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Ponzio NM, Alder J, Nucci M, Dannenfelser D, Hilton H, Linardopoulos N, Lutz C. Learning Science Communication Skills Using Improvisation, Video Recordings, and Practice, Practice, Practice. J Microbiol Biol Educ 2018; 19:19.1.15. [PMID: 29904514 PMCID: PMC5969400 DOI: 10.1128/jmbe.v19i1.1433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/27/2017] [Indexed: 06/08/2023]
Abstract
Doctoral students in science disciplines spend countless hours learning how to conduct cutting-edge research but very little time learning to communicate the nature and significance of their science to people outside their field. To narrow this disparity, we created an unusual course titled Communicating Science for doctoral science trainees at Rutgers University. Our goal was to help students develop an advanced ability to communicate their research clearly and accurately and to emphasize its value and significance to diverse audiences. Course design included classroom instruction supplemented with improvisation, video recordings, and ample opportunity for students to practice and receive immediate, constructive feedback in a supportive environment. A multidisciplinary faculty with expertise in science, education, communication, and theater arts taught this course. PhD students came from diverse scientific disciplines, ranging from biology and chemistry to civil engineering. Students also completed a capstone project in which they worked with a professional in the academic or private sector to explore a possible career aspiration. Assessment was in the form of feedback on students' oral and poster presentations, and written abstracts about their research. Student evaluations and comments about course format and content were mostly positive and also provided input for ways to improve the course. We discovered that the diversity of scientific backgrounds among our students enhanced their ability to learn how to communicate their science to others outside their disciplines. We are leveraging the success of our initial course offering to reach other student and faculty groups at Rutgers.
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Affiliation(s)
- Nicholas M. Ponzio
- Department of Pathology, Rutgers New Jersey Medical School and Rutgers School of Graduate Studies, Newark, NJ 07101
| | - Janet Alder
- Rutgers Robert Wood Johnson Medical School and Rutgers School of Graduate Studies, Piscataway, NJ 08854
| | - Mary Nucci
- Rutgers School of Environmental and Biological Sciences, New Brunswick, NJ 08901
| | - David Dannenfelser
- Theater Arts program – Rutgers School of Arts and Sciences, New Brunswick, NJ 08901
| | | | | | - Carol Lutz
- Rutgers New Jersey Medical School and Rutgers School of Graduate Studies, Newark, NJ 07101
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Hilton H, Kliman RM, Hey J. USING HITCHHIKING GENES TO STUDY ADAPTATION AND DIVERGENCE DURING SPECIATION WITHIN THE DROSOPHILA MELANOGASTER SPECIES COMPLEX. Evolution 2017; 48:1900-1913. [PMID: 28565154 DOI: 10.1111/j.1558-5646.1994.tb02222.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/1993] [Accepted: 03/10/1994] [Indexed: 11/29/2022]
Abstract
Several studies of intraspecific and interspecific DNA sequence variation from Drosophila loci have revealed a pattern of low intraspecific variation from genomic regions of low recombination. The mechanisms consistently invoked to explain these patterns are the selective sweep of advantageous mutations together with genetic hitchhiking of linked loci. To examine the effect of selective sweeps on genetic divergence during speciation, we studied two loci in different genomic regions thought to be subject to selective sweeps. We obtained DNA sequences from 1.1kb pair portions of the fourth chromosome locus cubitus interruptus Dominant (ciD ) and from the asense locus near the telomere of the X chromosome. At ciD , we found very low variation among multiple lines of Drosophila mauritiana and D. sechellia. This finding is consistent with an earlier report of very low variation in D. melanogaster and D. simulans at ciD and supports the conclusion of selective sweeps and genetic hitchhiking on the nonrecombining fourth chromosome. The pattern of variation found at asense suggests that a selective sweep has occurred recently at the tip of the X chromosome in D. simulans, but not in D. melanogaster or D. mauritiana. The data from ciD and asense are compared with data from three X chromosome loci (period, zeste, and yolk protein 2) that experience normal levels of recombination. By examining estimated genealogies and the rates at which different classes of mutations have accumulated, we conclude that selective sweeps are common occurrences on the fourth chromosome but less common near the tip of the X chromosome. An interesting pattern of low variation at ciD among D. simulans, D. mauritiana, and D. sechellia suggests that a selective sweep may have occurred among these forms even after divergence into separate species had begun.
