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Choudhary S, Iyer G, Smith BM, Li J, Sippel M, Criminisi A, Heymsfield SB. Development and validation of an accurate smartphone application for measuring waist-to-hip circumference ratio. NPJ Digit Med 2023; 6:168. [PMID: 37696899 PMCID: PMC10495406 DOI: 10.1038/s41746-023-00909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023] Open
Abstract
Waist-to-hip circumference ratio (WHR) is now recognized as among the strongest shape biometrics linked with health outcomes, although use of this phenotypic marker remains limited due to the inaccuracies in and inconvenient nature of flexible tape measurements when made in clinical and home settings. Here we report that accurate and reliable WHR estimation in adults is possible with a smartphone application based on novel computer vision algorithms. The developed application runs a convolutional neural network model referred to as MeasureNet that predicts a person's body circumferences and WHR using front, side, and back color images. MeasureNet bridges the gap between measurements conducted by trained professionals in clinical environments, which can be inconvenient, and self-measurements performed by users at home, which can be unreliable. MeasureNet's accuracy and reliability is evaluated using 1200 participants, measured by a trained staff member. The developed smartphone application, which is a part of Amazon Halo, is a major advance in digital anthropometry, filling a long-existing gap in convenient, accurate WHR measurement capabilities.
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Affiliation(s)
| | | | | | | | | | | | - Steven B Heymsfield
- Amazon Inc., Seattle, WA, USA
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, USA
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Koshkin V, Powles T, Iyer G, Loriot Y, Drakaki A, Duran Martinez I, De Santis M, Retz M, Jain R, Chan S, Ichimaru M, Galsky M. 1779TiP Phase II clinical study evaluating the efficacy and safety of disitamab vedotin in patients (pts) with HER2-expressing urothelial carcinoma (RC48G001). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1938] [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: 11/01/2022] Open
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Come JH, Senter TJ, Clark MP, Court JJ, Gale-Day Z, Gu W, Krueger E, Liang J, Morris M, Nanthakumar S, O'Dowd H, Maltais F, Iyer G, Andreassi J, Boucher C, Considine T, Moody CS, Taylor W, Mohanty AK, Huang Y, Zuccola H, Coll J, Bonanno KC, Gagnon KJ, Gan L, Lu F, Gao H, Chakilam A, Engtrakul J, Song B, Crawford D, Doyle E, Kramer T, Vought B, Phillips J, Kemper R, Sanders M, Swett R, Furey B, Winquist R, Bunnage ME, Jackson KL, Charifson PS, Magavi SS. Discovery and Optimization of Pyrazole Amides as Inhibitors of ELOVL1. J Med Chem 2021; 64:17753-17776. [PMID: 34748351 DOI: 10.1021/acs.jmedchem.1c00944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Accumulation of very long chain fatty acids (VLCFAs) due to defects in ATP binding cassette protein D1 (ABCD1) is thought to underlie the pathologies observed in adrenoleukodystrophy (ALD). Pursuing a substrate reduction approach based on the inhibition of elongation of very long chain fatty acid 1 enzyme (ELOVL1), we explored a series of thiazole amides that evolved into compound 27─a highly potent, central nervous system (CNS)-penetrant compound with favorable in vivo pharmacokinetics. Compound 27 selectively inhibits ELOVL1, reducing C26:0 VLCFA synthesis in ALD patient fibroblasts, lymphocytes, and microglia. In mouse models of ALD, compound 27 treatment reduced C26:0 VLCFA concentrations to near-wild-type levels in blood and up to 65% in the brain, a disease-relevant tissue. Preclinical safety findings in the skin, eye, and CNS precluded progression; the origin and relevance of these findings require further study. ELOVL1 inhibition is an effective approach for normalizing VLCFAs in models of ALD.
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Affiliation(s)
- Jon H Come
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Timothy J Senter
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Michael P Clark
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - John J Court
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Zachary Gale-Day
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Wenxin Gu
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Elaine Krueger
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Jianglin Liang
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Mark Morris
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Suganthini Nanthakumar
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Hardwin O'Dowd
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Francois Maltais
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Ganesh Iyer
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - John Andreassi
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Christina Boucher
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Tony Considine
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Cameron S Moody
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - William Taylor
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Arun K Mohanty
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Yulin Huang
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Harmon Zuccola
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Joyce Coll
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Kenneth C Bonanno
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Kevin J Gagnon
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Lu Gan
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Fan Lu
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Hong Gao
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Ananthisrinivas Chakilam
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Juntyma Engtrakul
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Bin Song
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Dan Crawford
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Elisabeth Doyle
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Tal Kramer
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Bryan Vought
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Jonathan Phillips
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Raymond Kemper
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Martin Sanders
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Rebecca Swett
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Brinley Furey
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Ray Winquist
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Mark E Bunnage
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Katrina L Jackson
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Paul S Charifson
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
| | - Sanjay S Magavi
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, Massachusetts 02210, United States
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Rydzewski N, Buehler D, Kendziorski C, Iyer G, Zhao S, Baschnagel A. Immune-Depleted Phenotype in Non-Small Cell Lung Cancer Brain Metastases Predicts for Worse Overall Survival. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.063] [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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Teraoka J, Nguyen K, Hart D, Peace S, Leard L, Iyer G, Gordon D, Zuckerman B, Pascual J, Ponzo J, Perez A, Budanova N, Gesthalter Y, Trinh B, Kukreja J, Hays S, Venado A. Decreasing 30-day Readmissions for Pleural Effusions after Lung Transplant. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1075] [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] Open
