1
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Churchill J, Sachdeva A, Jones C, Issa A, Fankhauser C, Hudson A, Tran A, Oliveira P, Johnson H, Lau M, Parnham A, Sangar V. P16 status is an independent predictor of overall survival in metastatic penile cancer in a large contemporary cohort. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00680-2] [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: 02/12/2023]
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2
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Adegboye O, Churchill J, Moorjani J, Johnson H, Capper S, Booker J, Parnham A, Lau M, Sangar V, Faivre-Finn C. Electronic patient-reported outcome measures (ePROMs) - ready for prime time in penile cancer care? Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00692-9] [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: 02/12/2023]
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3
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Lee E, Antonelli L, Issa A, James C, Oliveria P, Lau M, Sangar V, Parnham A, Fankhauser C. Risk of local recurrence in men with Penile Intraepithelial Neoplasia (PeIN) in the surgical margin after penile sparing surgery. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)02459-4] [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: 11/11/2022] Open
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4
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Peters N, Scott J, Issa A, Fankhauser C, Lee E, Churchill J, Oliveria P, Tran A, Lau M, Parnham A, Sangar V, Graham D. 1311P Penile cancer in North-West England: A 5-year analysis of epidemiology, risk factors and outcomes in a supraregional centre. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1444] [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: 11/30/2022] Open
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5
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Yu KH, Park J, Mittal A, Abou-Alfa GK, Dika IE, Epstein AS, Ilson DH, Kelsen DP, Ku GY, Li J, Park W, Varghese AM, Chou JFL, Capanu M, Cooper B, Bartlett A, McCarthy D, Sangar V, McCarthy B, O’Reilly EM. Circulating tumor and invasive cell expression profiling predicts effective therapy in pancreatic cancer. Cancer 2022; 128:2958-2966. [PMID: 35647938 PMCID: PMC10131181 DOI: 10.1002/cncr.34269] [Citation(s) in RCA: 1] [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: 03/02/2022] [Revised: 04/06/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Pancreatic adenocarcinoma (PDAC) remains a refractory disease; however, modern cytotoxic chemotherapeutics can induce tumor regression and extend life. A blood-based, pharmacogenomic, chemosensitivity assay using gene expression profiling of circulating tumor and invasive cells (CTICs) to predict treatment response was previously developed. The combination regimen of 5-fluorouracil, leucovorin, irinotecan, and oxaliplatin (FOLFIRINOX) and gemcitabine/nab-paclitaxel (G/nab-P) are established frontline approaches for treating advanced PDAC; however, there are no validated biomarkers for treatment selection. A similar unmet need exists for choosing second-line therapy. METHODS The chemosensitivity assay was evaluated in metastatic PDAC patients presenting for frontline treatment. A prospective study enrolled patients (n = 70) before receiving either FOLFIRINOX or G/nab-P at a 1:1 ratio. Six milliliters of peripheral blood was collected at baseline and at time of disease progression. CTICs were isolated, gene-expression profiling was performed, and the assay was used to predict effective and ineffective chemotherapeutic agents. Treating physicians were blinded to the assay prediction results. RESULTS Patients receiving an effective regimen as predicted by the chemosensitivity assay experienced significantly longer median progression-free survival (mPFS; 7.8 months vs. 4.2 months; hazard ratio [HR], 0.35; p = .0002) and median overall survival (mOS; 21.0 months vs. 9.7 months; HR, 0.40; p = .005), compared with an ineffective regimen. Assay prediction for effective second-line therapy was explored. The entire study cohort experienced favorable outcomes compared with historical controls, 7.1-month mPFS and 12.3-month mOS. CONCLUSIONS Chemosensitivity assay profiling is a promising tool for guiding therapy in advanced PDAC. Further prospective validation is under way (clinicaltrials.gov NCT03033927).
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Affiliation(s)
- Kenneth H. Yu
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Jennifer Park
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Avni Mittal
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ghassan K. Abou-Alfa
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Imane El Dika
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Andrew S. Epstein
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - David H. Ilson
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - David P. Kelsen
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Geoffrey Y. Ku
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Jia Li
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Wungki Park
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Anna M. Varghese
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | | | | | | | | | | | | | - Eileen M. O’Reilly
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
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Swinton M, Mariam N, Tan J, Afferi L, Lonati C, Moshini M, Lau M, Ramani V, Sangar V, Clarke N, Mistry H, Elumalai T, Hoskin P, Choudhury A. PD-0418 Resect or Preserve? Comparing treatment strategies in clinically node positive bladder cancer. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02853-5] [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: 11/28/2022]
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7
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Lee E, Issa A, Oliveira P, Lau M, Sangar V, Parnham M, Fankhauser C. Diagnostic accuracy of dynamic sentinel lymph node biopsy for penile cancer in men with non-palpable and palpable inguinal lymph nodes. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00763-1] [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: 11/16/2022]
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de Vries H, Lee H, Lam W, Djajadiningrat R, Ottenhof S, Roussel E, Kroon B, de Jong I, Oliveira P, Alnajjar H, Albersen M, Muneer A, Sangar V, Parnham A, Ayres B, Watkin N, Horenblas S, Stuiver M, Brouwer O. Clinicopathologic predictors of finding additional inguinal lymph node metastases in penile cancer patients following positive dynamic sentinel node biopsy: a European multicentre evaluation. BJU Int 2021; 130:126-132. [DOI: 10.1111/bju.15678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/24/2021] [Accepted: 12/11/2021] [Indexed: 11/28/2022]
Affiliation(s)
- H.M. de Vries
- Department of Urology Netherlands Cancer Institute Amsterdam Netherlands
| | - H.J. Lee
- Department of Urology St. George University Hospital NHS foundation trust London United Kingdom
| | - W. Lam