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Affiliation(s)
- Holly Hilton
- Rutgers University, Nelson Labs, P.O. Box 1059, Piscataway, New Jersey, 08855-1059
| | - Richard M Kliman
- Rutgers University, Nelson Labs, P.O. Box 1059, Piscataway, New Jersey, 08855-1059
| | - Jody Hey
- Rutgers University, Nelson Labs, P.O. Box 1059, Piscataway, New Jersey, 08855-1059
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Strulovici-Barel Y, Staudt MR, Krause A, Gordon C, Tilley AE, Harvey BG, Kaner RJ, Hollmann C, Mezey JG, Bitter H, Pillai SG, Hilton H, Wolff G, Stevenson CS, Visvanathan S, Fine JS, Crystal RG. Persistence of circulating endothelial microparticles in COPD despite smoking cessation. Thorax 2016; 71:1137-1144. [PMID: 27462120 DOI: 10.1136/thoraxjnl-2015-208274] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Increasing evidence links COPD pathogenesis with pulmonary capillary apoptosis. We previously demonstrated that plasma levels of circulating microparticles released from endothelial cells (EMPs) due to apoptosis are elevated in smokers with normal spirometry but low diffusion capacity, that is, with early evidence of lung destruction. We hypothesised that pulmonary capillary apoptosis persists with the development of COPD and assessed its reversibility in healthy smokers and COPD smokers following smoking cessation. METHODS Pulmonary function and high-resolution CT (HRCT) were assessed in 28 non-smokers, 61 healthy smokers and 49 COPD smokers; 17 healthy smokers and 18 COPD smokers quit smoking for 12 months following the baseline visit. Total EMP (CD42b-CD31+), pulmonary capillary EMP (CD42b-CD31+ACE+) and apoptotic EMP (CD42b-CD62E+/CD42b-CD31+) levels were quantified by flow cytometry. RESULTS Compared with non-smokers, healthy smokers and COPD smokers had elevated levels of circulating EMPs due to active pulmonary capillary endothelial apoptosis. Levels remained elevated over 12 months in healthy smokers and COPD smokers who continued smoking, but returned to non-smoker levels in healthy smokers who quit. In contrast, levels remained significantly abnormal in COPD smokers who quit. CONCLUSIONS Pulmonary capillary apoptosis is reversible in healthy smokers who quit, but continues to play a role in COPD pathogenesis in smokers who progressed to airflow obstruction despite smoking cessation. TRIAL REGISTRATION NUMBER NCT00974064; NCT01776398.
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Affiliation(s)
- Yael Strulovici-Barel
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Michelle R Staudt
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Anja Krause
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Cynthia Gordon
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Ann E Tilley
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Ben-Gary Harvey
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York.,Department of Pulmonary and Critical Care Medicine, Weill Medical College of Cornell University, New York, New York
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York.,Department of Pulmonary and Critical Care Medicine, Weill Medical College of Cornell University, New York, New York
| | - Charleen Hollmann
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Hans Bitter
- Hoffmann-La Roche, Nutley, New Jersey, USA.,Novartis
| | | | - Holly Hilton
- Hoffmann-La Roche, Nutley, New Jersey, USA.,PPD Labs
| | - Gerhard Wolff
- Hoffmann-La Roche, Nutley, New Jersey, USA.,Achillion Pharmaceuticals, Inc
| | | | - Sudha Visvanathan
- Hoffmann-La Roche, Nutley, New Jersey, USA.,Boehringer Ingelheim Pharmaceuticals
| | - Jay S Fine
- Hoffmann-La Roche, Nutley, New Jersey, USA.,Boehringer Ingelheim Pharmaceuticals
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, New York
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Mina-Osorio P, LaStant J, Keirstead N, Whittard T, Ayala J, Stefanova S, Garrido R, Dimaano N, Hilton H, Giron M, Lau KY, Hang J, Postelnek J, Kim Y, Min S, Patel A, Woods J, Ramanujam M, DeMartino J, Narula S, Xu D. Suppression of glomerulonephritis in lupus-prone NZB × NZW mice by RN486, a selective inhibitor of Bruton's tyrosine kinase. ACTA ACUST UNITED AC 2013; 65:2380-91. [PMID: 23754328 DOI: 10.1002/art.38047] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 05/30/2013] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Bruton's tyrosine kinase (BTK) plays a critical role in B cell development and function. We recently described a selective BTK inhibitor, RN486, that blocks B cell receptor (BCR) and Fcγ receptor signaling and is efficacious in animal models of arthritis. The aim of this study was to examine the potential efficacy of BTK in systemic lupus erythematosus (SLE), using an NZB × NZW mouse model of spontaneous SLE. METHODS Mice received RN486 or its vehicle (administered in chow) at a final concentration of 30 mg/kg for 8 weeks, starting at 32 weeks of age. RESULTS The administration of RN486 completely stopped disease progression, as determined by histologic and functional analyses of glomerular nephritis. The efficacy was associated with striking inhibition of B cell activation, as demonstrated by a significant reduction in CD69 expression in response to BCR crosslinking. RN486 markedly reduced the secretion of IgG anti-double-stranded DNA (anti-dsDNA) secretion, as determined by enzyme-linked immunosorbent and enzyme-linked immunospot assays. Flow cytometric analysis demonstrated depletion of CD138(high) B220(low) plasma cells in the spleen. RN486 inhibited secretion of IgG anti-dsDNA but not IgM anti-dsDNA, suggesting that pharmacologic blockade of BTK resembles the reported transgenic expression of low levels of endogenous BTK in B cells. In addition, RN486 may also impact the effector function of autoantibodies, as evidenced by a significant reduction in immune complex-mediated activation of human monocytes in vitro and down-regulation of the expression of macrophage-related and interferon-inducible genes in both the kidneys and spleens of treated mice. CONCLUSION Collectively, our data suggest that BTK inhibitors may simultaneously target autoantibody-producing and effector cells in SLE, thus constituting a promising therapeutic alternative for this disease.