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Liu D, Flory J, Lin A, Offin M, Falcon CJ, Murciano-Goroff YR, Rosen E, Guo R, Basu E, Li BT, Harding JJ, Iyer G, Jhaveri K, Gounder MM, Shukla NN, Roberts SS, Glade-Bender J, Kaplanis L, Schram A, Hyman DM, Drilon A. Characterization of on-target adverse events caused by TRK inhibitor therapy. Ann Oncol 2020; 31:1207-1215. [PMID: 32422171 PMCID: PMC8341080 DOI: 10.1016/j.annonc.2020.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 02/13/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The tropomyosin receptor kinase (TRK) pathway controls appetite, balance, and pain sensitivity. While these functions are reflected in the on-target adverse events (AEs) observed with TRK inhibition, these AEs remain under-recognized, and pain upon drug withdrawal has not previously been reported. As TRK inhibitors are approved by multiple regulatory agencies for TRK or ROS1 fusion-positive cancers, characterizing these AEs and corresponding management strategies is crucial. PATIENTS AND METHODS Patients with advanced or unresectable solid tumors treated with a TRK inhibitor were retrospectively identified in a search of clinical databases. Among these patients, the frequency, severity, duration, and management outcomes of AEs including weight gain, dizziness or ataxia, and withdrawal pain were characterized. RESULTS Ninety-six patients with 15 unique cancer histologies treated with a TRK inhibitor were identified. Weight gain was observed in 53% [95% confidence interval (CI), 43%-62%] of patients and increased with time on TRK inhibition. Pharmacologic intervention, most commonly with glucagon-like peptide 1 analogs or metformin, appeared to result in stabilization or loss of weight. Dizziness, with or without ataxia, was observed in 41% (95% CI, 31%-51%) of patients with a median time to onset of 2 weeks (range, 3 days to 16 months). TRK inhibitor dose reduction was the most effective intervention for dizziness. Pain upon temporary or permanent TRK inhibitor discontinuation was observed in 35% (95% CI, 24%-46%) of patients; this was more common with longer TRK inhibitor use. TRK inhibitor reinitiation was the most effective intervention for withdrawal pain. CONCLUSIONS TRK inhibition-related AEs including weight gain, dizziness, and withdrawal pain occur in a substantial proportion of patients receiving TRK inhibitors. This safety profile is unique relative to other anticancer therapies and warrants careful monitoring. These on-target toxicities are manageable with pharmacologic intervention and dose modification.
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Affiliation(s)
- D Liu
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J Flory
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - A Lin
- Department of Medicine, Weill Cornell Medical College, New York, USA; Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - M Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - C J Falcon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Y R Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - E Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Guo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - E Basu
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - B T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - J J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - G Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - K Jhaveri
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - M M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - N N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - S S Roberts
- Department of Medicine, Weill Cornell Medical College, New York, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J Glade-Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - L Kaplanis
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, USA
| | - A Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - D M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA
| | - A Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical College, New York, USA.
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Zhou M, Yuzhakov A, Benod CC, Xue L, Silver AD, Iyer G, Townson SA, Jin M, Perl NR, Kohlmann A, Mann AS, Akcay G, May EW. Abstract A06: Biophysical and biochemical characterization of KRAS G12C inhibition through the SMARTTM platform. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-a06] [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
RAS proteins are small GTPases involved in cell proliferation, survival, and differentiation, and are mutationally activated in about a third of all human cancers. These mutations drive cancer by impairing GTPase activity so that the RAS protein is found predominantly in its GTP-bound “on” conformation. Most KRAS isoform mutations are located at codon 12, a glycine in the P-loop of the GTPase active site. KRAS mutations in which the glycine is mutated to a cysteine (G12C) are particularly common in lung cancer. Despite its prevalence as an important oncogene and decades of research, the RAS protein remains an unexploited cancer target. We have developed a novel platform, SMART (Small Molecule Assisted Receptor Targeting), to disrupt the protein-protein interactions of so-called “undruggable” targets. Our compounds bind the immunophilin protein Cyclophilin A (CypA), and subsequently form a ternary complex with the target protein, KRAS. An electrophilic moiety on the ligand selectively forms a covalent bond with the cysteine of GTP-KRAS G12C, thus strengthening the stability of the ternary complex, partially occupying the effector face, and thus occluding the binding of downstream effector proteins, such as RAF. In a separate presentation, we describe a wide breadth of data to support the advancement of a small molecule specifically targeting the activated form of KRAS, with a focus on the cellular pharmacology. In this presentation, we highlight biophysical and biochemical findings that support our novel strategy for targeting GTP-KRAS G12C. SPR reveals the CypA-compound binary KD. A novel SPR protocol method was developed to examine CypA-compound-KRAS ternary complex formation, exploiting the A-B-A injection system of the Biacore 8K. LC-MS is used to characterize the crosslinking of our compounds to KRAS G12C in the presence of CypA, and full kinact/KI analysis is conducted with select compounds; in combination with SPR studies, the noncovalent KD of the ternary complex can be determined. Intrinsic warhead reactivity is measured through GSH adduct formation. TR-FRET studies probe the ability of ternary complexes to inhibit the binding of RAF to KRAS G12C. ITC and BLI are used to confirm ternary complex formation for selected compounds. In addition to guiding SAR, these studies characterize the degree of presenter (CypA) dependence, specificity of compound binding to the G12C mutant and to the GTP nucleotide-bound form of KRAS, and the ability to predict cellular efficacy. Our kinetic crosslinking experiments reveal single-digit micromolar KIs and a good kinact/KI ratio for our compounds relative to published literature on compounds targeting GDP-KRAS G12C. When these values are compared to SPR findings, the noncovalent KD contributes largely to KI, and thus noncovalent interactions play a bigger role in our compound’s interaction with RAS as compared to known GDP-KRAS G12C agents.
Citation Format: Minyun Zhou, Alexander Yuzhakov, Cindy C Benod, Linlong Xue, Alec D Silver, Ganesh Iyer, Sharon A. Townson, Meizhong Jin, Nicholas R. Perl, Anna Kohlmann, Alan S. Mann, Gizem Akcay, Earl W. May. Biophysical and biochemical characterization of KRAS G12C inhibition through the SMARTTM platform [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A06.
