoring system helps to ensure that PharmGKB clinical annotations continue to be a robust source of pharmacogenomic information.

  View details for DOI 10.1002/cpt.2350

  View details for PubMedID 34216021

• Response to: Unveiling the guidance heterogeneity for genome-informed drug treatment interventions among regulatory bodies and research consortia. Pharmacological research Huddart, R. n., Li, G. n., Sangkuhl, K. n., Thorn, C. F., Whirl-Carrillo, M. n., Caudle, K. E., Relling, M. V., Klein, T. E. 2020: 104838

  View details for DOI 10.1016/j.phrs.2020.104838

  View details for PubMedID 32407955

• Essential Characteristics of Pharmacogenomics Study Publications CLINICAL PHARMACOLOGY & THERAPEUTICS Thorn, C. F., Whirl-Carrillo, M., Hachad, H., Johnson, J. A., McDonagh, E. M., Ratain, M. J., Relling, M. V., Scott, S. A., Altman, R. B., Klein, T. E. 2019; 105 (1): 86–91

  View details for DOI 10.1002/cpt.1279

  View details for Web of Science ID 000454618200017

• Essential characteristics of pharmacogenomics study publications. Clinical pharmacology and therapeutics Thorn, C. F., Whirl-Carrillo, M., Hachad, H., Johnson, J. A., McDonagh, E. M., Ratain, M. J., Relling, M. V., Scott, S. A., Altman, R. B., Klein, T. E. 2018

  Abstract

  Pharmacogenomics (PGx) can be seen as a model for biomedical studies: it includes all disease areas of interest, spans in vitro studies to clinical trials, while focusing on the relationships between genes and drugs and the resulting phenotypes. This review will examine different characteristics of PGx study publications and provide examples of excellence in framing PGx questions and reporting their resulting data in a way that maximizes the knowledge that can be built upon them. This article is protected by copyright. All rights reserved.

  View details for PubMedID 30406943

• PharmGKB summary: clozapine pathway, pharmacokinetics PHARMACOGENETICS AND GENOMICS Thorn, C. F., Mueller, D. J., Altman, R. B., Klein, T. E. 2018; 28 (9): 214–22

  View details for PubMedID 30134346

• PharmGKB summary: pazopanib pathway, pharmacokinetics PHARMACOGENETICS AND GENOMICS Thorn, C. F., Sharma, M. R., Altman, R. B., Klein, T. E. 2017; 27 (8): 307–12

  View details for PubMedID 28678138

  View details for PubMedCentralID PMC5862561

• PharmGKB summary: isoniazid pathway, pharmacokinetics. Pharmacogenetics and genomics Klein, D. J., Boukouvala, S., McDonagh, E. M., Shuldiner, S. R., Laurieri, N., Thorn, C. F., Altman, R. B., Klein, T. E. 2016; 26 (9): 436-444

  View details for DOI 10.1097/FPC.0000000000000232

  View details for PubMedID 27232112

  View details for PubMedCentralID PMC4970941

• PharmGKB summary: pathways of acetaminophen metabolism at the therapeutic versus toxic doses PHARMACOGENETICS AND GENOMICS Mazaleuskaya, L. L., Sangkuhl, K., Thorn, C. F., FitzGerald, G. A., Altman, R. B., Klein, T. E. 2015; 25 (8): 416-426

  View details for DOI 10.1097/FPC.0000000000000150

  View details for Web of Science ID 000357993500007

  View details for PubMedCentralID PMC4498995

• PharmGKB summary: ibuprofen pathways PHARMACOGENETICS AND GENOMICS Mazaleuskaya, L. L., Theken, K. N., Gong, L., Thorn, C. F., FitzGerald, G. A., Altman, R. B., Klein, T. E. 2015; 25 (2): 96-106

  View details for DOI 10.1097/FPC.0000000000000113

  View details for Web of Science ID 000347393200006

  View details for PubMedID 25502615

  View details for PubMedCentralID PMC4355401

• PharmGKB summary: gemcitabine pathway PHARMACOGENETICS AND GENOMICS Alvarellos, M. L., Lamba, J., Sangkuhl, K., Thorn, C. F., Wang, L., Klein, D. J., Altman, R. B., Klein, T. E. 2014; 24 (11): 564-574

  View details for DOI 10.1097/FPC.0000000000000086

  View details for Web of Science ID 000343666300003

  View details for PubMedCentralID PMC4189987

• PharmGKB summary: uric acid-lowering drugs pathway, pharmacodynamics. Pharmacogenetics and genomics McDonagh, E. M., Thorn, C. F., Callaghan, J. T., Altman, R. B., Klein, T. E. 2014; 24 (9): 464-476

  View details for DOI 10.1097/FPC.0000000000000058

  View details for PubMedID 24915143

• PharmGKB summary: ifosfamide pathways, pharmacokinetics and pharmacodynamics. Pharmacogenetics and genomics Lowenberg, D., Thorn, C. F., Desta, Z., Flockhart, D. A., Altman, R. B., Klein, T. E. 2014; 24 (2): 133-138

  View details for DOI 10.1097/FPC.0000000000000019

  View details for PubMedID 24401834

• Incorporation of Pharmacogenomics into Routine Clinical Practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline Development Process. Current drug metabolism Caudle, K. E., Klein, T. E., Hoffman, J. M., Muller, D. J., Whirl-Carrillo, M., Gong, L., McDonagh, E. M., Sangkuhl, K., Thorn, C. F., Schwab, M., Agundez, J. A., Freimuth, R. R., Huser, V., Lee, M. T., Iwuchukwu, O. F., Crews, K. R., Scott, S. A., Wadelius, M., Swen, J. J., Tyndale, R. F., Stein, C. M., Roden, D., Relling, M. V., Williams, M. S., Johnson, S. G. 2014; 15 (2): 209-217

  Abstract

  The Clinical Pharmacogenetics Implementation Consortium (CPIC) publishes genotype-based drug guidelines to help clinicians understand how available genetic test results could be used to optimize drug therapy. CPIC has focused initially on well-known examples of pharmacogenomic associations that have been implemented in selected clinical settings, publishing nine to date. Each CPIC guideline adheres to a standardized format and includes a standard system for grading levels of evidence linking genotypes to phenotypes and assigning a level of strength to each prescribing recommendation. CPIC guidelines contain the necessary information to help clinicians translate patient-specific diplotypes for each gene into clinical phenotypes or drug dosing groups. This paper reviews the development process of the CPIC guidelines and compares this process to the Institute of Medicine's Standards for Developing Trustworthy Clinical Practice Guidelines.

  View details for PubMedID 24479687

• Clinical Pharmacogenetics Implementation Consortium Guidelines for Dihydropyrimidine Dehydrogenase Genotype and Fluoropyrimidine Dosing CLINICAL PHARMACOLOGY & THERAPEUTICS Caudle, K. E., Thorn, C. F., Klein, T. E., Swen, J. J., McLeod, H. L., Diasio, R. B., Schwab, M. 2013; 94 (6): 640-645

  Abstract

  The fluoropyrimidines are the mainstay chemotherapeutic agents for the treatment of many types of cancers. Detoxifying metabolism of fluoropyrimidines requires dihydropyrimidine dehydrogenase (DPD, encoded by the DPYD gene), and reduced or absent activity of this enzyme can result in severe, and sometimes fatal, toxicity. We summarize evidence from the published literature supporting this association and provide dosing recommendations for fluoropyrimidines based on DPYD genotype (updates at http://www.pharmgkb.org).