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Yin X, Luistro L, Zhong H, Smith M, Nevins T, Schostack K, Hilton H, Lin TA, Truitt T, Biondi D, Wang X, Packman K, Rosinski J, Berkofsky-Fessler W, Tang JP, Pant S, Geho D, Vega-Harring S, DeMario M, Levitsky H, Simcox M. RG7212 Anti-TWEAK mAb Inhibits Tumor Growth through Inhibition of Tumor Cell Proliferation and Survival Signaling and by Enhancing the Host Antitumor Immune Response. Clin Cancer Res 2013; 19:5686-98. [DOI: 10.1158/1078-0432.ccr-13-0405] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Buro-Auriemma LJ, Salit J, Hackett NR, Walters MS, Strulovici-Barel Y, Staudt MR, Fuller J, Mahmoud M, Stevenson CS, Hilton H, Ho MWY, Crystal RG. Cigarette smoking induces small airway epithelial epigenetic changes with corresponding modulation of gene expression. Hum Mol Genet 2013; 22:4726-38. [PMID: 23842454 DOI: 10.1093/hmg/ddt326] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers for genome-wide DNA methylation changes compared with nonsmokers, and whether changes in SAE DNA methylation were linked to the transcriptional output of these cells. Using genome-wide methylation analysis of SAE DNA of nonsmokers and smokers, the data identified 204 unique genes differentially methylated in SAE DNA of smokers compared with nonsmokers, with 67% of the regions with differential methylation occurring within 2 kb of the transcriptional start site. Among the genes with differential methylation were those related to metabolism, transcription, signal transduction and transport. For the differentially methylated genes, 35 exhibited a correlation with gene expression, 54% with an inverse correlation of DNA methylation with gene expression and 46% a direct correlation. These observations provide evidence that cigarette smoking alters the DNA methylation patterning of the SAE and that, for some genes, these changes are associated with the smoking-related changes in gene expression.
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Grimes DT, Riley KL, Field S, Patel SH, Keynton J, Hilton H, Greenfield A, Norris DP. Pkd1l1 as a molecular sensor of fluid flow during the breaking of left-right symmetry. Cilia 2012. [PMCID: PMC3555852 DOI: 10.1186/2046-2530-1-s1-p68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Su F, Xu L, Higgings B, Yang H, Packman K, Hilton H, Schostack K, Bollag G, Tsai J, Habets G. 372 Preclinical Characterization of RG7256, a Potent and Selective BRAF Inhibitor with Differentiation From Vemurafenib. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)72170-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cockayne DA, Cheng DT, Waschki B, Sridhar S, Ravindran P, Hilton H, Kourteva G, Bitter H, Pillai SG, Visvanathan S, Müller KC, Holz O, Magnussen H, Watz H, Fine JS. Systemic biomarkers of neutrophilic inflammation, tissue injury and repair in COPD patients with differing levels of disease severity. PLoS One 2012; 7:e38629. [PMID: 22701684 PMCID: PMC3373533 DOI: 10.1371/journal.pone.0038629] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 05/08/2012] [Indexed: 12/21/2022] Open
Abstract
The identification and validation of biomarkers to support the assessment of novel therapeutics for COPD continues to be an important area of research. The aim of the current study was to identify systemic protein biomarkers correlated with measures of COPD severity, as well as specific protein signatures associated with comorbidities such as metabolic syndrome. 142 protein analytes were measured in serum of 140 patients with stable COPD, 15 smokers without COPD and 30 non-smoking controls. Seven analytes (sRAGE, EN-RAGE, NGAL, Fibrinogen, MPO, TGF-α and HB-EGF) showed significant differences between severe/very severe COPD, mild/moderate COPD, smoking and non-smoking control groups. Within the COPD subjects, univariate and multivariate analyses identified analytes significantly associated with FEV(1), FEV(1)/FVC and DLCO. Most notably, a set of 5 analytes (HB-EGF, Fibrinogen, MCP-4, sRAGE and Sortilin) predicted 21% of the variability in DLCO values. To determine common functions/pathways, analytes were clustered in a correlation network by similarity of expression profile. While analytes related to neutrophil function (EN-RAGE, NGAL, MPO) grouped together to form a cluster associated with FEV(1) related parameters, analytes related to the EGFR pathway (HB-EGF, TGF-α) formed another cluster associated with both DLCO and FEV(1) related parameters. Associations of Fibrinogen with DLCO and MPO with FEV(1)/FVC were stronger in patients without metabolic syndrome (r = -0.52, p = 0.005 and r = -0.61, p = 0.023, respectively) compared to patients with coexisting metabolic syndrome (r = -0.25, p = 0.47 and r = -0.15, p = 0.96, respectively), and may be driving overall associations in the general cohort. In summary, our study has identified known and novel serum protein biomarkers and has demonstrated specific associations with COPD disease severity, FEV(1), FEV(1)/FVC and DLCO. These data highlight systemic inflammatory pathways, neutrophil activation and epithelial tissue injury/repair processes as key pathways associated with COPD.
