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Black TA, Paterson MJ, Timlick L, Cederwall J, Blais JM, Hollebone B, Orihel DM, Palace VP, Rodriguez-Gil JL, Hanson ML. The Challenges of Characterizing the Zooplankton Community Response Following Simulated Spills of Diluted Bitumen into Boreal Lake Limnocorrals. Bull Environ Contam Toxicol 2023; 110:46. [PMID: 36690874 DOI: 10.1007/s00128-022-03680-7] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
We attempted to characterize zooplankton community response following spills of the unconventional crude oil, diluted bitumen (dilbit), into 10-m diameter, ~ 100 m3, ~ 1.5-m deep boreal lake limnocorrals, including two controls and seven dilbit treatments ranging from 1.5 to 180 L (1:100,000 to 1:1,000 v/v, dilbit:water). Community composition and abundances were monitored weekly to bi-weekly over three months. Total zooplankton biomass and abundance seemingly collapsed in all limnocorrals, regardless of treatment, though some rotifer species persisted. As a result, it was not possible to determine the impacts of dilbit. We theorize several potential non-oil-related reasons for the sudden community collapse - including elevated zinc levels, fish grazing pressures, and sampling biases - and provide guidance for future work using in-lake enclosures.
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Affiliation(s)
- T A Black
- Department of Environment & Geography, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada.
| | - M J Paterson
- International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), R3B 0T4, Winnipeg, MB, Canada
| | - L Timlick
- International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), R3B 0T4, Winnipeg, MB, Canada
| | - J Cederwall
- Department of Biology, Queen's University, K7L 3N6, Kingston, ON, Canada
| | - J M Blais
- Department of Biology, University of Ottawa, K1N 9A7, Ottawa, ON, Canada
| | - B Hollebone
- Environment and Climate Change Canada, K1V 1H2, Ottawa, ON, Canada
| | - D M Orihel
- Department of Biology, Queen's University, K7L 3N6, Kingston, ON, Canada
| | - V P Palace
- International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), R3B 0T4, Winnipeg, MB, Canada
| | - J L Rodriguez-Gil
- Department of Environment & Geography, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada
- International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), R3B 0T4, Winnipeg, MB, Canada
| | - M L Hanson
- Department of Environment & Geography, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada
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Chapin WJ, Till JE, Hwang WT, Eads JR, Karasic TB, O'Dwyer PJ, Schneider CJ, Teitelbaum UR, Romeo J, Black TA, Christensen TE, Redlinger Tabery C, Anderson A, Slade M, LaRiviere M, Yee SS, Reiss KA, O'Hara MH, Carpenter EL. Multianalyte Prognostic Signature Including Circulating Tumor DNA and Circulating Tumor Cells in Patients With Advanced Pancreatic Adenocarcinoma. JCO Precis Oncol 2022; 6:e2200060. [PMID: 35939771 PMCID: PMC9384952 DOI: 10.1200/po.22.00060] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/24/2022] [Accepted: 06/15/2022] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is associated with a poor prognosis. Multianalyte signatures, including liquid biopsy and traditional clinical variables, have shown promise for improving prognostication in other solid tumors but have not yet been rigorously assessed for PDAC. MATERIALS AND METHODS We performed a prospective cohort study of patients with newly diagnosed locally advanced pancreatic cancer (LAPC) or metastatic PDAC (mPDAC) who were planned to undergo systemic therapy. We collected peripheral blood before systemic therapy and assessed circulating tumor cells (CTCs), cell-free DNA concentration (cfDNA), and circulating tumor KRAS (ctKRAS)-variant allele fraction (VAF). Association of variables with overall survival (OS) was assessed in univariate and multivariate survival analysis, and comparisons were made between models containing liquid biopsy variables combined with traditional clinical prognostic variables versus models containing traditional clinical prognostic variables alone. RESULTS One hundred four patients, 40 with LAPC and 64 with mPDAC, were enrolled. CTCs, cfDNA concentration, and ctKRAS VAF were all significantly higher in patients with mPDAC than patients with LAPC. ctKRAS VAF (cube root; 0.05 unit increments; hazard ratio, 1.11; 95% CI, 1.03 to 1.21; P = .01), and CTCs ≥ 1/mL (hazard ratio, 2.22; 95% CI, 1.34 to 3.69; P = .002) were significantly associated with worse OS in multivariate analysis while cfDNA concentration was not. A model selected by backward selection containing traditional clinical variables plus liquid biopsy variables had better discrimination of OS compared with a model containing traditional clinical variables alone (optimism-corrected Harrell's C-statistic 0.725 v 0.681). CONCLUSION A multianalyte prognostic signature containing CTCs, ctKRAS, and cfDNA concentration outperformed a model containing traditional clinical variables alone suggesting that CTCs, ctKRAS, and cfDNA provide prognostic information complementary to traditional clinical variables in advanced PDAC.