  View details for DOI 10.1038/clpt.2013.172

  View details for Web of Science ID 000327168400020

  View details for PubMedID 23988873

  View details for PubMedCentralID PMC3831181

• PharmGKB summary: tamoxifen pathway, pharmacokinetics. Pharmacogenetics and genomics Klein, D. J., Thorn, C. F., Desta, Z., Flockhart, D. A., Altman, R. B., Klein, T. E. 2013; 23 (11): 643-647

  View details for DOI 10.1097/FPC.0b013e3283656bc1

  View details for PubMedID 23962908

• PharmGKB summary: diuretics pathway, pharmacodynamics PHARMACOGENETICS AND GENOMICS Thorn, C. F., Ellison, D. H., Turner, S. T., Altman, R. B., Klein, T. E. 2013; 23 (8): 449-453

  View details for DOI 10.1097/FPC.0b013e3283636822

  View details for Web of Science ID 000323226500009

  View details for PubMedID 23788015

• Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6 and CYP2C19 Genotypes and Dosing of Tricyclic Antidepressants CLINICAL PHARMACOLOGY & THERAPEUTICS Hicks, J. K., Swen, J. J., Thorn, C. F., Sangkuhl, K., Kharasch, E. D., Ellingrod, V. L., Skaar, T. C., Mueller, D. J., Gaedigk, A., Stingl, J. C. 2013; 93 (5): 402-408

  Abstract

  Polymorphisms in CYP2D6 and CYP2C19 affect the efficacy and safety of tricyclics, with some drugs being affected by CYP2D6 only, and others by both polymorphic enzymes. Amitriptyline, clomipramine, doxepin, imipramine, and trimipramine are demethylated by CYP2C19 to pharmacologically active metabolites. These drugs and their metabolites, along with desipramine and nortriptyline, undergo hydroxylation by CYP2D6 to less active metabolites. Evidence from published literature is presented for CYP2D6 and CYP2C19 genotype-directed dosing of tricyclic antidepressants.

  View details for DOI 10.1038/clpt.2013.2

  View details for Web of Science ID 000317834800021

  View details for PubMedID 23486447

  View details for PubMedCentralID PMC3689226

• Valproic acid pathway: pharmacokinetics and pharmacodynamics PHARMACOGENETICS AND GENOMICS Ghodke-Puranik, Y., Thorn, C. F., Lamba, J. K., Leeder, J. S., Song, W., Birnbaum, A. K., Altman, R. B., Klein, T. E. 2013; 23 (4): 236-241

  View details for DOI 10.1097/FPC.0b013e32835ea0b2

  View details for Web of Science ID 000316109700008

  View details for PubMedID 23407051

• Clinical Pharmacogenetics Implementation Consortium Guidelines for Human Leukocyte Antigen-B Genotype and Allopurinol Dosing CLINICAL PHARMACOLOGY & THERAPEUTICS Hershfield, M. S., Callaghan, J. T., Tassaneeyakul, W., Mushiroda, T., Thorn, C. F., Klein, T. E., Lee, M. T. 2013; 93 (2): 153-158

  Abstract

  Allopurinol is the most commonly used drug for the treatment of hyperuricemia and gout. However, allopurinol is also one of the most common causes of severe cutaneous adverse reactions (SCARs), which include drug hypersensitivity syndrome, Stevens–Johnson syndrome, and toxic epidermal necrolysis. A variant allele of the human leukocyte antigen (HLA)-B, HLA-B*58:01, associates strongly with allopurinolinduced SCAR. We have summarized the evidence from the published literature and developed peer-reviewed guidelines for allopurinol use based on HLA-B genotype.

  View details for DOI 10.1038/clpt.2012.209

  View details for Web of Science ID 000314139100016

  View details for PubMedID 23232549

  View details for PubMedCentralID PMC3564416

• PharmGKB: the Pharmacogenomics Knowledge Base. Methods in molecular biology (Clifton, N.J.) Thorn, C. F., Klein, T. E., Altman, R. B. 2013; 1015: 311-320

  Abstract

  The Pharmacogenomics Knowledge Base, PharmGKB, is an interactive tool for researchers investigating how genetic variation affects drug response. The PharmGKB Web site, http://www.pharmgkb.org , displays genotype, molecular, and clinical knowledge integrated into pathway representations and Very Important Pharmacogene (VIP) summaries with links to additional external resources. Users can search and browse the knowledgebase by genes, variants, drugs, diseases, and pathways. Registration is free to the entire research community, but subject to agreement to use for research purposes only and not to redistribute. Registered users can access and download data to aid in the design of future pharmacogenetics and pharmacogenomics studies.

  View details for DOI 10.1007/978-1-62703-435-7_20

  View details for PubMedID 23824865

• Pharmacogenomics Knowledge for Personalized Medicine CLINICAL PHARMACOLOGY & THERAPEUTICS Whirl-Carrillo, M., MCDONAGH, E. M., Hebert, J. M., Gong, L., Sangkuhl, K., Thorn, C. F., Altman, R. B., Klein, T. E. 2012; 92 (4): 414-417

  Abstract

  The Pharmacogenomics Knowledgebase (PharmGKB) is a resource that collects, curates, and disseminates information about the impact of human genetic variation on drug responses. It provides clinically relevant information, including dosing guidelines, annotated drug labels, and potentially actionable gene-drug associations and genotype-phenotype relationships. Curators assign levels of evidence to variant-drug associations using well-defined criteria based on careful literature review. Thus, PharmGKB is a useful source of high-quality information supporting personalized medicine-implementation projects.

  View details for DOI 10.1038/clpt.2012.96

  View details for Web of Science ID 000309017000009

  View details for PubMedID 22992668

  View details for PubMedCentralID PMC3660037

• PharmGKB summary: very important pharmacogene information for GSTT1 PHARMACOGENETICS AND GENOMICS Thorn, C. F., Ji, Y., Weinshilboum, R. M., Altman, R. B., Klein, T. E. 2012; 22 (8): 646-651

  View details for DOI 10.1097/FPC.0b013e3283527c02

  View details for Web of Science ID 000306483500009

  View details for PubMedID 22643671

  View details for PubMedCentralID PMC3395771

• PharmGKB summary: phenytoin pathway PHARMACOGENETICS AND GENOMICS Thorn, C. F., Whirl-Carrillo, M., Leeder, J. S., Klein, T. E., Altman, R. B. 2012; 22 (6): 466-470

  View details for DOI 10.1097/FPC.0b013e32834aeedb

  View details for Web of Science ID 000303769700007

  View details for PubMedID 22569204

  View details for PubMedCentralID PMC3349446

• PharmGKB summary: caffeine pathway PHARMACOGENETICS AND GENOMICS Thorn, C. F., Aklillu, E., McDonagh, E. M., Klein, T. E., Altman, R. B. 2012; 22 (5): 389-395