- Department of Urology St. George University Hospital NHS foundation trust London United Kingdom
| | | | - S.R. Ottenhof
- Department of Urology Netherlands Cancer Institute Amsterdam Netherlands
| | - E. Roussel
- Department of Urology University Hospital Leuven Leuven Belgium
| | - B.K. Kroon
- Department of Urology Rijnstate Hospital Arnhem Netherlands
| | - I.J. de Jong
- Department of Urology University Medical Centre Groningen Groningen Netherlands
| | - P. Oliveira
- Department of Pathology The Christie NHS foundation trust Manchester United Kingdom
| | - H.M. Alnajjar
- Department of Urology and NIHR Biomedical Research Centre University College London Hospitals NHS foundation trust London United Kingdom
| | - M. Albersen
- Department of Urology University Hospital Leuven Leuven Belgium
| | - A. Muneer
- Department of Urology and NIHR Biomedical Research Centre University College London Hospitals NHS foundation trust London United Kingdom
- Division of Surgery and Interventional Science University College London Hospitals NHS foundation trust London United Kingdom
| | - V. Sangar
- Department of Urology The Christie NHS foundation trust London United Kingdom
- Manchester Academic Health Sciences Centre University of Manchester United Kingdom
| | - A. Parnham
- Department of Urology The Christie NHS foundation trust London United Kingdom
| | - B. Ayres
- Department of Urology St. George University Hospital NHS foundation trust London United Kingdom
| | - N. Watkin
- Department of Urology St. George University Hospital NHS foundation trust London United Kingdom
| | - S. Horenblas
- Department of Urology Netherlands Cancer Institute Amsterdam Netherlands
| | - M.M. Stuiver
- Department of Clinical Epidemiology Amsterdam University Medical Centres location AMC Amsterdam Netherlands
| | - O.R. Brouwer
- Department of Urology Netherlands Cancer Institute Amsterdam Netherlands
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Fankhauser C, M. De Vries H, Roussel E, Jakobsen J, Issa A, Lee E, Schifano N, Alnajjar H, Castiglione F, Pedro O, Lau M, Parnham A, Maarten A, Watkin N, Muneer A, Ayres B, Brouwer O, Sangar V. Risk factors for inguinal lymph node metastases in men with T1G2 penile cancer: a multi centre collaborative study. EUR UROL SUPPL 2021. [DOI: 10.1016/s2666-1683(21)03080-9] [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: 12/01/2022] Open
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De Vries H, Lee H, Lam W, Djajadiningrat R, Ottenhof S, Roussel E, Kroon B, Jong I, Oliveira P, Alnajjar H, Albersen M, Muneer A, Sangar V, Parnham A, Ayres B, Watkin N, Horenblas S, Stuiver M, Brouwer O. Developing a predictive model for additional lymph node metastases at inguinal lymph node dissection following positive sentinel node biopsy for penile cancer: An European multicentre evaluation. EUR UROL SUPPL 2021. [DOI: 10.1016/s2666-1683(21)03081-0] [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: 11/29/2022] Open
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11
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Fankhauser C, Issa A, Lee E, Oing C, Oliveira P, Parnham A, Oates J, Sangar V, Gulamhusein A, Clarke N. Radical hemiscrotectomy and en-bloc orchidectomy: Surgical technique, perioperative and oncologic outcomes of a supra-regional UK referral centre. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01615-8] [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: 10/20/2022]
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12
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De Vries H, Lee H, Roussel E, Kroon B, De Jong I, Albersen M, Muneer A, Sangar V, Parnham A, Ayres B, Watkin N, Horenblas S, Stuiver M, Brouwer O. Factors associated with additional tumour-bearing lymph nodes at completion ILND after positive DSNB for penile cancer staging: A European multicentre evaluation. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01058-7] [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: 11/29/2022]
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13
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Grogg J, Fronzaroli J, Bode P, Oliveira P, Lorch A, Beyer J, Eberli D, Sangar V, Hermanns T, Clarke N, Fankhauser C. Clinicopathological characteristics and outcomes in men with mesothelioma of the tunica vaginalis testis: Analysis of published case series data. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)36274-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Ayres B, Parnham A, Albersen M, Muneer A, Meyer C, Mancini M, Langenhuijsen H, Watkin N, Sangar V. What is the extent of variation in inguinal lymph node management by penile cancer specialists? An eUROGEN survey. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)32756-7] [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: 10/23/2022] Open
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15
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Baik J, Lee T, Oates J, Aziz O, Wilson M, Shenjere P, Shanks J, Oliveira P, Wylie J, Leahy M, Sangar V, Clarke N. Surgical outcomes of adult patients with abdominopelvic sarcomas. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)32944-x] [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: 11/26/2022] Open
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Baloni P, Sangar V, Yurkovich JT, Robinson M, Taylor S, Karbowski CM, Hamadeh HK, He YD, Price ND. Genome-scale metabolic model of the rat liver predicts effects of diet restriction. Sci Rep 2019; 9:9807. [PMID: 31285465 PMCID: PMC6614411 DOI: 10.1038/s41598-019-46245-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/25/2019] [Indexed: 12/19/2022] Open
Abstract
Mapping network analysis in cells and tissues can provide insights into metabolic adaptations to changes in external environment, pathological conditions, and nutrient deprivation. Here, we reconstructed a genome-scale metabolic network of the rat liver that will allow for exploration of systems-level physiology. The resulting in silico model (iRatLiver) contains 1,882 reactions, 1,448 metabolites, and 994 metabolic genes. We then used this model to characterize the response of the liver’s energy metabolism to a controlled perturbation in diet. Transcriptomics data were collected from the livers of Sprague Dawley rats at 4 or 14 days of being subjected to 15%, 30%, or 60% diet restriction. These data were integrated with the iRatLiver model to generate condition-specific metabolic models, allowing us to explore network differences under each condition. We observed different pathway usage between early and late time points. Network analysis identified several highly connected “hub” genes (Pklr, Hadha, Tkt, Pgm1, Tpi1, and Eno3) that showed differing trends between early and late time points. Taken together, our results suggest that the liver’s response varied with short- and long-term diet restriction. More broadly, we anticipate that the iRatLiver model can be exploited further to study metabolic changes in the liver under other conditions such as drug treatment, infection, and disease.