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Gordon D, Hays S, Singer J, Perez A, Venado A, Iyer G, Zuckerman B, Daulton C, Pascual J, Dewey K, Florez R, Shah R, Kolaitis N, Leard L, Kleinhenz M, Golden J, Trinh B, Deuse T, Kukreja J. Reducing Length of Stay after Lung Transplant through Implementation of Multi-Disciplinary Care Coordination Rounds. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.829] [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: 11/29/2022] Open
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Blitzer G, Wang A, Brown J, Burr A, Matkowskyj K, Schuppener L, Kovacs K, Witt J, Kendziorski C, Iyer G, Baschnagel A. Tumor Lymphocyte, Macrophage, and GITR Changes in Tissue Microarray and RNA Sequencing of Patients with and without Neoadjuvant Radiation Therapy for Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.278] [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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Burr A, Bayouth J, Bates A, Murphy T, Niewold N, Wang A, Francis D, Yadav P, Morris Z, Iyer G, Baschnagel A. Correlation of Serum Inflammatory Cytokine Levels and Pulmonary Toxicity Following Lung Irradiation. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1412] [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: 10/26/2022]
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Matos I, Goyal L, Cleary J, Voss M, Oh D, Bernstam FM, Ng C, Iyer G, Ishii N, Hu Y, Chessex AV, Pokorska-Bocci A, Nicolas V, Kirpicheva Y, Zanna C, Flaherty K, Tabernero J, Hyman D. Debio 1347 in patients with gastrointestinal cancers harboring an FGFR gene fusion: preliminary results. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz157.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sim R, Mueller S, Iyer G, Tan N, Soo K, Mahalakshmi R, Tan H. EP-1135 Effect of Primary Treatment on Neck Dissection Choice in Nasopharyngeal Carcinoma Regional Failure. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)31555-5] [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: 11/26/2022]
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Abstract
Urothelial malignancies, including carcinomas of the bladder, ureters, and renal pelvis comprised ∼8% of new cancer cases in the USA in 2016. In the metastatic setting, 15% of patients exhibit long-term survival following cisplatin-based chemotherapy and in patients with recurrent disease, response rates to second-line chemotherapy are generally 15%-20% with a 3-month progression-free survival. However, recent advances in immunotherapy represent an opportunity to significantly improve patient outcomes. Moreover, the advent of next-generation sequencing has resulted in both an improved understanding of the fundamental genetic changes that characterize urothelial carcinoma (UC) and identification of several candidate biomarkers of response to various therapies. Incorporation of prospective genotyping into clinical trials will allow for the identification and enrichment of patients most likely to respond to specific targeted therapies and chemotherapy. Combining different therapeutic classes to enhance outcomes is also an area of active research in UC.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/genetics
- Carcinoma, Transitional Cell/drug therapy
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/mortality
- Carcinoma, Transitional Cell/pathology
- Clinical Trials as Topic
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Genotyping Techniques
- High-Throughput Nucleotide Sequencing
- Humans
- Molecular Targeted Therapy/methods
- Mutation Rate
- Progression-Free Survival
- Urologic Neoplasms/drug therapy
- Urologic Neoplasms/genetics
- Urologic Neoplasms/pathology
- Urothelium/pathology
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Affiliation(s)
- G Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
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Audenet F, Isharwal S, Cha E, Donoghue M, Pietzak E, Sfakianos J, Bagrodia A, Dalbagni G, Donahue T, Rosenberg J, Bajorin D, Arcila M, Berger M, Taylor B, Al-Ahmadie H, Iyer G, Bochner B, Coleman J, Solit D. Classification phylogénétique des récidives vésicales après tumeur de la voie excrétrice urinaire supérieure. Prog Urol 2018. [DOI: 10.1016/j.purol.2018.07.133] [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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Audenet F, Isharwal S, Cha E, Donoghue M, Pietzak E, Sfakianos J, Bagrodia A, Dalbagni G, Donahue T, Rosenberg J, Bajorin D, Arcila M, Berger M, Taylor B, Al-Ahmadie H, Iyer G, Bochner B, Coleman J, Solit D. Spécificités moléculaires des tumeurs de la voie excrétrice urinaire supérieure. Prog Urol 2018. [DOI: 10.1016/j.purol.2018.07.132] [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: 11/24/2022]
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Teo MY, Bambury RM, Zabor EC, Jordan E, Al-Ahmadie H, Boyd ME, Bouvier N, Mullane SA, Cha EK, Roper N, Ostrovnaya I, Hyman DM, Bochner BH, Arcila ME, Solit DB, Berger MF, Bajorin DF, Bellmunt J, Iyer G, Rosenberg JE. Commentary on "DNA damage response and repair gene alterations are associated with improved survival in patients with platinum-treated advanced urothelial carcinoma.". Urol Oncol 2018; 36:345-346. [PMID: 29859727 DOI: 10.1016/j.urolonc.2018.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PURPOSE Platinum-based chemotherapy remains the standard treatment for advanced urothelial carcinoma by inducing DNA damage. We hypothesize that somatic alterations in DNA damage response and repair (DDR) genes are associated with improved sensitivity to platinum-based chemotherapy. EXPERIMENTAL DESIGN Patients with diagnosis of locally advanced and metastatic urothelial carcinoma treated with platinum-based chemotherapy who had exon sequencing with the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay were identified. Patients were dichotomized based on the presence/absence of alterations in a panel of 34 DDR genes. DDR alteration status was correlated with clinical outcomes and disease features. RESULTS One hundred patients were identified, of which 47 harbored alterations in DDR genes. Patients with DDR alterations had improved progression-free survival (9.3 vs. 6.0 months, log-rank P = 0.007) and overall survival (23.7 vs. 13.0 months, log-rank P = 0.006). DDR alterations were also associated with higher number mutations and copy-number alterations. A trend toward positive correlation between DDR status and nodal metastases and inverse correlation with visceral metastases were observed. Different DDR pathways also suggested variable effect on clinical outcomes. CONCLUSIONS Somatic DDR alteration is associated with improved clinical outcomes in platinum-treated patients with advanced urothelial carcinoma. Once validated, it can improve patient selection for clinical practice and future study enrollment.