  View details for DOI 10.1097/FPC.0b013e3283505d5e

  View details for Web of Science ID 000302783800008

  View details for PubMedID 22293536

  View details for PubMedCentralID PMC3381939

• Using ODIN for a PharmGKB revalidation experiment DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION Rinaldi, F., Clematide, S., Garten, Y., Whirl-Carrillo, M., Gong, L., Hebert, J. M., Sangkuhl, K., Thorn, C. F., Klein, T. E., Altman, R. B. 2012

  Abstract

  The need for efficient text-mining tools that support curation of the biomedical literature is ever increasing. In this article, we describe an experiment aimed at verifying whether a text-mining tool capable of extracting meaningful relationships among domain entities can be successfully integrated into the curation workflow of a major biological database. We evaluate in particular (i) the usability of the system's interface, as perceived by users, and (ii) the correlation of the ranking of interactions, as provided by the text-mining system, with the choices of the curators.

  View details for DOI 10.1093/database/bas021

  View details for Web of Science ID 000304924100001

  View details for PubMedID 22529178

  View details for PubMedCentralID PMC3332569

• Celecoxib pathways: pharmacokinetics and pharmacodynamics PHARMACOGENETICS AND GENOMICS Gong, L., Thorn, C. F., Bertagnolli, M. M., Grosser, T., Altman, R. B., Klein, T. E. 2012; 22 (4): 310-318

  View details for DOI 10.1097/FPC.0b013e32834f94cb

  View details for Web of Science ID 000301537400010

  View details for PubMedID 22336956

  View details for PubMedCentralID PMC3303994

• PharmGKB summary: very important pharmacogene information for G6PD PHARMACOGENETICS AND GENOMICS McDonagh, E. M., Thorn, C. F., Bautista, J. M., Youngster, I., Altman, R. B., Klein, T. E. 2012; 22 (3): 219-228

  View details for DOI 10.1097/FPC.0b013e32834eb313

  View details for Web of Science ID 000300409800008

  View details for PubMedID 22237549

  View details for PubMedCentralID PMC3382019

• PharmGKB summary: very important pharmacogene information for cytochrome P450, family 2, subfamily C, polypeptide 19 PHARMACOGENETICS AND GENOMICS Scott, S. A., Sangkuhl, K., Shuldiner, A. R., Hulot, J., Thorn, C. F., Altman, R. B., Klein, T. E. 2012; 22 (2): 159-165

  View details for DOI 10.1097/FPC.0b013e32834d4962

  View details for Web of Science ID 000299310600008

  View details for PubMedID 22027650

  View details for PubMedCentralID PMC3349992

• PharmGKB summary: very important pharmacogene information for CYP1A2 PHARMACOGENETICS AND GENOMICS Thorn, C. F., Aklillu, E., Klein, T. E., Altman, R. B. 2012; 22 (1): 73-77

  View details for DOI 10.1097/FPC.0b013e32834c6efd

  View details for Web of Science ID 000298249500009

  View details for PubMedID 21989077

  View details for PubMedCentralID PMC3346273

• PharmGKB summary: carbamazepine pathway PHARMACOGENETICS AND GENOMICS Thorn, C. F., Leckband, S. G., Kelsoe, J., Leeder, J. S., Mueller, D. J., Klein, T. E., Altman, R. B. 2011; 21 (12): 906-910

  View details for DOI 10.1097/FPC.0b013e328348c6f2

  View details for Web of Science ID 000296799900016

  View details for PubMedID 21738081

  View details for PubMedCentralID PMC3349991

• PharmGKB summary: methotrexate pathway PHARMACOGENETICS AND GENOMICS Mikkelsen, T. S., Thorn, C. F., Yang, J. J., Ulrich, C. M., French, D., Zaza, G., Dunnenberger, H. M., Marsh, S., McLeod, H. L., Giacomini, K., Becker, M. L., Gaedigk, R., Leeder, J. S., Kager, L., Relling, M. V., Evans, W., Klein, T. E., Altman, R. B. 2011; 21 (10): 679-686

  View details for DOI 10.1097/FPC.0b013e328343dd93

  View details for Web of Science ID 000294808900008

  View details for PubMedID 21317831

  View details for PubMedCentralID PMC3139712

• Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence PLOS GENETICS Dewey, F. E., Chen, R., Cordero, S. P., Ormond, K. E., Caleshu, C., Karczewski, K. J., Whirl-Carrillo, M., Wheeler, M. T., Dudley, J. T., Byrnes, J. K., Cornejo, O. E., Knowles, J. W., Woon, M., Sangkuhl, K., Gong, L., Thorn, C. F., Hebert, J. M., Capriotti, E., David, S. P., Pavlovic, A., West, A., Thakuria, J. V., Ball, M. P., Zaranek, A. W., Rehm, H. L., Church, G. M., West, J. S., Bustamante, C. D., Snyder, M., Altman, R. B., Klein, T. E., Butte, A. J., Ashley, E. A. 2011; 7 (9)

  Abstract

  Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

  View details for DOI 10.1371/journal.pgen.1002280

  View details for PubMedID 21935354

• PharmGKB summary: very important pharmacogene information for PTGS2 PHARMACOGENETICS AND GENOMICS Thorn, C. F., Grosser, T., Klein, T. E., Altman, R. B. 2011; 21 (9): 607-613

  View details for DOI 10.1097/FPC.0b013e3283415515

  View details for Web of Science ID 000293731200012

  View details for PubMedID 21063235

  View details for PubMedCentralID PMC3141084

• Doxorubicin pathways: pharmacodynamics and adverse effects PHARMACOGENETICS AND GENOMICS Thorn, C. F., Oshiro, C., Marsh, S., Hernandez-Boussard, T., McLeod, H., Klein, T. E., Altman, R. B. 2011; 21 (7): 440-446

  View details for DOI 10.1097/FPC.0b013e32833ffb56

  View details for Web of Science ID 000291633300011

  View details for PubMedID 21048526

  View details for PubMedCentralID PMC3116111

• PharmGKB summary: fluoropyrimidine pathways PHARMACOGENETICS AND GENOMICS Thorn, C. F., Marsh, S., Carrillo, M. W., McLeod, H. L., Klein, T. E., Altman, R. B. 2011; 21 (4): 237-242

  View details for DOI 10.1097/FPC.0b013e32833c6107

  View details for Web of Science ID 000288444500010

  View details for PubMedID 20601926

  View details for PubMedCentralID PMC3098754

• KCNH2 pharmacogenomics summary PHARMACOGENETICS AND GENOMICS Oshiro, C., Thorn, C. F., Roden, D. M., Klein, T. E., Altman, R. B. 2010; 20 (12): 775-777