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Affiliation(s)
- Priyanka Baloni
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Vineet Sangar
- Institute for Systems Biology, Seattle, WA, United States of America
| | - James T Yurkovich
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Max Robinson
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Scott Taylor
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Christine M Karbowski
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Hisham K Hamadeh
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America.,Genmab, Princeton, NJ, United States of America
| | - Yudong D He
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, United States of America.
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18
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Chio IIC, Jafarnejad SM, Ponz-Sarvise M, Rivera K, Öhlund D, Sangar V, Wright K, Fillippi D, Hao Y, Wilkinson JE, Tiriac H, Hammell M, Schmidt E, Park Y, Pappin D, Sonenberg N, Tuveson D. Abstract PR04: Nrf2 promotes mRNA translation in pancreatic cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.panca16-pr04] [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
Pancreatic Ductal Adenocarcinoma (PDA) is the 4th leading cause of cancer death in the USA. Lethality of PDA is largely ascribed to poor drug delivery and augmented cell survival pathways. We previously found that oncogenic Kras expression induced an important regulator of redox control, the transcription factor Nuclear factor erythroid-derived 2-like 2, Nfe2l2/Nrf2. Expression of Nrf2-dependent proteins is critical for neutralizing or eliminating toxicants and to maintain cellular redox homeostasis. The NRF2 transcriptional program is believed to protect neoplastic cells from oxidative stress, and may confer the resistance of these cells to chemotherapy. Thus, antagonizing NRF2 effector functions represents an attractive therapeutic strategy.
Activation of Nrf2 leads to alterations in cellular redox levels, to which cysteine residues are particularly reactive. Redox modifications on reactive cysteines may regulate the activity of their corresponding protein, rendering these proteins as candidate redox-sensitive effectors of NRF2. To decipher changes in the cysteine proteome, we devised a highly sensitive proteomic method that combines a selectively cleavable cysteine-reactive affinity tag to enrich for and identify reduced cysteines, with amine-reactive isobaric tags for relative and absolute quantification of the total proteome. Using this approach, we identified cysteines on translational regulatory proteins to be explicitly oxidized in Nrf2-deficient, Kras mutant cells. Both cap- dependent and -independent mRNA translation was impaired in Nrf2-deficient pancreatic cancer cells, and can be rescued upon supplementation with antioxidants. In addition to stimulating translation through maintaining the reduced state of specific cysteine residues, redox regulation by Nrf2 also promotes EGFR autocrine signaling through AKT in KRAS mutant cells to fuel cap-dependent translation initiation. These functions converge to promote global protein synthesis in PDA. As a consequence, combined inhibition of AKT signaling and glutathione synthesis hampered the survival of PDA cells in vitro and in vivo, presenting a new opportunity for therapeutic intervention.
This abstract is also being presented as Poster B02
Citation Format: Iok In Christine Chio, Seyed Mehdi Jafarnejad, Mariano Ponz-Sarvise, Keith Rivera, Daniel Öhlund, Vineet Sangar, Kevin Wright, Dea Fillippi, Yuan Hao, John Erby Wilkinson, Herve Tiriac, Molly Hammell, Edward Schmidt, Youngkyu Park, Darryl Pappin, Nahum Sonenberg, David Tuveson.{Authors}. Nrf2 promotes mRNA translation in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr PR04.
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Affiliation(s)
| | | | | | - Keith Rivera
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Daniel Öhlund
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Kevin Wright
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Dea Fillippi
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Yuan Hao
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Herve Tiriac
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Molly Hammell
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - Youngkyu Park
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | - Darryl Pappin
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
| | | | - David Tuveson
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY,
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19
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Chio IIC, Jafarnejad SM, Ponz-Sarvise M, Park Y, Rivera K, Palm W, Wilson J, Sangar V, Hao Y, Öhlund D, Wright K, Filippini D, Lee EJ, Da Silva B, Schoepfer C, Wilkinson JE, Buscaglia JM, DeNicola GM, Tiriac H, Hammell M, Crawford HC, Schmidt EE, Thompson CB, Pappin DJ, Sonenberg N, Tuveson DA. NRF2 Promotes Tumor Maintenance by Modulating mRNA Translation in Pancreatic Cancer. Cell 2016; 166:963-976. [PMID: 27477511 DOI: 10.1016/j.cell.2016.06.056] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 05/05/2016] [Accepted: 06/29/2016] [Indexed: 02/07/2023]
Abstract
Pancreatic cancer is a deadly malignancy that lacks effective therapeutics. We previously reported that oncogenic Kras induced the redox master regulator Nfe2l2/Nrf2 to stimulate pancreatic and lung cancer initiation. Here, we show that NRF2 is necessary to maintain pancreatic cancer proliferation by regulating mRNA translation. Specifically, loss of NRF2 led to defects in autocrine epidermal growth factor receptor (EGFR) signaling and oxidation of specific translational regulatory proteins, resulting in impaired cap-dependent and cap-independent mRNA translation in pancreatic cancer cells. Combined targeting of the EGFR effector AKT and the glutathione antioxidant pathway mimicked Nrf2 ablation to potently inhibit pancreatic cancer ex vivo and in vivo, representing a promising synthetic lethal strategy for treating the disease.
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Affiliation(s)
- Iok In Christine Chio
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Seyed Mehdi Jafarnejad
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Mariano Ponz-Sarvise
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Youngkyu Park
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Keith Rivera
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Wilhelm Palm
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John Wilson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Vineet Sangar
- Institute of Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA
| | - Yuan Hao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Daniel Öhlund
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kevin Wright
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dea Filippini
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Eun Jung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Brandon Da Silva
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Christina Schoepfer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John Erby Wilkinson
- Departments of Molecular & Integrative Physiology and Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan M Buscaglia
- Division of Gastroenterology, Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Gina M DeNicola
- Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10021, USA
| | - Herve Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Howard C Crawford
- Departments of Molecular & Integrative Physiology and Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Edward E Schmidt
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59718, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Darryl J Pappin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY 11724, USA.