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Saltz J, Sharma A, Iyer G, Bremer E, Wang F, Jasniewski A, DiPrima T, Almeida JS, Gao Y, Zhao T, Saltz M, Kurc T. A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images. Cancer Res 2017; 77:e79-e82. [PMID: 29092946 DOI: 10.1158/0008-5472.can-17-0316] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/17/2017] [Accepted: 09/01/2017] [Indexed: 11/16/2022]
Abstract
Well-curated sets of pathology image features will be critical to clinical studies that aim to evaluate and predict treatment responses. Researchers require information synthesized across multiple biological scales, from the patient to the molecular scale, to more effectively study cancer. This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features. All the services are deployed as containers and the user-facing interfaces as web-based applications. The set of containers and web applications presented in this article is used in cancer research studies of morphologic characteristics of tumor tissues. The software is free and open source. Cancer Res; 77(21); e79-82. ©2017 AACR.
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Affiliation(s)
- Joel Saltz
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York.
| | - Ashish Sharma
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia
| | - Ganesh Iyer
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia
| | - Erich Bremer
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Feiqiao Wang
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Alina Jasniewski
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Tammy DiPrima
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Jonas S Almeida
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Yi Gao
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York
| | - Tianhao Zhao
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York.,Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Mary Saltz
- Department of Radiology, Stony Brook University, Stony Brook, New York
| | - Tahsin Kurc
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York.,Scientific Data Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee
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Lai G, Nahar R, Lim T, Kwang X, Liew P, Lim J, Aung Z, Takano A, Lim W, Lau D, Tan W, Ang M, Toh C, Tan B, Devanand A, Too C, Gogna A, Ong B, Koh T, Kanesvaran R, Ng Q, Jain A, Yuan J, Lim T, Lim A, Hillmer A, Zhai W, Iyer G, Tan E, Tam W, Tan D. OA 09.07 Clonality of c-MET Copy Number Gain as a Determinant of Primary TKI Resistance in EGFR-Mutant NSCLC. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.380] [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: 10/18/2022]
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Abstract
Abstract
Although Tor has state-of-the art anticensorship measures, users in heavily censored environments will not be able to connect to Tor if they cannot configure their connections. We perform the first usability evaluation of Tor Launcher, the graphical user interface (GUI) that Tor Browser uses to configure connections to Tor. Our study shows that 79% (363 of 458) of user attempts to connect to Tor in simulated censored environments failed. We found that users were often frustrated during the process and tried options at random. In this paper, we measure potential usability issues, discuss design constraints unique to Tor, and provide recommendations based on what we learned to help more users connect to Tor while reducing the time they take to do so. Tor Browser incorporated the changes proposed by this study.
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Affiliation(s)
| | | | | | | | - Serge Egelman
- University of California , Berkeley and International Computer Science Institute
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Bhardwaj AK, Gupta G, Prajapati R, Joshi V, Patel M, Bhavsar J, More V, Jindal M, Bhattacharya A, Jogi G, Palaliya A, Jha S, Pandey M, Shukla D, Iyer G, Jadhav P, Goyal D, Desai A, Sekachev I, Vitupier G, Han X, Olivier T. Overview and status of ITER Cryostat manufacturing. Fusion Engineering and Design 2016. [DOI: 10.1016/j.fusengdes.2015.12.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Court JJ, Poisson C, Ardzinski A, Bilimoria D, Chan L, Chandupatla K, Chauret N, Collier PN, Das SK, Denis F, Dorsch W, Iyer G, Lauffer D, L'Heureux L, Li P, Luisi BS, Mani N, Nanthakumar S, Nicolas O, Rao BG, Ronkin S, Selliah S, Shawgo RS, Tang Q, Waal ND, Yannopoulos CG, Green J. Discovery of Novel Thiophene-Based, Thumb Pocket 2 Allosteric Inhibitors of the Hepatitis C NS5B Polymerase with Improved Potency and Physicochemical Profiles. J Med Chem 2016; 59:6293-302. [PMID: 27366941 DOI: 10.1021/acs.jmedchem.6b00541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The hepatitis C viral proteins NS3/4A protease, NS5B polymerase, and NS5A are clinically validated targets for direct-acting antiviral therapies. The NS5B polymerase may be inhibited directly through the action of nucleosides or nucleotide analogues or allosterically at a number of well-defined sites. Herein we describe the further development of a series of thiophene carboxylate allosteric inhibitors of NS5B polymerase that act at the thumb pocket 2 site. Lomibuvir (1) is an allosteric HCV NS5B inhibitor that has demonstrated excellent antiviral activity and potential clinical utility in combination with other direct acting antiviral agents. Efforts to further explore and develop this series led to compound 23, a compound with comparable potency and improved physicochemical properties.