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Affiliation(s)
- Debra A. Cockayne
- Inflammation Disease Therapy Area, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Donavan T. Cheng
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Benjamin Waschki
- Pulmonary Research Institute at Hospital Grosshansdorf, Grosshansdorf, Germany
- Center for Pneumology and Thoracic Surgery, Hospital Grosshandorf, Grosshansdorf, Germany
| | - Sriram Sridhar
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Palanikumar Ravindran
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Holly Hilton
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Galina Kourteva
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Hans Bitter
- Translational Research Sciences, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Sreekumar G. Pillai
- Inflammation Disease Therapy Area, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Sudha Visvanathan
- Inflammation Disease Therapy Area, Hoffmann-La Roche, Nutley, New Jersey, United States of America
| | - Kai-Christian Müller
- Center for Pneumology and Thoracic Surgery, Hospital Grosshandorf, Grosshansdorf, Germany
| | - Olaf Holz
- Center for Pneumology and Thoracic Surgery, Hospital Grosshandorf, Grosshansdorf, Germany
| | - Helgo Magnussen
- Pulmonary Research Institute at Hospital Grosshansdorf, Grosshansdorf, Germany
| | - Henrik Watz
- Pulmonary Research Institute at Hospital Grosshansdorf, Grosshansdorf, Germany
| | - Jay S. Fine
- Inflammation Disease Therapy Area, Hoffmann-La Roche, Nutley, New Jersey, United States of America
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Daouti S, Filipovic Z, Stern A, Tardell C, Zhang X, Lucas-McGady D, Higgins B, Huang KS, Gubler U, Li Y, Berkofsky-Fessler W, Hang J, Samokhin G, Seidl A, Niu H, Cai J, Hilton H, Thomas M, Pamulapati C, Mundigl O, Hansen S, Heimbrook DC, Packman KE. Abstract 4827: Humanized hepsin neutralizing antibody RO5486055 inhibits tumor growth and leads to accumulation of hepsin substrate laminin-332. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepsin is overexpressed in prostate and other cancers where it is implicated in promoting tumor growth, invasion, and metastasis. To further our understanding of the role of hepsin in prostate and breast cancer, a fully humanized monoclonal antibody that recognizes human and cynomolgus hepsin has been developed. RO5486055 selectively binds to hepsin but not related type II transmembrane serine proteases, and neutralizes hepsin serine protease activity with an IC50 in the single digit nM range. In LNCaP prostate cancer cells, both shRNA knockdown of the hepsin gene and RO5486055 treatment cause a similar accumulation of the β3 chain of laminin-332, a known hepsin substrate. With ip administration in mice, RO5486055 demonstrates dose-dependent exposure and a long serum half-life of 168-406 hours. RO5486055 attenuates tumor growth in the LNCaP prostate cancer and T-47D breast cancer xenograft models, but not in the CRW-22Rv1 prostate or MCF-7 breast cancer xenografts. In these models, it has been shown that the level of the β3 chain of laminin-332 detected by Western blot analysis predicts sensitivity to RO5486055-mediated growth inhibition. Moreover, accumulation of the β3 chain during RO5486055 treatment correlates with antitumor activity. In 8/10 hepsin-expressing patient-derived prostate tumors, an inverse correlation between hepsin and β3 chain expression is observed. The β3 chain of laminin-332 may therefore be useful as both a predictive and response biomarker for anti-hepsin therapy. RO5486055-mediated tumor growth inhibition is enhanced by combination with the EGFR-targeted antibody cetuximab in LNCaP prostate cancer xenografts, and by combination with hormone withdrawal in T-47D breast cancer xenografts. These preclinical results suggest that hepsin-directed therapy could be effective in prostate and breast cancer treatment.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4827. doi:1538-7445.AM2012-4827
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ying Li
- 1Hoffmann-La Roche, Inc., Nutley, NJ
| | | | | | | | | | | | - James Cai
- 1Hoffmann-La Roche, Inc., Nutley, NJ
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Su F, Viros A, Milagre C, Trunzer K, Bollag G, Spleiss O, Reis-Filho JS, Kong X, Koya RC, Flaherty KT, Chapman PB, Kim MJ, Hayward R, Martin M, Yang H, Wang Q, Hilton H, Hang JS, Noe J, Lambros M, Geyer F, Dhomen N, Niculescu-Duvaz I, Zambon A, Niculescu-Duvaz D, Preece N, Robert L, Otte NJ, Mok S, Kee D, Ma Y, Zhang C, Habets G, Burton EA, Wong B, Nguyen H, Kockx M, Andries L, Lestini B, Nolop KB, Lee RJ, Joe AK, Troy JL, Gonzalez R, Hutson TE, Puzanov I, Chmielowski B, Springer CJ, McArthur GA, Sosman JA, Lo RS, Ribas A, Marais R. RAS mutations in cutaneous squamous-cell carcinomas in patients treated with BRAF inhibitors. N Engl J Med 2012; 366:207-15. [PMID: 22256804 PMCID: PMC3724537 DOI: 10.1056/nejmoa1105358] [Citation(s) in RCA: 798] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Cutaneous squamous-cell carcinomas and keratoacanthomas are common findings in patients treated with BRAF inhibitors. METHODS We performed a molecular analysis to identify oncogenic mutations (HRAS, KRAS, NRAS, CDKN2A, and TP53) in the lesions from patients treated with the BRAF inhibitor vemurafenib. An analysis of an independent validation set and functional studies with BRAF inhibitors in the presence of the prevalent RAS mutation was also performed. RESULTS Among 21 tumor samples, 13 had RAS mutations (12 in HRAS). In a validation set of 14 samples, 8 had RAS mutations (4 in HRAS). Thus, 60% (21 of 35) of the specimens harbored RAS mutations, the most prevalent being HRAS Q61L. Increased proliferation of HRAS Q61L-mutant cell lines exposed to vemurafenib was associated with mitogen-activated protein kinase (MAPK)-pathway signaling and activation of ERK-mediated transcription. In a mouse model of HRAS Q61L-mediated skin carcinogenesis, the vemurafenib analogue PLX4720 was not an initiator or a promoter of carcinogenesis but accelerated growth of the lesions harboring HRAS mutations, and this growth was blocked by concomitant treatment with a MEK inhibitor. CONCLUSIONS Mutations in RAS, particularly HRAS, are frequent in cutaneous squamous-cell carcinomas and keratoacanthomas that develop in patients treated with vemurafenib. The molecular mechanism is consistent with the paradoxical activation of MAPK signaling and leads to accelerated growth of these lesions. (Funded by Hoffmann-La Roche and others; ClinicalTrials.gov numbers, NCT00405587, NCT00949702, NCT01001299, and NCT01006980.).