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Tian Q, Sangar V, Price ND. Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research. Mol Cell Proteomics 2016; 15:362-7. [PMID: 26407994 PMCID: PMC4739660 DOI: 10.1074/mcp.r115.053884] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/22/2015] [Indexed: 01/11/2023] Open
Abstract
High-throughput technologies present immense opportunities to characterize brain cancer biology at a systems level. However, proteomic studies of brain cancers are still relatively scarce. Here we discuss the latest proteomic technologies, their application to profiling and quantitation of brain proteomes and how we expect these technologies will be applied to study brain cancer proteomes in the future. Mass spectrometry based proteomics with increased specificity, coverage and throughput will be pervasive in proteomics investigations of brain. Generated data needs to be captured by the curation of databases, and application of creative data analysis strategies is needed to provide meaningful insights into brain functions and associated pathologies. Overall, proteomics applications to brain cancers are in the earliest stages and the expanded use of these technologies holds enormous potential to improve our understanding of brain functions and pathologies.
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Affiliation(s)
- Qiang Tian
- From the ‡Institute for Systems Biology, Seattle, WA 98109
| | - Vineet Sangar
- From the ‡Institute for Systems Biology, Seattle, WA 98109
| | - Nathan D Price
- From the ‡Institute for Systems Biology, Seattle, WA 98109
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Sangar V, Earls JC, Yu KH. Gene-pair classifier in circulating tumor and invasive cells to predict pharmacological response. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.3_suppl.279] [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: 11/20/2022] Open
Abstract
279 Background: Improved diagnostic tools for predicting treatment response and prognosis are needed in pancreatic adenocarcinoma (PDAC), the fourth leading cause of cancer mortality in the U.S. In this study, we explored the diagnostic potential of gene expression signatures from circulating tumorigenic and invasive cells (CTICs). Methods: We recruited 50 PDAC patients to participate in our IRB-approved study. 35 patients were evaluable for response to chemotherapy treatment. 10 mL of peripheral blood was collected from patients with unresectable PDAC prior to initiating chemotherapy and again at disease progression. Clinical data was prospectively collected. Blood was processed for isolation of circulating TP cells (Vita-Cap, Vitatex Inc.), total RNA was extracted and gene-expression analysis was performed (Affymetrix GeneChipHuman Genome U133 Plus 2.0 array). Using time to progression (TTP) as a threshold, twenty-five patients with TTP>120 days were labeled as responders and ten patients with TTP<=120 days were labeled as non-responders. Results: Network analysis of expression profiles revealed that the PTC1 and CDC25 pathways were significantly different in responders and non-responders. Both pathways contribute towards tumorigenesis, and enhance tumor resistance to therapeutic intervention in PDAC. Further investigation into these pathways revealed that the relative expression of ATM and XPO1 was the most accurate classifier (76% accuracy, Specificity = 80% and Sensitivity = 72%). Additionally, 18 out of 20 patients of the patients with ATM < XPO1expression pattern responded to treatment. Mechanistically, this observation suggests that ATM may be counteracting DNA damage inflicted by chemotherapy during G2/M transition of the cell cycle. Conclusions: Computational analysis of gene expression data from CTICs can reliably predict pharmacological response. Pathway analysis identifies gene interaction networks relevant to tumorigenesis and drug response. Data will be updated with longitudinal analysis of treatment response in both responders and non-responders to the treatment.
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Affiliation(s)
| | | | - Kenneth H. Yu
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
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22
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White ID, Wilson J, Aslet P, Baxter AB, Birtle A, Challacombe B, Coe J, Grover L, Payne H, Russell S, Sangar V, Van As N, Kirby M. Development of UK guidance on the management of erectile dysfunction resulting from radical radiotherapy and androgen deprivation therapy for prostate cancer. Int J Clin Pract 2015; 69:106-23. [PMID: 25283500 PMCID: PMC4309408 DOI: 10.1111/ijcp.12512] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
AIM To develop a management strategy (rehabilitation programme) for erectile dysfunction (ED) after radiotherapy (RT) or androgen deprivation therapy (ADT) for prostate cancer that is suitable for use in a UK NHS healthcare context. METHODS PubMed literature searches of ED management in this patient group together with a survey of 28 experts in the management of treatment-induced ED from across the UK were conducted. RESULTS Data from 19 articles and completed questionnaires were collated. The findings discussed in this article confirm that RT/ADT for prostate cancer can significantly impair erectile function. While many men achieve erections through PDE5-I use, others need combined management incorporating exercise and lifestyle modifications, psychosexual counselling and other erectile aids. This article offers a comprehensive treatment algorithm to manage patients with ED associated with RT/ADT. CONCLUSION Based on published research literature and survey analysis, recommendations are proposed for the standardisation of management strategies employed for ED after RT/ADT. In addition to implementing the algorithm, understanding the rationale for the type and timing of ED management strategies is crucial for clinicians, men and their partners.
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Affiliation(s)
- I D White
- Urology Unit, The Royal Marsden NHS Foundation Trust, London & Sutton, UK
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Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND. Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Mol Cell Proteomics 2014; 13:2618-31. [PMID: 24997998 DOI: 10.1074/mcp.m114.040428] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Glioblastoma multiforme is a highly invasive and aggressive brain tumor with an invariably poor prognosis. The overexpression of epidermal growth factor receptor (EGFR) is a primary influencer of invasion and proliferation in tumor cells and the constitutively active EGFRvIII mutant, found in 30-65% of Glioblastoma multiforme, confers more aggressive invasion. To better understand how EGFR contributes to tumor aggressiveness, we investigated the effect of EGFR on the secreted levels of 65 rationally selected proteins involved in invasion. We employed selected reaction monitoring targeted mass spectrometry using stable isotope labeled internal peptide standards to quantity proteins in the secretome from five GBM (U87) isogenic cell lines in which EGFR, EGFRvIII, and/or PTEN were expressed. Our results show that cell lines with EGFR overexpression and constitutive EGFRvIII expression differ remarkably in the expression profiles for both secreted and intracellular signaling proteins, and alterations in EGFR signaling result in reproducible changes in concentrations of secreted proteins. Furthermore, the EGFRvIII-expressing mutant cell line secretes the majority of the selected invasion-promoting proteins at higher levels than other cell lines tested. Additionally, the intracellular and extracellular protein measurements indicate elevated oxidative stress in the EGFRvIII-expressing cell line. In conclusion, the results of our study demonstrate that EGFR signaling has a significant effect on the levels of secreted invasion-promoting proteins, likely contributing to the aggressiveness of Glioblastoma multiforme. Further characterization of these proteins may provide candidates for new therapeutic strategies and targets as well as biomarkers for this aggressive disease.