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Affiliation(s)
- John J Court
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Carl Poisson
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Andrzej Ardzinski
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Darius Bilimoria
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Laval Chan
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Kishan Chandupatla
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathalie Chauret
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Philip N Collier
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Sanjoy Kumar Das
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Francois Denis
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Warren Dorsch
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Ganesh Iyer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - David Lauffer
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Lucille L'Heureux
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Pan Li
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Brian S Luisi
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nagraj Mani
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Suganthi Nanthakumar
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Olivier Nicolas
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - B Govinda Rao
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Steven Ronkin
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Subajini Selliah
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Rebecca S Shawgo
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Qing Tang
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Nathan D Waal
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
| | - Constantin G Yannopoulos
- Vertex Pharmaceuticals (Canada) Incorporated , 275 Boulevard Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Jeremy Green
- Vertex Pharmaceuticals Incorporated , 50 Northern Avenue, Boston, Massachusetts 02210, United States
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Jordan E, Won H, Toubaji A, Bagrodia A, Desai N, Bajorin D, Rosenberg J, Bochner B, Kim W, Berger M, Solit D, Al-Ahmadie H, Iyer G. 2650 Assessment of genomic alterations in bladder adenocarcinoma and urachal adenocarcinoma. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31467-8] [Citation(s) in RCA: 3] [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: 11/24/2022]
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Sudhir K, Priester J, Shum M, Atkin D, Foster A, Iyer G, Jin G, Keniston D, Kitayama S, Mobarak M, Qian Y, Tewari I, Wood W. Research Opportunities in Emerging Markets: an Inter-disciplinary Perspective from Marketing, Economics, and Psychology. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40547-015-0044-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Mouw K, Van Allen E, O’Connor K, Wagle N, Kim P, Al-Ahmadie H, Zhu C, Ostravnaya I, Iyer G, Signoretti S, Reuter V, Getz G, Kantoff P, Bochner B, Choueiri T, Bajorin D, Gabriel S, D’Andrea A, Garraway L, Rosenberg J. Somatic ERCC2 Mutations Confer Cisplatin Sensitivity in Muscle-Invasive Urothelial Cancer. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.481] [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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25
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Ganly I, Iyer G, Rahmati R, Dogan S, Kim L, Palmer F, Lee N, Patel S, Shah J. Risk Stratification Based on HPV and Smoking Status Independently Predicts Outcome in Patients With Oropharyngeal Cancer Treated With Surgery and Postoperative Radiation. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2013.11.047] [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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26
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Gu T, Iyer G, Cheng KSC. Parameter estimation and rate model simulation of partial breakthrough of bovine serum albumin on a column packed with large Q Sepharose anion-exchange particles. Sep Purif Technol 2013. [DOI: 10.1016/j.seppur.2013.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gallagher DJ, Vijai J, Hamilton RJ, Ostrovnaya I, Iyer G, Garcia-Grossman IR, Kim PH, Przybylo JA, Alanee S, Riches JC, Regazzi AM, Milowsky MI, Offit K, Bajorin DF. Germline single nucleotide polymorphisms associated with response of urothelial carcinoma to platinum-based therapy: the role of the host. Ann Oncol 2013; 24:2414-21. [PMID: 23897706 DOI: 10.1093/annonc/mdt225] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Variations in urothelial carcinoma (UC) response to platinum chemotherapy are common and frequently attributed to genetic and epigenetic variations of somatic DNA. We hypothesized that variations in germline DNA may contribute to UC chemosensitivity. PATIENTS AND METHODS DNA from 210 UC patients treated with platinum-based chemotherapy was genotyped for 80 single nucleotide polymorphisms (SNPs). Logistic regression was used to examine the association between SNPs and response, and a multivariable predictive model was created. Significant SNPs were combined to form a SNP score predicting response. Eleven UC cell lines were genotyped as validation. RESULTS Six SNPs were significantly associated with 101 complete or partial responses (48%). Four SNPs retained independence association and were incorporated into a response prediction model. Each additional risk allele was associated with a nearly 50% decrease in odds of response [odds ratio (OR) = 0.51, 95% confidence interval 0.39-0.65, P = 1.05 × 10(-7)). The bootstrap-adjusted area under the curves of this model was greater than clinical prognostic factors alone (0.78 versus 0.64). The SNP score showed a positive trend with chemosensitivity in cell lines (P = 0.115). CONCLUSIONS Genetic variants associated with response of UC to platinum-based therapy were identified in germline DNA. A model using these genetic variants may predict response to chemotherapy better than clinical factors alone.
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Affiliation(s)
- D J Gallagher
- Department of Medical Oncology and Cancer Genetics, Mater Hospital and St. James's Hospital, Dublin 7, Ireland.
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Iyer G, Ramaswamy S, Cheng KS, Sisowath N, Mehta U, Leahy A, Chung F, Asher D. Flow-Through Purification of Viruses- A Novel Approach to Vaccine Purification. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.provac.2012.04.015] [Citation(s) in RCA: 16] [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: 11/29/2022]
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Iyer G, Ramaswamy S, Asher D, Mehta U, Leahy A, Chung F, Cheng KS. Reduced surface area chromatography for flow-through purification of viruses and virus like particles. J Chromatogr A 2011; 1218:3973-81. [DOI: 10.1016/j.chroma.2011.04.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 04/28/2011] [Indexed: 11/26/2022]
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31
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Li JY, Chong M, Yong LT, Tan NC, Iyer G, Soo KC, Tan HK. O131. Giant Ameloblastoma: Is radical resection the choice of treatment? Oral Oncol 2011. [DOI: 10.1016/j.oraloncology.2011.06.242] [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: 11/27/2022]
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Al-Ahmadie H, Iyer G, Lin O, Gopalan A, Fine S, Tickoo S, Reuter VE, Bajorin DF, Milowsky MI, Solit DB. Alterations in genes regulating cell cycle and apoptosis in high-grade urothelial carcinoma. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.7_suppl.237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
237 Background: Dysregulations of cell cycle and inhibition of apoptosis are crucial factors in tumorigenesis of multiple malignancies, including urothelial carcinoma (UC). Deletions of TP53 and CDKN2A and amplification of MDM2 have been observed in UC, but their exact frequency and functional consequence is less known. We sought to determine the frequency of copy number alteration (CNA) and mutations of genes that regulate cell cycle or apoptosis in a panel of 96 cases of high-grade UC (HGUC) of bladder. Methods: 96 frozen cases of HGUC were studied, including 11 bladder small cell carcinomas. DNA was isolated and analyzed for CNA by comparative genomic hybridization (CGH) using a one million oligonucleotide probe array from Agilent. The targeted genes included TP53, MDM2, CCND1, CCNE1, CDKN2A/B, E2F3 and Rb1. Traditional Sanger sequencing for mutations within TP53, Rb1, and CDKN2A was also performed. Results: The frequency of CNA and mutations are listed in the table. Overall, 54 of 96 cases (56%) showed CNA (45) or mutation (13). Deletion of CDKN2A/B and amplification of E2F3 were the most common alterations in cell cycle regulatory genes (13 cases each, 14%), followed by amplification of CCND1 (11 cases, 11%). There was no co-amplification of CCND1 and CCNE1 in any sample. Rb1 deletion was present in five cases. CNA in E2F3 and Rb1 were mutually exclusive in 14 of 16 cases (88%) and were both present in two cases only. Mutations in TP53 were noted in 13 cases and deletions in nine. Amplification of MDM2 was noted in four cases, none of which overlapped with TP53 deletions or mutations. Overexpression of E2F3 was significantly more common in small cell carcinoma (5/11) compared to conventional UC (8/85, p = 0.006). Conclusions: Regulators of cell cycle and apoptosis are amplified, deleted or mutated in more than half of cases (56%) of high-grade urothelial carcinoma. The overwhelming majority of these abnormalities are nonoverlapping. Amplification of E2F3 seems to be overrepresented in small cell carcinoma of bladder. [Table: see text] No significant financial relationships to disclose.
