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Ahern TP, Collin LJ, Baurley JW, Kjærsgaard A, Nash R, Maliniak ML, Damkier P, Zwick ME, Isett RB, Christiansen PM, Ejlertsen B, Lauridsen KL, Christensen KB, Silliman RA, Sørensen HT, Tramm T, Hamilton-Dutoit S, Lash TL, Cronin-Fenton D. Metabolic Pathway Analysis and Effectiveness of Tamoxifen in Danish Breast Cancer Patients. Cancer Epidemiol Biomarkers Prev 2020; 29:582-590. [PMID: 31932415 PMCID: PMC7060091 DOI: 10.1158/1055-9965.epi-19-0833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/15/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Tamoxifen and its metabolites compete with estrogen to occupy the estrogen receptor. The conventional dose of adjuvant tamoxifen overwhelms estrogen in this competition, reducing breast cancer recurrence risk by nearly half. Phase I metabolism generates active tamoxifen metabolites, and phase II metabolism deactivates them. No earlier pharmacogenetic study has comprehensively evaluated the metabolism and transport pathways, and no earlier study has included a large population of premenopausal women. METHODS We completed a cohort study of 5,959 Danish nonmetastatic premenopausal breast cancer patients, in whom 938 recurrences occurred, and a case-control study of 541 recurrent cases in a cohort of Danish predominantly postmenopausal breast cancer patients, all followed for 10 years. We collected formalin-fixed paraffin-embedded tumor blocks and genotyped 32 variants in 15 genes involved in tamoxifen metabolism or transport. We estimated conventional associations for each variant and used prior information about the tamoxifen metabolic path to evaluate the importance of metabolic and transporter pathways. RESULTS No individual variant was notably associated with risk of recurrence in either study population. Both studies showed weak evidence of the importance of phase I metabolism in the clinical response to adjuvant tamoxifen therapy. CONCLUSIONS Consistent with prior knowledge, our results support the role of phase I metabolic capacity in clinical response to tamoxifen. Nonetheless, no individual variant substantially explained the modest phase I effect on tamoxifen response. IMPACT These results are consistent with guidelines recommending against genotype-guided prescribing of tamoxifen, and for the first time provide evidence supporting these guidelines in premenopausal women.
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Affiliation(s)
- Thomas P Ahern
- Department of Surgery, Larner College of Medicine at The University of Vermont, Burlington, Vermont
| | - Lindsay J Collin
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | | | - Anders Kjærsgaard
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Rebecca Nash
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Maret L Maliniak
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Per Damkier
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
- Emory Integrated Genomics Core, Emory University, Atlanta, Georgia
| | - R Benjamin Isett
- Emory Integrated Genomics Core, Emory University, Atlanta, Georgia
| | - Peer M Christiansen
- Breast Unit, Aarhus University Hospital/Randers Regional Hospital, Aarhus, Denmark
- Danish Breast Cancer Group, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bent Ejlertsen
- Danish Breast Cancer Group, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | | | - Rebecca A Silliman
- Boston University School of Medicine, Boston University, Boston, Massachusetts
| | - Henrik T Sørensen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Trine Tramm
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Timothy L Lash
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia.
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
- Winship Cancer Institute, Emory University, Atlanta, Georgia
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Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, Penubarthi S, Sun H, Baldwin DA, Fraser NW. Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection. PLoS One 2015; 10:e0117471. [PMID: 25710170 PMCID: PMC4339549 DOI: 10.1371/journal.pone.0117471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 12/23/2014] [Indexed: 01/01/2023] Open
Abstract
HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.