  View details for DOI 10.1097/FPC.0b013e3283349e9c

  View details for Web of Science ID 000284148300006

  View details for PubMedID 20150828

  View details for PubMedCentralID PMC3086352

• Thiopurine pathway PHARMACOGENETICS AND GENOMICS Zaza, G., Cheok, M., Krynetskaia, N., Thorn, C., Stocco, G., Hebert, J. M., McLeod, H., Weinshilboum, R. M., Relling, M. V., Evans, W. E., Klein, T. E., Altman, R. B. 2010; 20 (9): 573-574

  View details for DOI 10.1097/FPC.0b013e328334338f

  View details for Web of Science ID 000281295500008

  View details for PubMedID 19952870

  View details for PubMedCentralID PMC3098750

• PharmGKB summary: very important pharmacogene information for CYP2B6 PHARMACOGENETICS AND GENOMICS Thorn, C. F., Lamba, J. K., Lamba, V., Klein, T. E., Altman, R. B. 2010; 20 (8): 520-523

  View details for DOI 10.1097/FPC.0b013e32833947c2

  View details for Web of Science ID 000279865400007

  View details for PubMedID 20648701

  View details for PubMedCentralID PMC3086041

• Clinical assessment incorporating a personal genome LANCET Ashley, E. A., Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., Dudley, J. T., Ormond, K. E., Pavlovic, A., Morgan, A. A., Pushkarev, D., Neff, N. F., Hudgins, L., Gong, L., Hodges, L. M., Berlin, D. S., Thorn, C. F., Sangkuhl, K., Hebert, J. M., Woon, M., Sagreiya, H., Whaley, R., Knowles, J. W., Chou, M. F., Thakuria, J. V., Rosenbaum, A. M., Zaranek, A. W., Church, G. M., Greely, H. T., Quake, S. R., Altman, R. B. 2010; 375 (9725): 1525-1535

  Abstract

  The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context.We assessed a patient with a family history of vascular disease and early sudden death. Clinical assessment included analysis of this patient's full genome sequence, risk prediction for coronary artery disease, screening for causes of sudden cardiac death, and genetic counselling. Genetic analysis included the development of novel methods for the integration of whole genome and clinical risk. Disease and risk analysis focused on prediction of genetic risk of variants associated with mendelian disease, recognised drug responses, and pathogenicity for novel variants. We queried disease-specific mutation databases and pharmacogenomics databases to identify genes and mutations with known associations with disease and drug response. We estimated post-test probabilities of disease by applying likelihood ratios derived from integration of multiple common variants to age-appropriate and sex-appropriate pre-test probabilities. We also accounted for gene-environment interactions and conditionally dependent risks.Analysis of 2.6 million single nucleotide polymorphisms and 752 copy number variations showed increased genetic risk for myocardial infarction, type 2 diabetes, and some cancers. We discovered rare variants in three genes that are clinically associated with sudden cardiac death-TMEM43, DSP, and MYBPC3. A variant in LPA was consistent with a family history of coronary artery disease. The patient had a heterozygous null mutation in CYP2C19 suggesting probable clopidogrel resistance, several variants associated with a positive response to lipid-lowering therapy, and variants in CYP4F2 and VKORC1 that suggest he might have a low initial dosing requirement for warfarin. Many variants of uncertain importance were reported.Although challenges remain, our results suggest that whole-genome sequencing can yield useful and clinically relevant information for individual patients.National Institute of General Medical Sciences; National Heart, Lung And Blood Institute; National Human Genome Research Institute; Howard Hughes Medical Institute; National Library of Medicine, Lucile Packard Foundation for Children's Health; Hewlett Packard Foundation; Breetwor Family Foundation.

  View details for Web of Science ID 000277655100025

  View details for PubMedID 20435227

• Pharmacogenomics and bioinformatics: PharmGKB PHARMACOGENOMICS Thorn, C. F., Klein, T. E., Altman, R. B. 2010; 11 (4): 501-505

  Abstract

  The NIH initiated the PharmGKB in April 2000. The primary mission was to create a repository of primary data, tools to track associations between genes and drugs, and to catalog the location and frequency of genetic variations known to impact drug response. Over the past 10 years, new technologies have shifted research from candidate gene pharmacogenetics to phenotype-based pharmacogenomics with a consequent explosion of data. PharmGKB has refocused on curating knowledge rather than housing primary genotype and phenotype data, and now, captures more complex relationships between genes, variants, drugs, diseases and pathways. Going forward, the challenges are to provide the tools and knowledge to plan and interpret genome-wide pharmacogenomics studies, predict gene-drug relationships based on shared mechanisms and support data-sharing consortia investigating clinical applications of pharmacogenomics.

  View details for DOI 10.2217/PGS.10.15

  View details for Web of Science ID 000276769300008

  View details for PubMedID 20350130

  View details for PubMedCentralID PMC3098752

• PharmGKB summary: very important pharmacogene information for angiotensin-converting enzyme PHARMACOGENETICS AND GENOMICS Thorn, C. F., Klein, T. E., Altman, R. B. 2010; 20 (2): 143-146

  View details for DOI 10.1097/FPC.0b013e3283339bf3

  View details for Web of Science ID 000274306700011

  View details for PubMedID 19898265

  View details for PubMedCentralID PMC3098760

• Codeine and morphine pathway PHARMACOGENETICS AND GENOMICS Thorn, C. F., Klein, T. E., Altman, R. B. 2009; 19 (7): 556-558

  View details for DOI 10.1097/FPC.01b013e32832e0eac

  View details for Web of Science ID 000267619000009

  View details for PubMedID 19512957

• Etoposide pathway PHARMACOGENETICS AND GENOMICS Yang, J., Bogni, A., Schuetz, E. G., Ratain, M., Dolan, M. E., McLeod, H., Gong, L., Thorn, C., Relling, M. V., Klein, T. E., Altman, R. B. 2009; 19 (7): 552-553

  View details for DOI 10.1097/FPC.0b013e32832e0e7f

  View details for Web of Science ID 000267619000007

  View details for PubMedID 19512958

• Dosing algorithms to predict warfarin maintenance dose in Caucasians and African Americans CLINICAL PHARMACOLOGY & THERAPEUTICS Schelleman, H., Chen, J., Chen, Z., Christie, J., Newcomb, C. W., Brensinger, C. M., Price, M., Whitehead, A. S., Kealey, C., Thorn, C. F., Samaha, F. F., Kimmel, S. E. 2008; 84 (3): 332-339

  Abstract

  The objective of this study was to determine whether warfarin dosing algorithms developed for Caucasians and African Americans on the basis of clinical, environmental, and genetic factors will perform better than an empirical starting dose of 5 mg/day. From April 2002 through December 2005, 259 subjects (Caucasians and African Americans) who started using warfarin were prospectively followed until they reached maintenance dose. The Caucasian algorithm included 11 variables (R(2) = 0.43). This model (which predicted 51% of the doses to within 1 mg of the observed dose) performed better than 5 mg/day (which predicted 29% of the doses to within 5 +/- 1 mg). The African-American algorithm included 10 variables (R(2) = 0.28). This model predicted 37% of the doses to within 1 mg of the observed dose, representing a small improvement compared with 5 mg/day (which predicted 34% of the doses to within 1 mg of 5 mg/day). These results were similar to the results we obtained from testing other published algorithms. The dosing algorithms explained <45% of the observed variability in Caucasians, and the algorithms performed only marginally better for African Americans when compared with giving 5 mg empirically.