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Affiliation(s)
- H. Al-Ahmadie
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - G. Iyer
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - O. Lin
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - A. Gopalan
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - S. Fine
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - S. Tickoo
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - V. E. Reuter
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - D. F. Bajorin
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - D. B. Solit
- Memorial Sloan-Kettering Cancer Center, New York, NY
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Kim S, Iyer G, Nadarajah A, Frantz JM, Spongberg AL. Polyacrylamide Hydrogel Properties for Horticultural Applications. International Journal of Polymer Analysis and Characterization 2010. [DOI: 10.1080/1023666x.2010.493271] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Iyer G, Tillekeratne LV, Coleman MR, Nadarajah A. Equilibrium swelling behavior of thermally responsive metal affinity hydrogels, Part I: Compositional effects. POLYMER 2008. [DOI: 10.1016/j.polymer.2008.06.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Iyer G, Tillekeratne LV, Coleman MR, Nadarajah A. Equilibrium swelling behavior of thermally responsive metal affinity hydrogels, Part II: Solution effects. POLYMER 2008. [DOI: 10.1016/j.polymer.2008.06.036] [Citation(s) in RCA: 4] [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: 11/29/2022]
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Iyer G, Iyer P, Tillekeratne LMV, Coleman MR, Nadarajah A. Controlling Phase Transition Behavior of Thermally Responsive Metal Affinity Hydrogels: A Molecular Design Approach. Macromolecules 2007. [DOI: 10.1021/ma0706881] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ganesh Iyer
- Department of Chemical & Environmental Engineering and Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, Ohio 43606
| | - Pallavi Iyer
- Department of Chemical & Environmental Engineering and Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, Ohio 43606
| | - L. M. Viranga Tillekeratne
- Department of Chemical & Environmental Engineering and Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, Ohio 43606
| | - Maria R. Coleman
- Department of Chemical & Environmental Engineering and Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, Ohio 43606
| | - Arunan Nadarajah
- Department of Chemical & Environmental Engineering and Department of Medicinal and Biological Chemistry, University of Toledo, Toledo, Ohio 43606
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Iyer G, Yoon YS, Coleman MR, Nadarajah A. Development of environmentally responsive hydrogels with metal affinity behavior. J Appl Polym Sci 2007. [DOI: 10.1002/app.26294] [Citation(s) in RCA: 4] [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: 11/08/2022]
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39
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Wira C, Lewandowski C, Martinez-Capolino C, Iyer G, Sherwin R, Kummer J, Rivers E. 66. Ann Emerg Med 2006. [DOI: 10.1016/j.annemergmed.2006.07.514] [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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Michalet X, Pinaud FF, Bentolila LA, Tsay JM, Doose S, Li JJ, Iyer G, Weiss S. Peptide-coated semiconductor nanocrystals for biomedical applications. Proc SPIE Int Soc Opt Eng 2005; 5704:10.1117/12.589498. [PMID: 29176922 PMCID: PMC5701801 DOI: 10.1117/12.589498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
We have developed a new functionalization approach for semiconductor nanocrystals based on a single-step exchange of surface ligands with custom-designed peptides. This peptide-coating technique yield small, monodisperse and very stable water-soluble NCs that remain bright and photostable. We have used this approach on several types of core and core-shell NCs in the visible and near-infrared spectrum range and used fluorescence correlation spectroscopy for rapid assessment of the colloidal and photophysical properties of the resulting particles. This peptide coating strategy has several advantages: it yields probes that are immediately biocompatible; it is amenable to improvements of the different properties (solubilization, functionalization, etc) via rational design, parallel synthesis, or molecular evolution; it permits the combination of several functions on individual NCs. These functionalized NCs have been used for diverse biomedical applications. Two are discussed here: single-particle tracking of membrane receptor in live cells and combined fluorescence and PET imaging of targeted delivery in live animals.