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Affiliation(s)
- William J. Chapin
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jacob E. Till
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA
| | - Jennifer R. Eads
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Thomas B. Karasic
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peter J. O'Dwyer
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charles J. Schneider
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Ursina R. Teitelbaum
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Janae Romeo
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Theresa E. Christensen
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Colleen Redlinger Tabery
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | | | - Michael LaRiviere
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kim A. Reiss
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mark H. O'Hara
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Sen M, Hausler RM, Dulmage K, Black TA, Murphy W, Pletcher Jr CH, Wang L, Chen C, Yee SS, Bornheimer SJ, Maxwell KN, Stanger BZ, Moore JS, Thompson JC, Carpenter EL. Transcriptional profiling of single tumour cells from pleural effusions reveals heterogeneity of epithelial to mesenchymal transition and extra-cellular matrix marker expression. Clin Transl Med 2022; 12:e888. [PMID: 35811459 PMCID: PMC9271990 DOI: 10.1002/ctm2.888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Moen Sen
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan M. Hausler
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Keely Dulmage
- Life Science InnovationBD Technologies and InnovationsDurhamNorth CarolinaUSA
| | - Taylor A. Black
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - William Murphy
- Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Charles H. Pletcher Jr
- Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ling Wang
- Life Science InnovationBD Technologies and InnovationsDurhamNorth CarolinaUSA
| | - Chang Chen
- Life Science InnovationBD Technologies and InnovationsDurhamNorth CarolinaUSA
| | - Stephanie S. Yee
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Kara N. Maxwell
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ben Z. Stanger
- Department of Medicine, Division of Gastroenterology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jonni S. Moore
- Department of Pathology and Laboratory Medicine, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jeffrey C. Thompson
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology GroupUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Erica L. Carpenter
- Department of Medicine, Division of Hematology and Oncology, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Black TA, White MS, Blais JM, Hollebone B, Orihel DM, Palace VP, Rodriguez-Gil JL, Hanson ML. Surface oil is the primary driver of macroinvertebrate impacts following spills of diluted bitumen in freshwater. Environ Pollut 2021; 290:117929. [PMID: 34416496 DOI: 10.1016/j.envpol.2021.117929] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
The response of freshwater invertebrates following accidental releases of oil is not well understood. This knowledge gap is more substantial for unconventional oils such as diluted bitumen (dilbit). We evaluated the effects of dilbit on insect emergence and benthic invertebrates by conducting experimental spills in limnocorrals (10-m diameter; ~100-m3) deployed in a boreal lake at the IISD-Experimental Lakes Area, Canada. The study included seven dilbit treatments (spill volumes ranged from 1.5 L [1:66,000, oil:water, v/v] to 180 L [1:590, oil:water, v/v]), two controls, and additional lake reference sites, monitored for 11 weeks. Invertebrate emergence declined at the community level following oil addition in a significantly volume-dependent manner, and by 93-100 % over the 11 weeks following the spill in the highest treatment. Dilbit altered community structure of benthic invertebrates, but not abundance. One-year post-spill and following oil removal using traditional skimming and absorption techniques, benthic richness and abundance were greater among all treatments than the previous year. These results indicate that recovery in community composition is possible following oil removal from a lake ecosystem. Research is needed concerning the mechanisms by which surface oil directly affect adult invertebrates, whether through limiting oviposition, limiting emergence, or both. The response of benthic communities to sediment tar mats is also warranted.
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Affiliation(s)
- T A Black
- Department of Environment & Geography, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
| | - M S White
- Ecometrix, 6800 Campobello Road, Mississauga, Ontario, Canada.
| | - J M Blais
- Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 9A7, Canada.
| | - B Hollebone
- Emergencies Science and Technology Division, Environment and Climate Change Canada, Ottawa, Ontario, K1V 1H2, Canada.
| | - D M Orihel
- School of Environmental Studies and Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
| | - V P Palace
- International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), Winnipeg, Manitoba, R3B 0T4, Canada.
| | - J L Rodriguez-Gil
- Department of Environment & Geography, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada; Department of Biology, University of Ottawa, Ottawa, Ontario, K1N 9A7, Canada; International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA), Winnipeg, Manitoba, R3B 0T4, Canada.