  View details for DOI 10.1038/clpt.2008.101

  View details for Web of Science ID 000258582700012

  View details for PubMedID 18596683

  View details for PubMedCentralID PMC2538606

• An XML-based interchange format for genotype-phenotype data HUMAN MUTATION Whirl-Carrillo, M., Woon, M., Thorn, C. E., Klein, T. E., Altman, R. B. 2008; 29 (2): 212-219

  Abstract

  Recent advances in high-throughput genotyping and phenotyping have accelerated the creation of pharmacogenomic data. Consequently, the community requires standard formats to exchange large amounts of diverse information. To facilitate the transfer of pharmacogenomics data between databases and analysis packages, we have created a standard XML (eXtensible Markup Language) schema that describes both genotype and phenotype data as well as associated metadata. The schema accommodates information regarding genes, drugs, diseases, experimental methods, genomic/RNA/protein sequences, subjects, subject groups, and literature. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB; www.pharmgkb.org) has used this XML schema for more than 5 years to accept and process submissions containing more than 1,814,139 SNPs on 20,797 subjects using 8,975 assays. Although developed in the context of pharmacogenomics, the schema is of general utility for exchange of genotype and phenotype data. We have written syntactic and semantic validators to check documents using this format. The schema and code for validation is available to the community at http://www.pharmgkb.org/schema/index.html (last accessed: 8 October 2007).

  View details for DOI 10.1002/humu.20662

  View details for Web of Science ID 000253033000002

  View details for PubMedID 17994540

• Apolipoprotein E genotype and warfarin dosing among Caucasians and African Americans PHARMACOGENOMICS JOURNAL Kimmel, S. E., Christie, J., Kealey, C., Chen, Z., Price, M., Thorn, C. F., Brensinger, C. M., Newcomb, C. W., Whitehead, A. S. 2008; 8 (1): 53-60

  Abstract

  Warfarin sodium is a vitamin K antagonist that is plagued by large variability in patient response, including higher dose requirements among African Americans. Polymorphisms in the gene encoding apolipoprotein E (APOE) may partly explain this variability by altering transport of vitamin K to the liver. In a prospective cohort study of 232 individuals (52.2% Caucasian and 47.8% African American) initiating warfarin therapy, the weekly maintenance dose was significantly higher for African Americans than for Caucasians (mean 42.9 versus mean 36.9 mg, P=0.018), and the epsilon4 allele was more common among African Americans (37.8 versus 26.4% for Caucasians). In multivariable analyses, the presence of the epsilon4 allele was associated with a statistically significantly higher warfarin dose among African Americans (median 45.0 mg in epsilon4 carriers versus 35.0 mg in non-epsilon4 carriers, P=0.014) but not Caucasians (38.1 versus 35.0 mg, P=0.60). In addition, warfarin maintenance dose increased among African Americans according to genotype previously associated with differential hepatic chylomicron clearance (epsilon2/epsilon2 or epsilon2/epsilon3: 30.0 mg; epsilon3/epsilon3: 35.0 mg; epsilon3/epsilon4 or epsilon4/epsilon4: 45.0 mg; P=0.012), although the epsilon4/epsilon4 genotype was rare and not clearly associated with higher doses. The association of APOE with warfarin dosing was independent of CYP2C9 and VKORC1 polymorphisms. APOE polymorphisms thus may be important determinants of warfarin maintenance dose and could explain at least some of the observed racial differences in dose requirements.

  View details for DOI 10.1038/sj.tpj.6500445

  View details for Web of Science ID 000252455600008

  View details for PubMedID 17325732

• Warfarin response and vitamin K epoxide reductase complex 1 in African Americans and Caucasians CLINICAL PHARMACOLOGY & THERAPEUTICS Schelleman, H., Chen, Z., Kealey, C., Whitehead, A. S., Christie, J., Price, M., Brensinger, C. M., Newcomb, C. W., Thorn, C. F., Samaha, F. F., Kimmel, S. E. 2007; 81 (5): 742-747

  Abstract

  The objective of this study was to determine whether two vitamin K epoxide reductase complex 1 (VKORC1) polymorphisms contribute to the variability in warfarin response, particularly in African Americans. The effect of the VKORC1 1173C/T and -1639G/A polymorphisms was examined in a prospective cohort study of 338 warfarin users. Subjects carrying an 1173T allele had a lower warfarin maintenance dose compared with subjects with the CC genotype in African Americans (-12.10 mg/week+/-4.93; P=0.02) and Caucasians (-14.41 mg/week+/-3.28; P<0.001). Before reaching maintenance dose, only Caucasians with the T allele had significantly increased risk of international normalized ratio >3 (odds ratio=3.10; 95% confidence interval: 1.73-5.55) compared with Caucasians with the CC genotype. Polymorphisms in the VKORC1 gene are associated with warfarin maintenance dose requirements among both African Americans and Caucasians. However, these polymorphisms may not be as useful in predicting over-anticoagulation among African Americans.

  View details for DOI 10.1038/sj.clpt.6100144

  View details for Web of Science ID 000245921500023

  View details for PubMedID 17329985

• Warfarin and cytochrome P4502C9 genotype: possible ethnic variation in warfarin sensitivity PHARMACOGENOMICS Kealey, C., Chen, Z., Christie, J., Thorn, C. F., Whitehead, A. S., Price, M., Samaha, F. F., Kimmel, S. E. 2007; 8 (3): 217-225

  Abstract

  Warfarin is a widely prescribed, efficacious oral anticoagulant. S-warfarin, the more active form, is metabolized by the cytochrome P450 (CYP)2C9 enzyme. The aim was to evaluate the influence of two CYP2C9 functional polymorphisms (*2 and *3) on warfarin dose in African-Americans, an unstudied population and Caucasians, and also to assess the effect of these polymorphisms on anticoagulation response after accounting for nongenetic factors and genetic factors that might also impact the dose-response relationship of warfarin.A prospective cohort of 362 patients with a target international normalized ratio of between 2.0 and 3.0 were genotyped. Warfarin sensitivity stratified by genotype was investigated using univariate and multivariate analyses.The maintenance dose of warfarin was significantly related to genotype (p < 0.01) (variant carriers: 31.25 mg/week; wild-type: 37.5 mg/week), even after adjustment for possible confounding factors (p = 0.046). However, the effect of genotype was restricted to Caucasians, in whom variant carriers had a significantly lower maintenance dose compared with wild-type homozygotes (unadjusted: p < 0.01; adjusted: p = 0.02). There was a greater risk of over-anticoagulation among Caucasian variant carriers, although this was only observed prior to reaching maintenance dose. For African-American variant carriers, there was no difference in warfarin response based on CYP2C9 genotype.CYP2C9 *2 and *3 variants provide predictive information in anticoagulation response. However, these variants may not be useful in African-Americans or as a marker of long-term over-anticoagulation once a stable dose is reached.