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Affiliation(s)
- X Michalet
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - F F Pinaud
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - L A Bentolila
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - J M Tsay
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - S Doose
- Applied Laserphysics & Laserspectroscopy, University of Bielefeld 33615 Bielefeld, Germany
| | - J J Li
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - G Iyer
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
| | - S Weiss
- Dpt of Chemistry & Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095
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Hu W, Feng Z, Eveleigh J, Iyer G, Pan J, Amin S, Chung FL, Tang MS. The major lipid peroxidation product, trans-4-hydroxy-2-nonenal, preferentially forms DNA adducts at codon 249 of human p53 gene, a unique mutational hotspot in hepatocellular carcinoma. Carcinogenesis 2002; 23:1781-9. [PMID: 12419825 DOI: 10.1093/carcin/23.11.1781] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.8] [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] [Indexed: 02/07/2023] Open
Abstract
Trans-4-hydroxy-2-nonenal (4-HNE), a major electrophilic by-product of lipid peroxidation, is able to interact with DNA to form exocyclic guanine adducts. 4-HNE is a mutagen and a significant amount of 4-HNE-guanine adduct has been detected in normal cells. Recently, it has been reported that exposure of the wild-type p53 human lymphoblastoid cell line to 4-HNE causes a high frequency of G to T transversion mutations at the third base of codon 249 (-AGG*-) in the p53 gene, a mutational hotspot in human cancers, particularly hepatocellular carcinoma. These findings raise a possibility that 4-HNE could be an important etiological agent for human cancers that have a mutation at codon 249 of the p53 gene. However, to date, the sequence specificity of 4-HNE-DNA binding remains unclear due to the lack of methodology. To address this question, we have developed a method, using UvrABC nuclease, a nucleotide excision repair enzyme complex isolated from Escherichia coli, to map the distribution of 4-HNE-DNA adducts in human p53 gene at the nucleotide sequence level. We found that 4-HNE-DNA adducts are preferentially formed at the third base of codon 249 in the p53 gene. The preferential binding of 4-HNE was also observed at codon 174, which has the same sequence and the same nearest neighbor sequences (-GAGG*C-) as codon 249. These results suggest that 4-HNE may be an important etiological agent for human cancers that have a mutation at codon 249 of the p53 gene.
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Affiliation(s)
- Wenwei Hu
- Department of Environmental Medicine, Pathology and Medicine, New York University School of Medicine, Tuxedo, NY 10987, USA
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42
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Ananthasubramaniam K, Iyer G, Karthikeyan V. Giant left atrium secondary to tight mitral stenosis leading to acquired Lutembacher syndrome: a case report with emphasis on role of echocardiography in assessment of Lutembacher syndrome. J Am Soc Echocardiogr 2001; 14:1033-5. [PMID: 11593210 DOI: 10.1067/mje.2001.111265] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lutembacher syndrome is an unusual clinical entity of congenital secundum atrial septal defect in combination with rheumatic mitral stenosis. Although this classic form is seldom seen by the adult cardiologist, spontaneous Lutembacher syndrome as discussed later or the iatrogenic variant is not infrequently encountered. The pathophysiologic, clinical, and hemodynamic differences of mitral valve disease in the presence of atrial septal defect compared with isolated mitral stenosis are highlighted in this case review. Special emphasis has also been given to echocardiographic evaluation of this syndrome complex, particularly in the setting of percutaneous mitral valvuloplasty, which produces the iatrogenic form of Lutembacher syndrome.
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Affiliation(s)
- K Ananthasubramaniam
- Henry Ford Heart and Vascular Institute and the Department of Internal Medicine, Detroit, Michigan 48202, USA.
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43
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Abstract
How do people perceive routine events, such as making a bed, as these events unfold in time? Research on knowledge structures suggests that people conceive of events as goal-directed partonomic hierarchies. Here, participants segmented videos of events into coarse and fine units on separate viewings; some described the activity of each unit as well. Both segmentation and descriptions support the hierarchical bias hypothesis in event perception: Observers spontaneously encoded the events in terms of partonomic hierarchies. Hierarchical organization was strengthened by simultaneous description and, to a weaker extent, by familiarity. Describing from memory rather than perception yielded fewer units but did not alter the qualitative nature of the descriptions. Although the descriptions were telegraphic and without communicative intent, their hierarchical structure was evident to naive readers. The data suggest that cognitive schemata mediate between perceptual and functional information about events and indicate that these knowledge structures may be organized around object/action units.
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Affiliation(s)
- J M Zacks
- Department of Psychology, Stanford University, USA.
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Fitzgerald LW, Iyer G, Conklin DS, Krause CM, Marshall A, Patterson JP, Tran DP, Jonak GJ, Hartig PR. Messenger RNA editing of the human serotonin 5-HT2C receptor. Neuropsychopharmacology 1999; 21:82S-90S. [PMID: 10432493 DOI: 10.1016/s0893-133x(99)00004-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA encoding the rat serotonin 5-HT2C receptor undergoes editing whereby one to four adenosines are converted to inosines. This conversion can change up to three codons out of a stretch of five in the second intracellular loop of the receptor. RNA editing of the rat 5-HT2C receptor that changes all three codons was shown previously to alter intracellular signaling by 5-HT without changing its receptor-binding affinity. We analyzed 5-HT2C receptor editing in human brain and hypothalamic RNA samples and confirmed that all four adenosine editing sites observed in rat were also present in human samples. Additionally, we identified a novel editing site in the middle edited codon that extends the repertoire of 5-HT2C receptors by six additional protein isoforms. We observed that editing reduces both the binding affinity and functional potency of agonists for recombinant human 5-HT2C receptor isoforms. This effect on binding affinity was proportional to the agonist's intrinsic activity, with full agonists most affected, and antagonists showing no effect. These data suggest that RNA editing may alter coupling energetics within the ternary complex, thereby altering agonist binding affinities, G protein coupling, and functional responses. RNA editing may thus provide a novel mechanism for regulating 5-HT synaptic signaling and plasticity.