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Affiliation(s)
- Vineet Sangar
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Cory C Funk
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Ulrike Kusebauch
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - David S Campbell
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Robert L Moritz
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
| | - Nathan D Price
- From the ‡Institute for Systems Biology, 401 Terry Ave N, Seattle, Washington, 98109
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Yu KH, Sangar V, Ricigliano M, Hidalgo M, O'Reilly EM, Abou-Alfa GK, Lowery MA, Crotty JF, Gary K, Cooper B, Lapidus RG, Sadowska M. Pharmacogenomic modeling of pancreatic cancer (PDAC) for prediction of chemotherapy response and resistance in second-line treatment setting. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.4130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kenneth H. Yu
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | - Manuel Hidalgo
- START Madrid, Centro Integral Oncológico Clara Campal, Hospital Universitario Norte Sanchinarro, Madrid, Spain
| | | | - Ghassan K. Abou-Alfa
- Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | - Kristen Gary
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Brandon Cooper
- University of Maryland Greenebaum Cancer Center, Baltimore, MD
| | - Rena G. Lapidus
- University of Maryland Greenebaum Cancer Center, Baltimore, MD
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25
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Kirby MG, White ID, Butcher J, Challacombe B, Coe J, Grover L, Hegarty P, Jackson G, Lowndes A, Payne H, Rees J, Sangar V, Thompson A. Development of UK recommendations on treatment for post-surgical erectile dysfunction. Int J Clin Pract 2014; 68:590-608. [PMID: 24188207 PMCID: PMC4279873 DOI: 10.1111/ijcp.12338] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
AIM To develop a management strategy (rehabilitation programme) for postsurgical erectile dysfunction (ED) among men experiencing ED associated with treatment of prostate, bladder or rectal cancer that is suitable for use in a UK NHS healthcare context. METHODS PubMed literature searches of ED management together with a survey of 13 experts in the management of ED from across the UK were conducted. RESULTS Data from 37 articles and completed questionnaires were collated. The results discussed in this study demonstrate improved objective and subjective clinical outcomes for physical parameters, sexual satisfaction, and rates of both spontaneous erections and those associated with ED treatment strategies. CONCLUSION Based on the literature and survey analysis, recommendations are proposed for the standardisation of management strategies employed for postsurgical ED.
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Affiliation(s)
- M G Kirby
- The Prostate Centre, London and the University of Hertfordshire, London, UK
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26
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Randhawa M, Sangar V, Tucker-Samaras S, Southall M. Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway. PLoS One 2014; 9:e90367. [PMID: 24603693 PMCID: PMC3946127 DOI: 10.1371/journal.pone.0090367] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/31/2014] [Indexed: 11/18/2022] Open
Abstract
Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin.
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Affiliation(s)
- Manpreet Randhawa
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
- * E-mail:
| | - Vineet Sangar
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Samantha Tucker-Samaras
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
| | - Michael Southall
- Johnson & Johnson Skin Research Center, CPPW, a Division of Johnson & Johnson Consumer Companies, Inc., Skillman, New Jersey, United States of America
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Bai JPF, Fontana RJ, Price ND, Sangar V. Systems pharmacology modeling: an approach to improving drug safety. Biopharm Drug Dispos 2013; 35:1-14. [PMID: 24136298 DOI: 10.1002/bdd.1871] [Citation(s) in RCA: 19] [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] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 12/15/2022]
Abstract
Advances in systems biology in conjunction with the expansion in knowledge of drug effects and diseases present an unprecedented opportunity to extend traditional pharmacokinetic and pharmacodynamic modeling/analysis to conduct systems pharmacology modeling. Many drugs that cause liver injury and myopathies have been studied extensively. Mitochondrion-centric systems pharmacology modeling is important since drug toxicity across a large number of pharmacological classes converges to mitochondrial injury and death. Approaches to systems pharmacology modeling of drug effects need to consider drug exposure, organelle and cellular phenotypes across all key cell types of human organs, organ-specific clinical biomarkers/phenotypes, gene-drug interaction and immune responses. Systems modeling approaches, that leverage the knowledge base constructed from curating a selected list of drugs across a wide range of pharmacological classes, will provide a critically needed blueprint for making informed decisions to reduce the rate of attrition for drugs in development and increase the number of drugs with an acceptable benefit/risk ratio.
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Affiliation(s)
- Jane P F Bai
- Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, 20993, USA
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28
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Yu KH, Sangar V, Ricigliano M, Hidalgo M, Abou-Alfa GK, Lowery MA, Saltz L, Crotty JF, Gary K, Yin J, Choi EY, O'Reilly EM. Use of pharmacogenomic modeling in pancreatic cancer for prediction of chemotherapy response and resistance. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.15_suppl.4017] [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: 11/20/2022] Open
Abstract
4017 Background: Pancreatic adenocarcinoma (PDAC) is uniformly lethal and is the 4th leading cause of cancer mortality. Despite this, modern cytotoxics (C) can induce tumor responses and extend life. Xenograft models have shown that pharmacogenomic (PGx) modeling of C can predict efficacy. Chemo-sensitivity and gene expression profiling of circulating tumor and invasive cells (CTICs) isolated from peripheral blood may predict tumor response, progression and resistance. Methods: A prospective MSKCC study has completed planned accrual of 50 patients. 10 mL of peripheral blood is collected from patients with unresectable PDAC prior to C and at disease progression. Clinical data is prospectively collected. CTICs are isolated (Vita-Cap, Vitatex Inc.), total RNA is extracted and gene-expression analysis is performed. PGx models for twelve chemotherapy drug combinations used in PDAC were created from the GI50 data obtained from the NCI-60 cell lines (CellPath Therapeutics, Inc., Baltimore, MD). Expression data were normalized through GCRMA then probed to identify expression differences between patients with short v long TTP and within patients at baseline v at time of progression. The analysis was performed at the pathway and individual gene level. Results: CTICs were isolated, and gene expression and chemo-sensitivity patterns were obtained in all 50 patients prior to initiating C and in 20 patients at 1st line disease progression. Preliminary analysis demonstrates clinical benefit for patients treated with C predicted to be effective versus ineffective (TTP 7.3 mo v 3.7 mo, p=0.017, HR 0.30). Changes in chemo-sensitivity patterns were evident at disease progression, reflecting treatment resistance. Pathway analysis revealed that E2F1 and NFκB pathways are associated with prognosis, PLC and RB1 pathways become disrupted with disease progression. Conclusions: Isolation and gene expression profiling of CTICs can be performed reliably in unresectable PDAC. Preliminary analysis suggests that C profiling can predict response. Repeat PGx profiling identifies key pathways associated with treatment resistance. Clinical trial information: NCT01474564.