  View details for DOI 10.2217/14622416.8.3.217

  View details for Web of Science ID 000244875000006

  View details for PubMedID 17324110

• Vitamin K epoxide reductase complex 1 variant influences warfarin response in African Americans Schelleman, H., Chen, Z., Whitehead, A. S., Christie, J., Price, M., Kealey, C., Brensinger, C. M., Newcomb, C. W., Thorn, C. F., Kimmel, S. E. LIPPINCOTT WILLIAMS & WILKINS. 2007: E223

  View details for Web of Science ID 000244482200058

• Cytotoxic doses of ketoconazole affect expression of a subset of hepatic genes JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A-CURRENT ISSUES Casley, W. L., Ogrodowczyk, C., Larocque, L., Jaentschke, B., LeBlanc-Westwood, C., Menzies, J., Whitehouse, L., Hefford, M., Aubin, R. A., Thorn, C. F., Whitehead, A. S., Li, X. 2007; 70 (22): 1946-1955

  Abstract

  Ketoconazole is a widely prescribed antifungal drug, which has also been investigated as an anticancer therapy in both clinical and pre-clinical settings. However, severe hepatic injuries were reported to be associated with the use of ketoconazole, even in patients routinely monitored for their liver functions. Several questions concerning ketoconazole-induced hepatic injury remain unanswered, including (1) does ketoconazole alter cytochrome P450 expression at the transcriptional level?, (2) what types of gene products responsible for cytotoxicity are induced by ketoconazole?, and (3) what role do the major metabolites of ketoconazole play in this pathophysiologic process? A mouse model was employed to investigate hepatic gene expression following hepatotoxic doses of ketoconazole. Hepatic gene expression was analyzed using a toxicogenomic microarray platform, which is comprised of cDNA probes generated from livers exposed to various hepatoxicants. These hepatoxicants fall into five well-studied toxicological categories: peroxisome proliferators, aryl hydrocarbon receptor agonists, noncoplanar polychlorinated biphenyls, inflammatory agents, and hypoxia-inducing agents. Nine genes encoding enzymes involved in Phase I metabolism and one Phase II enzyme (glutathione S-transferase) were found to be upregulated. Serum amyloid A (SAA1/2) and hepcidin were the only genes that were downregulated among the 2364 genes assessed. In vitro cytotoxicity and transcription analyses revealed that SAA and hepcidin are associated with the general toxicity of ketoconazole, and might be usefully explored as generalized surrogate markers of xenobiotic-induced hepatic injury. Finally, it was shown that the primary metabolite of ketoconazole (de-N-acetyl ketoconazole) is largely responsible for the hepatoxicity and the downregulation of SAA and hepcidin.

  View details for DOI 10.1080/15287390701551407

  View details for Web of Science ID 000251297200008

  View details for PubMedID 17966066

• Comparison of health status between the United States and England JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Thorn, C. F. 2006; 296 (19): 2312

  View details for DOI 10.1001/jama.296.19.2312-b

  View details for Web of Science ID 000241998700011

  View details for PubMedID 17105789

• Clinical implications of pharmacogenomics of statin treatment PHARMACOGENOMICS JOURNAL Mangravite, L. M., Thorn, C. F., Krauss, R. M. 2006; 6 (6): 360-374

  View details for DOI 10.1038/sj.tpj.6500384

  View details for Web of Science ID 000242403500002

  View details for PubMedID 16550210

• A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION Rubin, D. L., Thorn, C. F., Klein, T. E., Altman, R. B. 2005; 12 (2): 121-129

  Abstract

  Biomedical databases summarize current scientific knowledge, but they generally require years of laborious curation effort to build, focusing on identifying pertinent literature and data in the voluminous biomedical literature. It is difficult to manually extract useful information embedded in the large volumes of literature, and automated intelligent text analysis tools are becoming increasingly essential to assist in these curation activities. The goal of the authors was to develop an automated method to identify articles in Medline citations that contain pharmacogenetics data pertaining to gene-drug relationships.The authors built and evaluated several candidate statistical models that characterize pharmacogenetics articles in terms of word usage and the profile of Medical Subject Headings (MeSH) used in those articles. The best-performing model was used to scan the entire Medline article database (11 million articles) to identify candidate pharmacogenetics articles.A sampling of the articles identified from scanning Medline was reviewed by a pharmacologist to assess the precision of the method. The authors' approach identified 4,892 pharmacogenetics articles in the literature with 92% precision. Their automated method took a fraction of the time to acquire these articles compared with the time expected to be taken to accumulate them manually. The authors have built a Web resource (http://pharmdemo.stanford.edu/pharmdb/main.spy) to provide access to their results.A statistical classification approach can screen the primary literature to pharmacogenetics articles with high precision. Such methods may assist curators in acquiring pertinent literature in building biomedical databases.

  View details for DOI 10.1197/jamia.M1640

  View details for Web of Science ID 000227842000003

  View details for PubMedID 15561790

  View details for PubMedCentralID PMC551544

• PharmGKB: the pharmacogenetics and pharmacogenomics knowledge base. Methods in molecular biology (Clifton, N.J.) Thorn, C. F., Klein, T. E., Altman, R. B. 2005; 311: 179-191

  Abstract

  The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) is an interactive tool for researchers investigating how genetic variation effects drug response. The PharmGKB web site, www.pharmgkb.org, displays genotype, molecular, and clinical primary data integrated with literature, pathway representations, protocol information, and links to additional external resources. Users can search and browse the knowledge base by genes, drugs, diseases, and pathways. Registration is free to the entire research community but subject to an agreement to respect the rights and privacy of the individuals whose information is contained within the database. Registered users can access and download primary data to aid in the design of future pharmacogenetics and pharmacogenomics studies.

  View details for PubMedID 16100408

• A common <i>ABCC2</i> promoter polymorphism is not a determinant of the risk of spina bifida BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY Jensen, L. E., Wall, A. M., Cook, M., Hoess, K., Thorn, C. F., Whitehead, A. S., Mitchell, L. E. 2004; 70 (6): 396-399

  Abstract

  There is compelling evidence that the risk of spina bifida, a malformation of the caudal neural tube, is associated with maternal and/or embryonic disturbances in folate/homocysteine metabolism. Hence, functional variants of genes that influence folate/homocysteine metabolism constitute a biologically plausible group of candidate risk factors for spina bifida and other neural tube defects. One such candidate is ABCC2, the gene encoding ABCC2, (a.k.a. canalicular multispecific organic anion transporter [cMOAT], multidrug resistance related protein 2 [MRP2]), a member of the ABC transporter family that effluxes natural folates and anti-folate drugs such as methotrexate.The association between the risk of spina bifida and both the maternal and embryonic ABCC2 C(-24)T genotype was evaluated by using the transmission disequilibrium test and log-linear modeling.These analyses provided no evidence that the risk of spina bifida was significantly related to either the maternal or embryonic ABCC2 C(-24)T genotype.The results of the present analyses suggest that the C(-24)T variant of the ABCC2 gene is not a major determinant of spina bifida risk.