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Affiliation(s)
- Fei Su
- Hoffmann-La Roche, Nutley, NJ, USA
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Mikaelian I, Buness A, Hirkaler G, Fernandes R, Coluccio D, Geng W, Visalli T, Bachynsky M, Berkofsky-Fessler W, Kanwal C, Hilton H, Nicklaus R, Hoflack JC, Dunn M, Sanders M, Giron M, Boyle B, Singer T, Dick LS. Serum cardiac troponin I concentrations transiently increase in rats given rosiglitazone. Toxicol Lett 2011; 201:110-5. [DOI: 10.1016/j.toxlet.2010.12.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 12/10/2010] [Accepted: 12/13/2010] [Indexed: 12/25/2022]
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Lin TA, Kourteva G, Hilton H, Li H, Tare NS, Carvajal V, Hang JS, Wei X, Renzetti LM. The mRNA level of Charcot-Leyden crystal protein/galectin-10 is a marker for CRTH2 activation in human whole blood in vitro. Biomarkers 2010; 15:646-54. [PMID: 20858065 DOI: 10.3109/1354750x.2010.511266] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
CRTH2 is one of the prostaglandin D₂ receptors and plays a proinflammatory role in allergic diseases. Gene expression markers in whole blood induced by CRTH2 activation have not previously been reported. Using microarray analyses of 54 675 genes, we revealed modest gene expression changes in human whole blood stimulated in vitro by a selective CRTH2 agonist, DK-PGD₂. Five genes were found to exhibit 1.5- to 2.6-fold changes in expression. The expression of Charcot-Leyden crystal protein/galectin-10 (CLC/Gal-10) in particular was consistently enhanced in human whole blood stimulated by DK-PGD₂, as confirmed by quantitative real-time polymerase chain reaction analyses. DK-PGD(2)-induced increases in blood CLC/Gal-10 mRNA levels were largely attenuated by the CRTH2 antagonist CAY10471.Thus, the DK-PGD₂-induced CLC/Gal-10 mRNA level can serve as a potential marker for monitoring pharmacodynamic effects of blood exposure to CRTH2 modulating agents.
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Affiliation(s)
- Tai-An Lin
- Pharma Research and Early Development, Hoffmann-La Roche Inc., Nutley, NJ 07110, USA.
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Hicks A, Kourteva G, Hilton H, Li H, Lin TA, Liao W, Li Y, Wei X, March T, Benson J, Renzetti LM. Cellular and molecular characterization of ozone-induced pulmonary inflammation in the Cynomolgus monkey. Inflammation 2010; 33:144-56. [PMID: 19941046 DOI: 10.1007/s10753-009-9168-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We investigated the cellular and molecular effects of ozone exposure in Cynomolgus monkeys. Thirty-six Cynomolgus monkeys were exposed to single or repeat ozone challenge. Pulmonary inflammation was assessed using bronchoalveolar lavage fluid (BAL) and histology. Gene expression profiling in lung and blood was performed. Ozone challenge evoked BAL cellular inflammation and increases in total protein, alkaline phosphatase and cytokines. Lung histology revealed cellular inflammation and epithelial necrosis. Gene expression profiling identified oxidative phosphorylation, immune response and cell adhesion pathways altered in response to ozone, with common and unique profiles in lung and blood. Lipocalin 2, CD177, the FK-506 and S100A8 binding proteins and ST-2 represent novel peripheral biomarkers of ozone toxicity. Repeat ozone challenge evoked reproducible inflammation but attenuated cell damage. These studies provide data on the molecular mechanisms and biomarker identification of ozone-evoked toxicity, and support the use of the Cynomolgus monkey as a model of human ozone challenge.