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Affiliation(s)
- Kenneth H. Yu
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Manuel Hidalgo
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | | | | | - Leonard Saltz
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Kristen Gary
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Jing Yin
- University of Maryland, Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD
| | - Eun Yong Choi
- University of Maryland, Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD
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Sangar V, Ricigliano M, O'Reilly EM, Abou-Alfa GK, Lowery MA, Saltz L, Crotty JF, Gary K, Choi EY, Yin J, Hidalgo M, Yu KH. Use of pharmacogenomic modeling in pancreatic cancer for prediction of chemotherapy response and resistance. J Clin Oncol 2013. [DOI: 10.1200/jco.2013.31.4_suppl.142] [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: 11/20/2022] Open
Abstract
142 Background: Pancreatic adenocarcinoma (PDAC) is uniformly lethal; despite this, modern cytotoxics (C) can induce tumor responses and extend life. Xenograft models have shown that pharmacogenomic (PGx) modeling of C can predict efficacy. Chemo-sensitivity and gene expression profiling of tumor progenitor (TP) cells isolated from peripheral blood may predict tumor response, progression and resistance. Methods: A prospective MSKCC study is ongoing with 46 of 60 planned patients accrued. 10 mL of peripheral blood is collected from patients with unresectable PDAC prior to C and at disease progression. Clinical data is prospectively collected. Circulating TP cells are isolated (Vita-Cap, Vitatex Inc.), total RNA is extracted and gene-expression analysis is performed. PGx models for twelve chemotherapy drug combinations used in PDAC were created from the GI50 data obtained from the NCI-60 cell lines (CellPath Therapeutics, Inc., Baltimore, MD). Expression data were normalized through GCRMA then probed to identify expression differences between the 35 patients with continued disease response and the 11 patients with disease progression. Analysis was performed at the pathway and individual gene level. Results: TP cells were isolated and gene expression and chemo-sensitivity patterns were obtained in all 46 evaluable patients prior to initiating C and in all 11 patients at 1st line disease progression. Preliminary analysis demonstrates clinical benefit for patients treated with C predicted to be effective versus C predicted to be ineffective (TTP 4.4 mo versus 2.7 mo, p=0.016). Changes in chemo-sensitivity patterns were evident at disease progression, reflecting treatment resistance. Hedgehog pathway over-expression was associated with resistance to gemcitabine but clinical response to 5-FU based treatment. Pathway analysis revealed that ErbB3, ARE/Nrf2 and Insulin pathways distinguished patients with disease progression. Conclusions: Isolation and gene expression profiling of TP cells can be performed reliably in unresectable PDAC. Preliminary analysis suggests that C profiling can predict response. Repeat PGx profiling identifies key pathways associated with treatment resistance. Clinical trial information: NCT01474564.
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Affiliation(s)
| | | | | | | | | | - Leonard Saltz
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Kristen Gary
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Eun Yong Choi
- University of Maryland Greenebaum Cancer Center, Baltimore, MD
| | - Jing Yin
- University of Maryland Greenebaum Cancer Center, Baltimore, MD
| | - Manuel Hidalgo
- Clinical Research Programme, Spanish National Cancer Research Center \(CNIO\), Madrid, Spain
| | - Kenneth H. Yu
- Memorial Sloan-Kettering Cancer Center, New York, NY
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Sangar V, Eddy JA, Simeonidis E, Price ND. Mechanistic modeling of aberrant energy metabolism in human disease. Front Physiol 2012; 3:404. [PMID: 23112774 PMCID: PMC3480659 DOI: 10.3389/fphys.2012.00404] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 10/01/2012] [Indexed: 01/21/2023] Open
Abstract
Dysfunction in energy metabolism—including in pathways localized to the mitochondria—has been implicated in the pathogenesis of a wide array of disorders, ranging from cancer to neurodegenerative diseases to type II diabetes. The inherent complexities of energy and mitochondrial metabolism present a significant obstacle in the effort to understand the role that these molecular processes play in the development of disease. To help unravel these complexities, systems biology methods have been applied to develop an array of computational metabolic models, ranging from mitochondria-specific processes to genome-scale cellular networks. These constraint-based (CB) models can efficiently simulate aspects of normal and aberrant metabolism in various genetic and environmental conditions. Development of these models leverages—and also provides a powerful means to integrate and interpret—information from a wide range of sources including genomics, proteomics, metabolomics, and enzyme kinetics. Here, we review a variety of mechanistic modeling studies that explore metabolic functions, deficiency disorders, and aberrant biochemical pathways in mitochondria and related regions in the cell.