  View details for DOI 10.1002/bdra.20023

  View details for Web of Science ID 000222419100004

  View details for PubMedID 15211708

• TGF-β down-regulates IL-1α-induced TLR2 expression in murine hepatocytes JOURNAL OF LEUKOCYTE BIOLOGY Matsumura, T., Hayashi, H., Takii, T., Thorn, C. F., Whitehead, A. S., Inoue, J. I., Onozaki, K. 2004; 75 (6): 1056-1061

  Abstract

  We have previously reported that the proinflammatory cytokine interleukin (IL)-1α can up-regulate functional Toll-like receptor 2 (TLR2) expression in primary-cultured murine hepatocytes, and bacterial lipopeptide (BLP) is capable of signaling through TLR2 to induce serum amyloid A (SAA) expression in hepatocytes. In the present study, we investigated the effect of the anti-inflammatory cytokine transforming growth factor-β (TGF-β) on TLR2 expression in primary-cultured murine hepatocytes. At the mRNA and protein levels, TGF-β up-regulated TLR2 expression but inhibited TLR2 expression induced by IL-1α at 24 h. BLP-induced SAA promoter activity could be augmented by pretreatment with IL-1α but not TGF-β or the combination of TGF-β and IL-1α. TLR2 promoter activity and nuclear factor (NF)-κB activation by IL-1α were inhibited by TGF-β treatment. Pretreatment with TGF-β strongly suppressed IL-1α-induced TLR2 promoter activity and NF-κB activation, which was consistent with the down-regulation of type I IL-1 receptor (IL-1RI) mRNA expression. IL-1α up-regulated IL-1RI mRNA, but it was inhibited by the treatment with TGF-β. These results suggest that TGF-β suppresses the induction of TLR2 expression by IL-1α through down-regulation of IL-1RI expression. These results also demonstrate the disparity between IL-1α and TGF-β in regulating TLR2-mediated SAA production in hepatocytes.

  View details for DOI 10.1189/jlb.0104108

  View details for Web of Science ID 000221918800014

  View details for PubMedID 29350829

• Phase I trial of UFT/leucovorin and irinotecan in patients with advanced cancer EUROPEAN JOURNAL OF CANCER Veronese, M. L., Stevenson, J. P., Sun, W., Redlinger, M., Algazy, K., Giantonio, B., Hahn, S., Vaughn, D., Thorn, C., Whitehead, A. S., Haller, D. G., O'Dwyer, P. J. 2004; 40 (4): 508-514

  Abstract

  UFT (BMS-200604, Uftoral) is an oral fluoropyrimidine that combines uracil and the 5-fluorouracil (5-FU) prodrug, ftorafur, in a 4:1 molar ratio with single-agent activity in breast and gastrointestinal cancers. In vitro studies have shown that irinotecan downregulates thymidylate synthase (TS) expression in tumour cells, leading to synergy between irinotecan and 5-FU that is maximal when irinotecan is given 24 h prior to 5-FU. Given this observed synergy and the confirmatory clinical activity of combination therapy with 5-FU, leucovorin (LV) and irinotecan, we performed a phase I trial to determine the maximum tolerated doses (MTD) of UFT, LV, and irinotecan. Treatment consisted of irinotecan administered as a 90-min intravenous (i.v.) infusion on day 1 followed by twice daily oral UFT/LV on days 2-15, repeated every 21 days. Initial doses were irinotecan 200 mg/m(2) and UFT 200 mg/m(2)/day, with LV dose fixed at 60 mg/day. 31 patients received a total of 130 cycles of UFT/LV and irinotecan. 3 of 9 patients experienced grade 3/4 diarrhoea at the highest dose level of irinotecan 310 mg/m(2) and UFT 300 mg/m(2)/day. Other toxicities included neutropenia, anaemia, alopecia, nausea/vomiting and fatigue. Further dose escalation was not pursued since this level of toxicity was appropriate for future phase II study. One patient with colorectal cancer experienced a partial response and 9 patients with non-small cell lung, colorectal and gastro-oesophageal junction carcinomas had disease stabilisation lasting 4-26 (median 6) cycles. Methylenetetrahydrofolate reductase (MTHFR) C677T genotype was analysed in peripheral mononuclear cells (PMNs) obtained from 24 patients. 2 patients had the homozygous TT polymorphism and 1 of them had grade 3 diarrhoea at the first dose level. Irinotecan on day 1 followed by a 14-day course of oral UFT/LV beginning on day 2 is well tolerated, and suitable for testing in several tumour types. Doses recommended for further study on this schedule are irinotecan 310 mg/m(2) and UFT 300 mg/m(2)/day, with LV 60 mg/day.

  View details for DOI 10.1016/j.ejca.2003.10.022

  View details for Web of Science ID 000220029600017

  View details for PubMedID 14962716

• Regulation of the human acute phase serum amyloid a genes by tumour necrosis factor-α, interleukin-6 and glucocorticoids in hepatic and epithelial cell lines SCANDINAVIAN JOURNAL OF IMMUNOLOGY Thorn, C. F., Lu, Z. Y., Whitehead, A. S. 2004; 59 (2): 152-158

  Abstract

  The major acute-phase protein serum amyloid A, A-SAA, is upregulated by a variety of inflammatory stimuli, including cytokines and glucocorticoids (GCs). Elevated systemic concentrations of both A-SAA and tumour necrosis factor (TNF)-alpha are a feature of inflammatory diseases, such as rheumatoid arthritis and inflammatory bowel disease. Here, we examine the roles of TNF-alpha, interleukin-6 (IL-6) and GCs on the transcriptional regulation of the two human A-SAA genes (SAA1 and SAA2) and show that these stimuli have different effects on the SAA1 and SAA2 promoters in HepG2 hepatoma and KB epithelial cell lines. Both genes are induced modestly by TNF-alpha and IL-6 alone and synergistically by TNF-alpha plus IL-6. The TNF-driven induction of SAA1, but not that of SAA2, can be enhanced by GCs in both cell lines, whereas GCs alone can upregulate SAA1 only in epithelial cells. The upregulation of both genes by cytokines, and of SAA1 by GCs, is more rapid in epithelial cells than hepatoma cells. We established that the order in which either cell line was treated with TNF-alpha and IL-6 influenced A-SAA promoter transcriptional activation. Treatment with TNF-alpha followed by IL-6 resulted in a much greater induction of both A-SAA genes than treatment with IL-6 followed by TNF-alpha.