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15
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Mikaelian I, Buness A, de Vera-Mudry MC, Kanwal C, Coluccio D, Rasmussen E, Char HW, Carvajal V, Hilton H, Funk J, Hoflack JC, Fielden M, Herting F, Dunn M, Suter-Dick L. Primary endothelial damage is the mechanism of cardiotoxicity of tubulin-binding drugs. Toxicol Sci 2010; 117:144-51. [PMID: 20624997 DOI: 10.1093/toxsci/kfq189] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The use of tubulin binders (TBs) in the treatment of cancer often is associated with cardiotoxicity, the mechanism of which has not been elucidated. To test the hypothesis that interstitial cells of the myocardium are the primary target of TBs, we evaluated the acute effects of a single iv administration of three reference TBs: colchicine (0.2 and 2 mg/kg), vinblastine (0.5 and 3 mg/kg), and vincristine (0.1 and 1 mg/kg) 6 and 24 h after dosing. Mitotic arrest was identified at 24 h in all high-dose groups based on an increase in the number of mitotic figures in the interstitium coupled with a decrease in the number of Ki67-positive interstitial cells. Analysis of the myocardial transcriptomic data further supported G2/M cell cycle arrest 6 h after dosing with the high-dose groups of all three compounds. Apoptotic figures and an increase in the number of cleaved caspase 3-positive cells were identified at 6 and 24 h at the highest dose of each compound predominantly in interstitial cells, whereas a few cardiomyocytes were affected as well. Transcriptomic profiling of the myocardium further suggested that some of the affected interstitial cells were endothelial cells based on the upregulation of genes typically associated with vascular damage and downregulation of endothelial cell-specific molecule 1 and apelin. Taken together, these data identify endothelial cells of the myocardium as the primary target of the cardiotoxicity of TBs and identify cell cycle arrest as the mechanism of this toxicity.
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Affiliation(s)
- Igor Mikaelian
- Non-Clinical Safety, Bldg 100/310, Hoffmann-La Roche, Inc., Nutley, New Jersey 07110, USA.
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16
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Riley G, Baker J, Romero R, Hilton H, Blanco G. P34 Exploring IGFN1 in cardiac muscle. Neuromuscul Disord 2010. [DOI: 10.1016/s0960-8966(10)70049-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Luistro L, He W, Smith M, Packman K, Vilenchik M, Carvajal D, Roberts J, Cai J, Berkofsky-Fessler W, Hilton H, Linn M, Flohr A, Jakob-Røtne R, Jacobsen H, Glenn K, Heimbrook D, Boylan JF. Preclinical profile of a potent gamma-secretase inhibitor targeting notch signaling with in vivo efficacy and pharmacodynamic properties. Cancer Res 2009; 69:7672-80. [PMID: 19773430 DOI: 10.1158/0008-5472.can-09-1843] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Notch signaling is an area of great interest in oncology. RO4929097 is a potent and selective inhibitor of gamma-secretase, producing inhibitory activity of Notch signaling in tumor cells. The RO4929097 IC50 in cell-free and cellular assays is in the low nanomolar range with >100-fold selectivity with respect to 75 other proteins of various types (receptors, ion channels, and enzymes). RO4929097 inhibits Notch processing in tumor cells as measured by the reduction of intracellular Notch expression by Western blot. This leads to reduced expression of the Notch transcriptional target gene Hes1. RO4929097 does not block tumor cell proliferation or induce apoptosis but instead produces a less transformed, flattened, slower-growing phenotype. RO4929097 is active following oral dosing. Antitumor activity was shown in 7 of 8 xenografts tested on an intermittent or daily schedule in the absence of body weight loss or Notch-related toxicities. Importantly, efficacy is maintained after dosing is terminated. Angiogenesis reverse transcription-PCR array data show reduced expression of several key angiogenic genes. In addition, comparative microarray analysis suggests tumor cell differentiation as an additional mode of action. These preclinical results support evaluation of RO4929097 in clinical studies using an intermittent dosing schedule. A multicenter phase I dose escalation study in oncology is under way.
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Affiliation(s)
- Leopoldo Luistro
- Discovery Oncology, Discovery Chemistry, In Silico Sciences, Non-clinical Safety, Drug Metabolism, and RNA Therapeutics, Hoffmann-La Roche, Inc., Nutley, New Jersey, USA
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18
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Berkofsky-Fessler W, Nguyen TQ, Delmar P, Molnos J, Kanwal C, DePinto W, Rosinski J, McLoughlin P, Ritland S, DeMario M, Tobon K, Reidhaar-Olson JF, Rueger R, Hilton H. Preclinical biomarkers for a cyclin-dependent kinase inhibitor translate to candidate pharmacodynamic biomarkers in phase I patients. Mol Cancer Ther 2009; 8:2517-25. [PMID: 19755512 DOI: 10.1158/1535-7163.mct-09-0083] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A genomics-based approach to identify pharmacodynamic biomarkers was used for a cyclin-dependent kinase inhibitory drug. R547 is a potent cyclin-dependent kinase inhibitor with a potent antiproliferative effect at pharmacologically relevant doses and is currently in phase I clinical trials. Using preclinical data derived from microarray experiments, we identified pharmacodynamic biomarkers to test in blood samples from patients in clinical trials. These candidate biomarkers were chosen based on several criteria: relevance to the mechanism of action of R547, dose responsiveness in preclinical models, and measurable expression in blood samples. We identified 26 potential biomarkers of R547 action and tested their clinical validity in patient blood samples by quantitative real-time PCR analysis. Based on the results, eight genes (FLJ44342, CD86, EGR1, MKI67, CCNB1, JUN, HEXIM1, and PFAAP5) were selected as dose-responsive pharmacodynamic biomarkers for phase II clinical trials.