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Rangiah K, Tippornwong M, Sangar V, Austin D, Tétreault MP, Rustgi AK, Blair IA, Yu KH. Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. J Proteome Res 2009; 8:5153-64. [PMID: 19769411 PMCID: PMC2783939 DOI: 10.1021/pr900518v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [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] [Indexed: 01/11/2023]
Abstract
The complexity and heterogeneity of the plasma proteome have presented significant challenges in the identification of protein changes associated with tumor development. We used cell culture as a model system and identified differentially expressed, secreted proteins which may constitute serological biomarkers. A stable isotope labeling by amino acids in cell culture (SILAC) approach was used to label the entire secreted proteomes of the CT26 murine colon cancer cell line and normal young adult mouse colon (YAMC) cell line, thereby creating a stable isotope labeled proteome (SILAP) standard. This SILAP standard was added to unlabeled murine CT26 colon cancer cell or normal murine YAMC colon epithelial cell secreted proteome samples. A multidimensional approach combining isoelectric focusing (IEF), strong cation exchange (SCX) followed by reversed phase liquid chromatography was used for extensive protein and peptide separation. A total of 614 and 929 proteins were identified from the YAMC and CT26 cell lines, with 418 proteins common to both cell lines. Twenty highly abundant differentially expressed proteins from these groups were selected for liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) analysis in sera. Differential secretion into the serum was observed for several proteins when Apc(min) mice were compared with control mice. These findings were then confirmed by Western blot analysis.
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Affiliation(s)
- Kannan Rangiah
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Montri Tippornwong
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Vineet Sangar
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - David Austin
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Marie-Pier Tétreault
- Division of Gastroenterology, Departments of Medicine & Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Anil K. Rustgi
- Division of Gastroenterology, Departments of Medicine & Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Ian A. Blair
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
| | - Kenneth H. Yu
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6160
- Corresponding author: Center for Cancer Pharmacology, University of Pennsylvania School of Medicine, 856 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160. Tel: 215-573-9885. Fax: 215-573-9889.
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Yu KH, Barry CG, Austin D, Busch CM, Sangar V, Rustgi AK, Blair IA. Stable isotope dilution multidimensional liquid chromatography-tandem mass spectrometry for pancreatic cancer serum biomarker discovery. J Proteome Res 2009; 8:1565-76. [PMID: 19199705 PMCID: PMC2652408 DOI: 10.1021/pr800904z] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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A novel approach to pancreatic cancer biomarker discovery has been developed, which employs a stable isotope labeled proteome (SILAP) standard coupled with extensive multidimensional separation coupled with tandem mass spectrometry (MS/MS). Secreted proteins from CAPAN-2 human pancreatic cancer derived cells were collected after conducting stable isotope labeling by amino acids in cell culture (SILAC). The resulting SILAP standard contained <0.5% of individual unlabeled proteins. Pooled sera from patients with early stage pancreatic cancer or controls were prepared, and an equal amount of the SILAP standard was added to each sample. Proteins were separated by isoelectric focusing (IEF) prior to two-dimensional liquid chromatography (2D-LC)–MS/MS analysis. A total of 1065 proteins were identified of which 121 proteins were present at 1.5-fold or greater concentrations in the sera of patients with pancreatic cancer. ELISA validation of these findings was successfully performed for two proteins, ICAM-1 and BCAM. Results of these studies have provided proof of principle that a SILAP standard derived from the CAPAN-2 secreted proteome can be used in combination with extensive multidimensional LC-MS/MS for the identification and relative quantitation of potential biomarkers of pancreatic cancer. This technique allows for the detection of low-abundance proteins, and focuses only on biologically relevant proteins derived from pancreatic cancer cells. CAPAN-2 human pancreatic ductal adenocarcinoma-derived cells were grown in [13C6, 15N1]leucine, [13C6,15N2]lysine. One-hundred twenty-one proteins were present at 1.5-fold or greater concentrations in the sera of patients with pancreatic cancer. Results of these studies have provided proof of principle that a SILAP standard derived from the CAPAN-2 secreted proteome can be used in combination with extensive multidimensional LC−MS/MS for the identification and relative quantification of potential biomarkers of pancreatic cancer.
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Affiliation(s)
- Kenneth H Yu
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Shah SJ, Yu KH, Sangar V, Parry SI, Blair IA. Identification and quantification of preterm birth biomarkers in human cervicovaginal fluid by liquid chromatography/tandem mass spectrometry. J Proteome Res 2009; 8:2407-17. [PMID: 19271751 DOI: 10.1021/pr8010342] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spontaneous preterm birth (PTB) before 37 completed weeks of gestation resulting from preterm labor (PTL) is a leading contributor of perinatal morbidity and mortality. Early identification of at-risk women by reliable screening tests could alleviate this health issue; however, conventional methods such as obstetric history and clinical risk factors, uterine activity monitoring, biochemical markers, and cervical sonography for screening women at risk for PTB have proven unsuccessful in lowering the rate of PTB. Cervicovaginal fluid (CVF) might prove to be a useful, readily available biological fluid for identifying diagnostic PTB biomarkers. Human columnar epithelial endocervical-1 (End1) and vaginal (Vk2) cell secretomes were employed to generate a stable isotope labeled proteome (SILAP) standard to facilitate characterization and relative quantification of proteins present in CVF. The SILAP standard was prepared using stable isotope labeling by amino acids in cell culture (SILAC) of End1 and Vk2 through seven passages. The labeled secreted proteins from both cell lines were combined and characterized by liquid-chromatography-tandem mass spectrometry (LC-MS/MS). In total, 1211 proteins were identified in the End1-Vk2 SILAP standard, with 236 proteins being consistently identified in each of the replicates analyzed. Individual proteins were found to contain <0.5% of the endogenous unlabeled forms. Identified proteins were screened to provide a set of 15 candidates that have either previously been identified as potential PTB biomarkers or could be linked mechanistically to PTB. Stable isotope dilution LC-multiple reaction monitoring (MRM/MS) assays were then developed for conducting relative quantification of the 15 candidate biomarkers in human CVF samples from term and PTB cases. Three proteins were significantly elevated in PTB cases (desmoplakin isoform 1, stratifin, and thrombospondin 1 precursor), providing a foundation for further validation in larger patient cohorts.