  View details for DOI 10.1111/j.0300-9475.2004.01369.x

  View details for Web of Science ID 000188893100005

  View details for PubMedID 14871291

• Tissue-specific regulation of the human acute-phase serum amyloid A genes, <i>SAA1</i> and <i>SAA2</i>, by glucocorticoids in hepatic and epithelial cells EUROPEAN JOURNAL OF IMMUNOLOGY Thorn, C. F., Lu, Z. Y., Whitehead, A. S. 2003; 33 (9): 2630-2639

  Abstract

  The human acute-phase protein serum amyloid A (A-SAA), encoded by the SAA1 and SAA2 genes, is dramatically induced by pro-inflammatory mediators during the acute-phase response to infection or injury. Circulating A-SAA is predominantly synthesized by the liver. However, other tissues are the source of locally produced A-SAA. Here, we establish that the qualitative and kinetic aspects of SAA1 and SAA2 transcription following treatment of HepG2 hepatoma cells and KB epithelial cells with glucocorticoids and cytokines are quite distinct. Untreated HepG2 cells do not express A-SAA mRNA and glucocorticoids, when administered alone, fail to induce either SAA1 or SAA2. In contrast, untreated KB cells constitutively express SAA1 mRNA. Following cytokine stimulation, both A-SAA genes are rapidly up-regulated to similar extents. As in the hepatoma cell line, co-stimulation of KB cells with glucocorticoids places SAA1 at a transcriptional advantage over SAA2. Interestingly, SAA1 can be significantly induced by glucocorticoids alone in KB cells. The effects of glucocorticoids on SAA1 in both cell lines is glucocorticoid receptor-dependent. Differential regulation of A-SAA expression in these cell lines may reflect different temporal and spatial requirements for A-SAA synthesis in response to different inflammatory challenges.

  View details for DOI 10.1002/eji.200323985

  View details for Web of Science ID 000185323200029

  View details for PubMedID 12938239

• Differential transcription of the mouse acute phase serum amyloid A genes in response to pro-inflammatory cytokines AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS Thorn, C. F., Whitehead, A. S. 2002; 9 (4): 229-236

  Abstract

  The acute phase members of the mouse serum amyloid A (Saa) family, Saa1, Saa2 and Saa3, are highly similar at both the nucleotide and protein sequence levels. Saa1 and Saa2 in the BALB/c strain are 72% identical over the first 500 bp upstream of their transcription start sites and to date have been considered to be coordinately regulated. Furthermore, based on their homology with the upstream regions of the human SAA1 and SAA2 genes, it has been assumed that they are Type I acute phase proteins (APPs), i.e. they are primarily regulated by IL-1 and TNF. Here we establish that the BALB/c Saa1, Saa2 and Saa3 genes, in fact, respond differently to IL-1, TNF and IL-6. The Saa1 and Saa2 promoters are strongly induced by IL-6, with synergistic upregulation of Saa2, but not of Saa1, by IL-1 or TNF. In contrast, the Saa3 promoter is strongly induced by IL-1, moderately induced by TNF and only minimally induced by IL-6. We also define important sequence differences between the Saa promoters of Type A (BALB/c and ICR/Swiss) and Type B (129/Ola) strains of mice, that have dramatic qualitative and quantitative consequences for Saa1 and Saa2 regulation. These findings mandate careful strain selection prior to embarking on studies involving mouse models of secondary amyloidosis or cytokine inactivation.

  View details for DOI 10.3109/13506120209114098

  View details for Web of Science ID 000180409500002

  View details for PubMedID 12557750

• Differential glucocorticoid enhancement of the cytokine-driven transcriptional activation of the human acute phase serum amyloid a genes, <i>SAA1</i> and <i>SAA2</i> JOURNAL OF IMMUNOLOGY Thorn, C. F., Whitehead, A. S. 2002; 169 (1): 399-406

  Abstract

  The human acute phase serum amyloid A (A-SAA) genes, SAA1 and SAA2, have a high degree of sequence identity that extends approximately 450 bp upstream of their transcription start sites. Each promoter contains analogously positioned functional binding sites for the transcription factors NF-kappaB and NF-IL6. In human HepG2 hepatoma cells transfected with SAA promoter luciferase reporter constructs, administration of IL-1 and IL-6, singly or in combination, induced SAA1 and SAA2 transcriptional readouts that were qualitatively indistinguishable. However, under induced conditions, the SAA2 promoter had a significant quantitative transcriptional advantage over the SAA1 promoter. The application of the synthetic glucocorticoid dexamethasone in the context of cytokine stimulation enhanced the transcriptional activity of the SAA1, but not the SAA2, promoter such that readout from the former became equivalent to that from the latter. A putative glucocorticoid response element (GRE) is present (between residues -208 and -194) only in the SAA1 gene; a similar sequence in the corresponding region of the SAA2 gene is disrupted by a nine-residue insertion. The SAA1 GRE was shown to be functionally active and the SAA2 disrupted GRE was shown to be functionally inactive in experiments using reporter constructs carrying SAA1 and SAA2 promoters that had been modified by site-specific mutagenesis. Quantitative analysis of transcript-specific RT-PCR products, derived from SAA1 and SAA2 mRNAs after treatment of HepG2 cells with cytokines in the presence or absence of dexamethasone, confirmed that the endogenous SAA1 gene has a cytokine-driven transcriptional disadvantage that is superseded by a marginal transcriptional advantage when glucocorticoids are present.

  View details for DOI 10.4049/jimmunol.169.1.399

  View details for Web of Science ID 000176360400051

  View details for PubMedID 12077270

• <i>In vitro</i> evaluation of an enhanced human serum amyloid a (<i>SAA2</i>) promoter-regulated soluble TNF receptor fusion protein for anti-inflammatory gene therapy SCANDINAVIAN JOURNAL OF IMMUNOLOGY Rygg, M., Uhlar, C. M., Thorn, C., Jensen, L. E., Gaughan, D. J., Varley, A. W., Munford, R. S., Göke, R., Chen, Y., Whitehead, A. S. 2001; 53 (6): 588-595

  Abstract

  Tumour necrosis factor (TNF)-alpha contributes to the pathogenesis of many inflammatory diseases. Recombinant soluble TNF receptor fusion proteins (sTNFR:Ig) are potent TNF antagonists, both in vitro and in vivo. The concentration of serum amyloid A (SAA) increases by up to 1000-fold during inflammation, largely owing to cytokine-driven transcriptional upregulation. A reporter plasmid, comprising the proximal 0.7 kb of the human SAA2 promoter fused to a luciferase gene, was used in transient transfection experiments in human HepG2 hepatoma cells to assess the quantitative and qualitative TNF antagonist properties of a construct in which sTNFR:Ig synthesis is under the control of a chimera of the SAA2 promoter and a tat/HIV element. The SAA2-tat/HIV-sTNFR:Ig construct retained the fine-tuned cytokine responsiveness of the SAA2 promoter, while exhibiting the quantitatively enhanced level of protein expression conferred by the tat/HIV element. It produced a biologically significant TNF inhibition that was at least as strong as that achieved using a CMV promoter-driven sTNFR:Ig construct. There was a dose- and time-dependent relationship between the pro-inflammatory cytokine used, and the generation of TNF antagonist activity by SAA2-tat/HIV-sTNFR:Ig. Although sTNFR:Ig protein can be induced by either TNF-alpha or interleukin (IL)-1beta, its antagonist activity is limited to the former cytokine. The SAA2-tat/HIV-sTNFR:Ig construct, and derivatives thereof, may therefore be ideally suited to gene therapy applications that require the local production of potent and specific immune modifiers only when there is active pathology. It may consequently be of particular use in the future treatment of diseases such as rheumatoid arthritis.

  View details for DOI 10.1046/j.1365-3083.2001.00919.x

  View details for Web of Science ID 000169483700008

  View details for PubMedID 11422907