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19
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Affiliation(s)
- H. Hilton
- William R. Pritchard Veterinary Medical Teaching Hospital
| | - N. Pusterla
- Department of Medicine and Epidemiology; School of Veterinary Medicine; University of California, Davis; One Shields Avenue Davis CA 95161 USA
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20
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Hilton H, Galuppo L, Puchalski S, Johnson L, Robinson K, Mohr F, Maher O, Pusterla N. Successful Treatment of Invasive Pulmonary Aspergillosis in a Neonatal Foal. J Vet Intern Med 2009; 23:375-8. [DOI: 10.1111/j.1939-1676.2009.0272.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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21
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22
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Hilton H, Aleman M, Textor J, Nieto J, Pevec W. Ultrasound-Guided Balloon Thrombectomy for Treatment of Aorto-Iliac-Femoral Thrombosis in a Horse. J Vet Intern Med 2008; 22:679-83. [DOI: 10.1111/j.1939-1676.2008.0095.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Kourteva GT, Hilton H, Wei X, Li YL, March T, Benson J, Rosinski JA, Hicks A. Lung and Blood Gene Expression Profiles from Cynomolgus Monkeys Exposed to Ozone. FASEB J 2008. [DOI: 10.1096/fasebj.22.2_supplement.212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Mikaelian I, Coluccio D, Morgan KT, Johnson T, Ryan AL, Rasmussen E, Nicklaus R, Kanwal C, Hilton H, Frank K, Fritzky L, Wheeldon EB. Temporal Gene Expression Profiling Indicates Early Up-regulation of Interleukin-6 in Isoproterenol-induced Myocardial Necrosis in Rat. Toxicol Pathol 2008; 36:256-64. [DOI: 10.1177/0192623307312696] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Gene expression was evaluated in the myocardium of male Wistar rats after a single subcutaneous administration of 0.5 mg of isoproterenol, a β-adrenergic agonist that causes acute tachycardia with subsequent myocardial necrosis. Histology of the heart, clinical chemistry, and hematology were evaluated at 9 time points (0.5 hours to 14 days postinjection). Myocardial gene expression was evaluated at 4 time points (1 hour to 3 days). Contraction bands and loss of cross-striation were identified on phosphotungstic acid-hematoxylin-stained sections 0.5 hours postdosing. Plasma troponin I elevation was detected at 0.5 hours, peaked at 3 hours, and returned to baseline values at 3 days postdosing. Interleukin 6 (Il6) expression spiked at 1 to 3 hours and was followed by a short-lived, time-dependent dysregulation of its downstream targets. Concurrently and consistent with the kinetics of the histologic findings, many pathways indicative of necrosis/apoptosis (p38 mitogen-activated protein kinase [MAPK] signaling, NF-κB signaling) and adaptation to hypertension (PPAR signaling) were overrepresented at 3 hours. The 1-day and 3-day time points indicated an adaptive response, with down-regulation of the fatty acid metabolism pathway, up-regulation of the fetal gene program, and superimposed inflammation and repair at 3 days. These results suggest early involvement of Il6 in isoproterenol-induced myocardial necrosis and emphasize the value of early time points in transcriptomic studies.
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Affiliation(s)
- Igor Mikaelian
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Denise Coluccio
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | | | - Teona Johnson
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Amber L. Ryan
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Erik Rasmussen
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Rosemary Nicklaus
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Charu Kanwal
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Holly Hilton
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Karl Frank
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Luke Fritzky
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
| | - Eric B. Wheeldon
- Hoffmann-La Roche Inc., Non-Clinical Drug Safety, Nutley, New Jersey, USA and
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25
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Tovar C, Rosinski J, Filipovic Z, Higgins B, Kolinsky K, Hilton H, Zhao X, Vu BT, Qing W, Packman K, Myklebost O, Heimbrook DC, Vassilev LT. Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. Proc Natl Acad Sci U S A 2006; 103:1888-93. [PMID: 16443686 PMCID: PMC1413632 DOI: 10.1073/pnas.0507493103] [Citation(s) in RCA: 535] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The p53 tumor suppressor retains its wild-type conformation and transcriptional activity in half of all human tumors, and its activation may offer a therapeutic benefit. However, p53 function could be compromised by defective signaling in the p53 pathway. Using a small-molecule MDM2 antagonist, nutlin-3, to probe downstream p53 signaling we find that the cell-cycle arrest function of the p53 pathway is preserved in multiple tumor-derived cell lines expressing wild-type p53, but many have a reduced ability to undergo p53-dependent apoptosis. Gene array analysis revealed attenuated expression of multiple apoptosis-related genes. Cancer cells with mdm2 gene amplification were most sensitive to nutlin-3 in vitro and in vivo, suggesting that MDM2 overexpression may be the only abnormality in the p53 pathway of these cells. Nutlin-3 also showed good efficacy against tumors with normal MDM2 expression, suggesting that many of the patients with wild-type p53 tumors may benefit from antagonists of the p53-MDM2 interaction.