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Affiliation(s)
- Jaewook Oh
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Iryna F. Sanders
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Eric Z. Chen
- Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - John W. Tobias
- Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - R. Benjamin Isett
- Penn Molecular Profiling Facility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Sindura Penubarthi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Hao Sun
- Department of Chemical Pathology, The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences, Hong Kong SAR, China
| | - Don A. Baldwin
- Pathonomics LLC, Philadelphia, PA, 19104, United States of America
| | - Nigel W. Fraser
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States of America
- * E-mail:
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Saba NF, Wilson M, Doho G, DaSilva J, Benjamin Isett R, Newman S, Chen ZG, Magliocca K, Rossi MR. Mutation and Transcriptional Profiling of Formalin-Fixed Paraffin Embedded Specimens as Companion Methods to Immunohistochemistry for Determining Therapeutic Targets in Oropharyngeal Squamous Cell Carcinoma (OPSCC): A Pilot of Proof of Principle. Head Neck Pathol 2014; 9:223-35. [PMID: 25236499 PMCID: PMC4424213 DOI: 10.1007/s12105-014-0566-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 08/17/2014] [Indexed: 11/24/2022]
Abstract
The role of molecular methods in the diagnosis of head and neck cancer is rapidly evolving and holds great potential for improving outcomes for all patients who suffer from this diverse group of malignancies . However, there is considerable debate as to the best clinical approaches, particularly for Next Generation Sequencing (NGS). The choices of NGS methods such as whole exome, whole genome, whole transcriptomes (RNA-Seq) or multiple gene resequencing panels, each have strengths and weakness based on data quality, the size of the data, the turnaround time for data analysis, and clinical actionability. There have also been a variety of gene expression signatures established from microarray studies that correlate with relapse and response to treatment, but none of these methods have been implemented as standard of care for oropharyngeal squamous cell carcinoma (OPSCC). Because many genomic methodologies are still far from the capabilities of most clinical laboratories, we chose to explore the use of a combination of off the shelf targeted mutation analysis and gene expression analysis methods to complement standard anatomical pathology methods. Specifically, we have used the Ion Torrent AmpliSeq cancer panel in combination with the NanoString nCounter Human Cancer Reference Kit on 8 formalin-fixed paraffin embedded (FFPE) OPSCC tumor specimens, (4) HPV-positive and (4) HPV-negative. Differential expression analysis between HPV-positive and negative groups showed that expression of several genes was highly likely to correlate with HPV status. For example, WNT1, PDGFA and OGG1 were all over-expressed in the positive group. Our results show the utility of these methods with routine FFPE clinical specimens to identify potential therapeutic targets which could be readily applied in a clinical trial setting for clinical laboratories lacking the instrumentation or bioinformatics infrastructure to support comprehensive genomics workflows. To the best of our knowledge, these preliminary experiments are among the earliest to combine both mutational and gene expression profiles using Ion Torrent and NanoString technologies. This reports serves as a proof of principle methodology in OPSCC.
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Affiliation(s)
- Nabil F. Saba
- />Department of Otolaryngology and Head and Neck Oncology Program, Winship Cancer Institute of Emory University, Emory University School of Medicine, Atlanta, GA USA , />Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
| | - Malania Wilson
- />Emory Integrated Genomics Core, Emory University School of Medicine, Atlanta, GA USA
| | - Gregory Doho
- />Emory Integrated Genomics Core, Emory University School of Medicine, Atlanta, GA USA
| | - Juliana DaSilva
- />Emory Integrated Genomics Core, Emory University School of Medicine, Atlanta, GA USA
| | - R. Benjamin Isett
- />Emory Integrated Genomics Core, Emory University School of Medicine, Atlanta, GA USA
| | - Scott Newman
- />Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA USA
| | - Zhuo Georgia Chen
- />Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
| | - Kelly Magliocca
- />Department of Otolaryngology and Head and Neck Oncology Program, Winship Cancer Institute of Emory University, Emory University School of Medicine, Atlanta, GA USA , />Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Michael R. Rossi
- />Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA USA , />Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA USA
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Mueller PW, Lyons J, Kerr G, Haase CP, Isett RB. Standard enrichment methods for targeted next-generation sequencing in high-repeat genomic regions. Genet Med 2014; 15:910-1. [PMID: 24196000 DOI: 10.1038/gim.2013.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Patricia W Mueller
- Molecular Risk Assessment Laboratory, Newborn Screening and Molecular Biology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Erdogan B, Facey C, Qualtieri J, Tedesco J, Rinker E, Isett RB, Tobias J, Baldwin DA, Thompson JE, Carroll M, Kim AS. Diagnostic microRNAs in myelodysplastic syndrome. Exp Hematol 2011; 39:915-926.e2. [DOI: 10.1016/j.exphem.2011.06.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/07/2011] [Accepted: 06/02/2011] [Indexed: 02/06/2023]
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Bosinger SE, Li Q, Gordon SN, Klatt NR, Duan L, Xu L, Francella N, Sidahmed A, Smith AJ, Cramer EM, Zeng M, Masopust D, Carlis JV, Ran L, Vanderford TH, Paiardini M, Isett RB, Baldwin DA, Else JG, Staprans SI, Silvestri G, Haase AT, Kelvin DJ. Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. J Clin Invest 2010; 119:3556-72. [PMID: 19959874 DOI: 10.1172/jci40115] [Citation(s) in RCA: 259] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 10/19/2009] [Indexed: 01/07/2023] Open
Abstract
Natural SIV infection of sooty mangabeys (SMs) is nonprogressive despite chronic virus replication. Strikingly, it is characterized by low levels of immune activation, while pathogenic SIV infection of rhesus macaques (RMs) is associated with chronic immune activation. To elucidate the mechanisms underlying this intriguing phenotype, we used high-density oligonucleotide microarrays to longitudinally assess host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs was consistently associated with a robust innate immune response, including widespread upregulation of IFN-stimulated genes (ISGs) in blood and lymph nodes. While SMs exhibited a rapid resolution of ISG expression and immune activation, both responses were observed chronically in RMs. Systems biology analysis indicated that expression of the lymphocyte inhibitory receptor LAG3, a marker of T cell exhaustion, correlated with immune activation in SIV-infected RMs but not SMs. Our findings suggest that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low levels of immune activation characteristic of SMs chronically infected with SIV.