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Affiliation(s)
- L W Fitzgerald
- CNS Diseases Research, DuPont Pharmaceuticals Research Laboratories, Wilmington, Delaware 19880, USA
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45
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Fitzgerald LW, Conklin DS, Krause CM, Marshall AP, Patterson JP, Tran DP, Iyer G, Kostich WA, Largent BL, Hartig PR. High-affinity agonist binding correlates with efficacy (intrinsic activity) at the human serotonin 5-HT2A and 5-HT2C receptors: evidence favoring the ternary complex and two-state models of agonist action. J Neurochem 1999; 72:2127-34. [PMID: 10217294 DOI: 10.1046/j.1471-4159.1999.0722127.x] [Citation(s) in RCA: 45] [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: 11/20/2022]
Abstract
Many modern models of receptor-G protein function assume that there is a direct relationship between high-affinity agonist binding and efficacy. The validity of this assumption has been recently questioned for the serotonin 5-HT2A receptor. We examined the intrinsic activities of various ligands in activating phosphoinositide hydrolysis and measured their respective binding affinities to the high- and low-affinity states of the 5-HT2C (VNV isoform) and 5-HT(2A) receptors. Ligand binding affinities for the high-affinity state of the receptors were determined using 1-(4-[125I]iodo-2,5-dimethoxyphenyl)2-aminopropane, whereas [3H]mesulergine and N-[3H]methylspiperone were used, in the presence of excess guanine nucleotide [guanosine 5'-O-(3-thiotriphosphate)], to define binding to the low-affinity state of the 5-HT2C and 5-HT2A receptors, respectively. Antagonists labeled the high- and low-affinity states of each receptor with comparable affinities. Previously identified inverse agonists of the 5-HT2C receptor behaved as silent antagonists in our systems even when the receptor was overexpressed at a relatively high density. In contrast, the ability of agonists to bind differentially to the high- and low-affinity states of the 5-HT2A and 5-HT2C receptors was highly correlated (r2 = 0.86 and 0.96, respectively) with their intrinsic activities. These data suggest that high-affinity agonist states can account for agonist efficacy at human 5-HT2A or 5-HT2C receptors without the need for considering additional transition or active states of the receptor-ligand complex. The procedure described herein may expedite drug discovery efforts by predicting intrinsic activities of ligands solely from ligand binding assays.
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Affiliation(s)
- L W Fitzgerald
- CNS Diseases Research, DuPont Pharmaceuticals Research Laboratories, Wilmington, Delaware 19880, USA
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Chan SY, Louie MC, Piccotti JR, Iyer G, Ling X, Yang ZY, Nabel GJ, Bishop DK. Genetic vaccination-induced immune responses to the human immunodeficiency virus protein Rev: emergence of the interleukin 2-producing helper T lymphocyte. Hum Gene Ther 1998; 9:2187-96. [PMID: 9794203 DOI: 10.1089/hum.1998.9.15-2187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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] [Indexed: 11/12/2022] Open
Abstract
Rev M10 is a trans-dominant negative inhibitor of HIV replication. Hence, stable transduction of CD4+ T cells with Rev M10 represents a novel gene therapy aimed at inhibiting HIV replication within these cells, thereby slowing the progression of AIDS. However, the immune system may recognize Rev M10 as foreign and target transduced cells for elimination. In the current study, mice were genetically immunized with a plasmid encoding Rev M10, to (1) identify immune parameters that may be induced by Rev M10 gene transfer, (2) determine the impact of repeated introduction of the Rev M10-encoding plasmid on the immune response to the transgene product, and (3) determine if cotransfection with a plasmid encoding TGFbeta1 would suppress the response. Kinetic studies revealed that Rev-specific IL-2-producing helper T lymphocytes (HTLs) appeared following the second genetic immunization, peaked after the third, and persisted at peak levels for at least 6 weeks. Rev-specific HTLs were CD4+, and the development of these cells was ablated by cotransfection with TGFbeta1. Other cytokines were not readily detectable when immune splenocytes were restimulated with Rev in vitro, and Rev-specific IgG antibodies were not present in the sera of these mice. To our knowledge, this represents the first report that genetic immunization with Rev M10 induces an immune response that is dominated by IL-2-producing HTLs. Further, this study demonstrates the potential utility of introducing immunosuppressive genes as a means to control the immune response to foreign transgene products.
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Affiliation(s)
- S Y Chan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor 48109, USA
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Abstract
Gastrin gene expression is regulated by developmental cues, pH, and inflammation. These processes are mediated by various extracellular ligands, e.g., growth factors, cytokines, and neuropeptides that also stimulate c-fos gene expression. Therefore, to determine whether Fos is required for stimulation of the gastrin promoter, a c-fos sense expression vector was coexpressed with a gastrin reporter construct in a GH4 rat pituitary cell line. We found that epidermal growth factor (EGF) and tumor necrosis factor-alpha (TNF-alpha) transiently stimulate an increase in Fos protein that precedes stimulation of the gastrin promoter. However, the induction mediated by TNF-alpha was weaker than that mediated by EGF, indicating minimal overlap of the signaling pathways activated by EGF and TNF-alpha. Accordingly, overexpression of c-fos mRNA facilitated primarily EGF rather than TNF-alpha induction of the gastrin promoter. Expression of the c-fos gene in the absence of ligand did not stimulate the gastrin promoter. Thus c-fos gene expression is required but is not sufficient for induction of the gastrin promoter by EGF.
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Affiliation(s)
- P Marks
- Department of Internal Medicine, University of Michigan, Ann Arbor, USA
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48
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Bazzi MN, Iyer G. Chronic diarrhea and vomiting in an elderly woman. Hosp Pract (Off Ed) 1993; 28:26-7. [PMID: 8227247 DOI: 10.1080/21548331.1993.11442870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- M N Bazzi
- Wayne State University School of Medicine, Detroit
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49
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Mohandas KM, Swaroop VS, Desai DC, Dhir V, Nagral A, Iyer G. Upper esophageal webs, iron deficiency anemia, and esophageal cancer. Am J Gastroenterol 1991; 86:117-8. [PMID: 1986539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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50
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