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Affiliation(s)
- Christian Tovar
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - James Rosinski
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Zoran Filipovic
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Brian Higgins
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Kenneth Kolinsky
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Holly Hilton
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Xiaolan Zhao
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Binh T. Vu
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Weiguo Qing
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Kathryn Packman
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
| | - Ola Myklebost
- Institute for Cancer Research, Norwegian
Radium Hospital, 0310 Oslo, Norway
| | | | - Lyubomir T. Vassilev
- *Roche Research Center, Hoffmann-La Roche Inc., Nutley, NJ
07110; and
- To whom correspondence should be
addressed. E-mail:
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26
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Türeci O, Bian H, Nestle FO, Raddrizzani L, Rosinski JA, Tassis A, Hilton H, Walstead M, Sahin U, Hammer J. Cascades of transcriptional induction during dendritic cell maturation revealed by genome-wide expression analysis. FASEB J 2003; 17:836-47. [PMID: 12724343 DOI: 10.1096/fj.02-0724com] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dendritic cells (DC) are central regulators of immunity. Signal-induced maturation of DCs is assumed to be the starting point for specific immune responses. To further understand this process, we analyzed the alteration of transcript profiles along the time course of CD40 ligand-induced maturation of human myeloid DCs by Affymetrix GeneChip microarrays covering >6800 genes. Besides rediscovery of genes already described as associated with DC maturation proving reliability of the methods used, we identified clusterin as novel maturation marker. Looking across the time course, we observed synchronized kinetics of distinct functional groups of molecules whose temporal coregulation underscores known cellular events during dendritic cell maturation. For example, an early-peaking wave of inflammatory chemokines was followed by a sustained increase of constitutive chemokines and accompanied by slow but continuous induction of survival proteins. After an immediate but transient induction of cytokine-responsive transcripts, there was an increased expression of a group of genes involved in not only the regulation of cytokine effects, but also of transcription in general. Our results demonstrate that microarray studies along time courses combined with real-time PCR not only discover new marker molecules with functional implications, but also dissect the molecular kinetics of biological processes identifying complex pathways of regulation.
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Affiliation(s)
- Ozlem Türeci
- III. Department of Internal Medicine, University of Mainz, Germany.
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27
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Türeci O, Ding J, Hilton H, Bian H, Ohkawa H, Braxenthaler M, Seitz G, Raddrizzani L, Friess H, Buchler M, Sahin U, Hammer J. Computational dissection of tissue contamination for identification of colon cancer-specific expression profiles. FASEB J 2003; 17:376-85. [PMID: 12631577 DOI: 10.1096/fj.02-0478com] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Microarray profiles of bulk tumor tissues reflect gene expression corresponding to malignant cells as well as to many different types of contaminating normal cells. In this report, we assess the feasibility of querying baseline multitissue transcriptome databases to dissect disease-specific genes. Using colon cancer as a model tumor, we show that the application of Boolean operators (AND, OR, BUTNOT) for database searches leads to genes with expression patterns of interest. The BUTNOT operator for example allows the assignment of "expression signatures" to normal tissue specimens. These expression signatures were then used to computationally identify contaminating cells within conventionally dissected tissue specimens. The combination of several logic operators together with an expression database based on multiple human tissue specimens can resolve the problem of tissue contamination, revealing novel cancer-specific gene expression. Several markers, previously not known to be colon cancer associated, are provided.
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Affiliation(s)
- Ozlem Türeci
- III. Medizinische Klinik und Poliklinik, Johannes Gutenberg Universität Mainz, D-55131 Mainz, Germany.
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Abstract
The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa-maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged approximately 700, 000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.
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Affiliation(s)
- H Hilton
- Department of Plant Sciences and Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, New Jersey 08903, USA
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29
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Abstract
Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize-maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians-but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length.
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Affiliation(s)
- A Eyre-Walker
- Department of Plant Sciences and Center for Theoretical and Applied Genetics, Rutgers University, New Brunswick, NJ 08902, USA
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Abstract
The virilis phylad of the Drosophila virilis group consists of five closely related taxa: D. virilis, D. lummei, D. novamexicana, D. americana americana and D. americana texana. DNA sequences from a 2.1-kb pair portion of the period locus were generated in four to eight individuals from each of the five taxa. We found evidence of recombination and high levels of variation within species. We found no evidence of recent natural selection. Surprisingly there was no evidence of divergence between D. a. americana and D. a. texana, and they collectively appear to have had a large historical effective population size. The ranges of these two taxa overlap in a large hybrid zone that has been delineated in the eastern U.S. on the basis of the geographic pattern of a chromosomal fusion. Also surprisingly, D. novamexicana appears to consist of two distinct groups each with low population size and no gene flow between them.
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Affiliation(s)
- H Hilton
- Department of Biological Sciences, Rutgers University, Piscataway, NJ 08855-1059, USA.
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Hilton H, Kliman RM, Hey J. Using Hitchhiking Genes to Study Adaptation and Divergence During Speciation Within the Drosophila melanogaster Species Complex. Evolution 1994. [DOI: 10.2307/2410516] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Glenn RE, Colbert J, Gimbel J, Hilton H, Lamansky G, Rushlo J, Schiffman E. University of Iowa's study of retail dentistry raises some concerns. Dent Econ 1982; 72:32-6. [PMID: 6951747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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