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Affiliation(s)
- Steven E Bosinger
- Department of Pathology and Laboratory Medicine, and Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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Wang WX, Wilfred BR, Baldwin DA, Isett RB, Ren N, Stromberg A, Nelson PT. Focus on RNA isolation: obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue. Biochim Biophys Acta 2008; 1779:749-57. [PMID: 18316046 DOI: 10.1016/j.bbagrm.2008.01.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are present in all known plant and animal tissues and appear to be somewhat concentrated in the mammalian nervous system. Many different miRNA expression profiling platforms have been described. However, relatively little research has been published to establish the importance of 'upstream' variables in RNA isolation for neural miRNA expression profiling. We tested whether apparent changes in miRNA expression profiles may be associated with tissue processing, RNA isolation techniques, or different cell types in the sample. RNA isolation was performed on a single brain sample using eight different RNA isolation methods, and results were correlated using a conventional miRNA microarray and then cross-referenced to Northern blots. Differing results were seen between samples obtained using different RNA isolation techniques and between microarray and Northern blot results. Another complication of miRNA microarrays is tissue-level heterogeneity of cellular composition. To investigate this phenomenon, miRNA expression profiles were determined and compared between highly-purified primary cerebral cortical cell preparations of rat primary E15-E18 neurons versus rat primary E15-E18 astrocytes. Finally, to assess the importance of dissecting human brain gray matter from subjacent white matter in cerebral cortical studies, miRNA expression profiles were compared between gray matter and immediately contiguous white matter. The results suggest that for microarray studies, cellular composition is important, and dissecting white matter from gray matter improves the specificity of the results. Based on these data, recommendations for miRNA expression profiling in neural tissues, and considerations worthy of further study, are discussed.
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Affiliation(s)
- Wang-Xia Wang
- Sanders-Brown Center on Aging and Department of Pathology, University of Kentucky, Lexington, Kentucky 40536-0230, USA
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Nouzova M, Holtan N, Oshiro MM, Isett RB, Munoz-Rodriguez JL, List AF, Narro ML, Miller SJ, Merchant NC, Futscher BW. Epigenomic changes during leukemia cell differentiation: analysis of histone acetylation and cytosine methylation using CpG island microarrays. J Pharmacol Exp Ther 2004; 311:968-81. [PMID: 15302897 DOI: 10.1124/jpet.104.072488] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dysregulation of epigenetic control is an important participant in carcinogenesis. The PML/RAR alpha translocation in acute promyelocytic leukemia (APL) is an example where the resultant fusion protein recruits histone deacetylase complexes to target genes resulting in their inappropriate transcriptional repression. All-trans-retinoic acid (ATRA) acts as a ligand that relieves this repression and produces an epigenetic transcriptional reprogramming of the cancer cell. CpG island microarrays were used to analyze the DNA methylation and histone acetylation state of the human APL cell line NB4 before and after differentiation with ATRA as well as normal peripheral blood mononuclear cells (PBMC). Over 70 CpG islands within 1 kb of transcription start of a known gene are aberrantly methylated in NB4 cells compared with PBMC; however, no changes in cytosine methylation were detected following ATRA-induced differentiation. With respect to histone H4 acetylation, over 100 single-copy CpG islands within 1 kb of transcription start of a known human gene became hyperacetylated following ATRA-induced differentiation. One CpG island was aberrantly methylated in NB4 cells, but became hyperacetylated and was induced following ATRA treatment and was associated with the HoxA1 gene, suggesting it may be a target gene of ATRA in APL. In addition to single-copy sequences, a selective increase in acetylation was detected in satellite DNA when compared with other high-copy sequences, such as Alu or rDNA. In summary, ATRA stimulates complex epigenomic changes during leukemic cell differentiation, and monitoring these changes may help to identify new targets of epigenetic dysfunction.
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Affiliation(s)
- M Nouzova
- Arizona Cancer Center, 1515 N. Campbell Ave., Tucson AZ 85724-5024, USA
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