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Affiliation(s)
- Sumit J Shah
- Center for Excellence in Environmental Toxicology, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6160, USA
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Shah SJ, Yu KH, Sangar V, Parry SI, Blair IA. Identification and Quantification of Preterm Birth Biomarkers in Human Cervicovaginal Fluid by Liquid Chromatography/Tandem Mass Spectrometry. J Proteome Res 2009. [DOI: 10.1021/pr900441w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sangar V, Lesk VI, Lesk AM. On the use of overlapping lattices for screening to find pairs of nearby points in two and three dimensions. Comput Biol Chem 2008; 32:212-4. [DOI: 10.1016/j.compbiolchem.2008.02.002] [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] [Received: 01/31/2008] [Accepted: 02/01/2008] [Indexed: 11/25/2022]
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Sangar V, Blankenberg DJ, Altman N, Lesk AM. Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 2007; 8:294. [PMID: 17686158 PMCID: PMC1976327 DOI: 10.1186/1471-2105-8-294] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [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: 02/05/2007] [Accepted: 08/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex. The assumption that homologs share function--the basis of transfer of annotations in databases--must therefore be regarded with caution. Here, we present a quantitative study of sequence and function divergence, based on the Gene Ontology classification of function. We determined the relationship between sequence divergence and function divergence in 6828 protein families from the PFAM database. Within families there is a broad range of sequence similarity from very closely related proteins--for instance, orthologs in different mammals--to very distantly-related proteins at the limit of reliable recognition of homology. RESULTS We correlated the divergence in sequences determined from pairwise alignments, and the divergence in function determined by path lengths in the Gene Ontology graph, taking into account the fact that many proteins have multiple functions. Our results show that, among homologous proteins, the proportion of divergent functions decreases dramatically above a threshold of sequence similarity at about 50% residue identity. For proteins with more than 50% residue identity, transfer of annotation between homologs will lead to an erroneous attribution with a totally dissimilar function in fewer than 6% of cases. This means that for very similar proteins (about 50 % identical residues) the chance of completely incorrect annotation is low; however, because of the phenomenon of recruitment, it is still non-zero. CONCLUSION Our results describe general features of the evolution of protein function, and serve as a guide to the reliability of annotation transfer, based on the closeness of the relationship between a new protein and its nearest annotated relative.
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Affiliation(s)
- Vineet Sangar
- Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel J Blankenberg
- Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Naomi Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Arthur M Lesk
- Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
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Boddu J, Jiang C, Sangar V, Olson T, Peterson T, Chopra S. Comparative structural and functional characterization of sorghum and maize duplications containing orthologous myb transcription regulators of 3-deoxyflavonoid biosynthesis. Plant Mol Biol 2006; 60:185-99. [PMID: 16429259 DOI: 10.1007/s11103-005-3568-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 09/28/2005] [Indexed: 05/06/2023]
Abstract
Sequence characterization of the genomic region of sorghum yellow seed 1 shows the presence of two genes that are arranged in a head to tail orientation. The two duplicated gene copies, y1 and y2 are separated by a 9.084 kbp intergenic region, which is largely composed of highly repetitive sequences. The y1 is the functional copy, while the y2 may represent a pseudogene; there are several sequence indels and rearrangements within the putative coding region of y2. The y1 gene encodes a R2R3 type of Myb domain protein that regulates the expression of chalcone synthase, chalcone isomerase and dihydroflavonol reductase genes required for the biosynthesis of 3-deoxyflavonoids. Expression of y1 can be observed throughout the plant and it represents a combination of expression patterns produced by different alleles of the maize p1. Comparative sequence analysis within the coding regions and flanking sequences of y1, y2 and their maize and teosinte orthologs show local rearrangements and insertions that may have created modified regulatory regions. These micro-colinearity modifications possibly are responsible for differential patterns of expression in maize and sorghum floral and vegetative tissues. Phylogenetic analysis indicates that sorghum y1 and y2 sequences may have arisen by gene duplication mechanisms and represent an evolutionarily parallel event to the duplication of maize p2 and p1 genes.
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Affiliation(s)
- Jayanand Boddu
- Department of Crop & Soil Sciences, Pennsylvania State University, PA 16802, USA
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Chopra S, Cocciolone SM, Bushman S, Sangar V, McMullen MD, Peterson T. The maize unstable factor for orange1 is a dominant epigenetic modifier of a tissue specifically silent allele of pericarp color1. Genetics 2003; 163:1135-46. [PMID: 12663550 PMCID: PMC1462483 DOI: 10.1093/genetics/163.3.1135] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [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: 11/13/2022] Open
Abstract
We have characterized Unstable factor for orange1 (Ufo1), a dominant, allele-specific modifier of expression of the maize pericarp color1 (p1) gene. The p1 gene encodes an Myb-homologous transcriptional activator of genes required for biosynthesis of red phlobaphene pigments. The P1-wr allele specifies colorless kernel pericarp and red cobs, whereas Ufo1 modifies P1-wr expression to confer pigmentation in kernel pericarp, as well as vegetative tissues, which normally do not accumulate significant amounts of phlobaphene pigments. In the presence of Ufo1, P1-wr transcript levels and transcription rate are increased in kernel pericarp. The P1-wr allele contains approximately six p1 gene copies present in a hypermethylated and multicopy tandem array. In P1-wr Ufo1 plants, methylation of P1-wr DNA sequences is reduced, whereas the methylation state of other repetitive genomic sequences was not detectably affected. The phenotypes produced by the interaction of P1-wr and Ufo1 are unstable, exhibiting somatic mosaicism and variable penetrance. Moreover, the changes in P1-wr expression and methylation are not heritable: meiotic segregants that lack Ufo1 revert to the normal P1-wr expression and methylation patterns. These results demonstrate the existence of a class of modifiers of gene expression whose effects are associated with transient changes in DNA methylation of specific loci.
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Affiliation(s)
- Surinder Chopra
- Department of Zoology and Genetics and Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
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Maddineni S, Sangar V, King H, Betts C, O'Flynn K, Lupton E, George N, Ramani V, Clarke N. A phase I dose escalation and pharmacokinetic trial of intra-vesical gemcitabine in the treatment of recurrent superficial transitional cell carcinoma of the bladder. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1569-9056(03)80759-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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