| | - M L Hanson
- Department of Environment & Geography, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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Till JE, Black TA, Gentile C, Abdalla A, Wang Z, Sangha HK, Roth JJ, Sussman R, Yee SS, O'Hara MH, Thompson JC, Aggarwal C, Hwang WT, Elenitoba-Johnson KSJ, Carpenter EL. Optimization of Sources of Circulating Cell-Free DNA Variability for Downstream Molecular Analysis. J Mol Diagn 2021; 23:1545-1552. [PMID: 34454115 DOI: 10.1016/j.jmoldx.2021.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/10/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
Circulating cell-free DNA (ccfDNA) is used increasingly as a cancer biomarker for prognostication, as a correlate for tumor volume, or as input for downstream molecular analysis. Determining optimal blood processing and ccfDNA quantification are crucial for ccfDNA to serve as an accurate biomarker as it moves into the clinical realm. Whole blood was collected from 50 subjects, processed to plasma, and used immediately or frozen at -80°C. Plasma ccfDNA was extracted and concentration was assessed by real-time quantitative PCR (qPCR), fluorimetry, and droplet digital PCR (ddPCR). For the 24 plasma samples from metastatic pancreatic cancer patients, the variant allele fractions (VAF) of KRAS G12/13 pathogenic variants in circulating tumor DNA (ctDNA) were measured by ddPCR. Using a high-speed (16,000 × g) or slower-speed (4100 × g) second centrifugation step showed no difference in ccfDNA yield or ctDNA VAF. A two- versus three-spin centrifugation protocol also showed no difference in ccfDNA yield or ctDNA VAF. A higher yield was observed from fresh versus frozen plasma by qPCR and fluorimetry, whereas a higher yield was observed for frozen versus fresh plasma by ddPCR, however, no difference was observed in ctDNA VAF. Overall, our findings suggest factors to consider when implementing a ccfDNA extraction and quantification workflow in a research or clinical setting.
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Affiliation(s)
- Jacob E Till
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Caren Gentile
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aseel Abdalla
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zhuoyang Wang
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hareena K Sangha
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacquelyn J Roth
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robyn Sussman
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark H O'Hara
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey C Thompson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kojo S J Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Raymond and Ruth Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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6
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Johnson ATC, Kehayias C, Carpenter EL, Piltz-Seymour J, Tanyi JL, Otto C, Lee YE, Black TA, Yee SS, Preti G. Nanoanalysis of plasma volatile organic compounds using novel DNA-decorated carbon nanotube vapor sensors to noninvasively distinguish ovarian and pancreatic cancer from benign and control samples. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.5544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5544 Background: All cells release volatile organic compounds (VOCs) which emanate from body fluids. Our previous preliminary proof of concept study demonstrated that VOCs released from tissue and plasma from ovarian cancer patients are distinct from those released from samples of patients with benign tumors and controls. We seek to create a sensitive and specific, high-throughput screening test for cancer based on analysis of VOCs using novel nanosensors, first targeting cancers with limited clinical screening modalities. In this study we use these sensors to distinguish vapor characteristics in plasma samples from patients with ovarian and pancreatic cancer from benign specimens and controls. Methods: VOCs emanating from.5 mL of thawed, previously banked plasma samples from 93 total individuals were analyzed using a 10-channel nanoelectronic olfaction (“e-nose”) system based on single-stranded DNA-decorated single-walled carbon nanotube (DNA-NT) vapor sensors. Analysis was performed on samples from 20 patients with ovarian cancer, 20 with benign ovarian tumors and 20 age-matched women as well as 13 patients with pancreatic cancer, 10 patients with benign pancreatic disease, and 10 age- and sex-matched controls. All ovarian cancer patients and comparators were non-smokers, while 1 pancreatic patient and 1 corresponding control were current smokers. The sample set included cancer patients with both early- and late-stage disease. All cancer specimens were obtained proximal to initial diagnosis and prior to initiation of therapy. With a test time of approximately 20 minutes per sample, the array output for each individual sample creates a vector in a 10-dimensional sensor space. The ability of the nanosensor array to discriminate between malignant, benign, and healthy groups was investigated using linear discriminant analysis (LDA), support vector machine (SVM), k-nearest neighbors (KNN), and random forest classification algorithms. Each algorithm was trained and tested according to leave-one-out and repeated stratified k-fold cross-validation methods. Results: Compared to their corresponding benign and control specimens, the DNA-NT sensor array was able to discriminate the VOCs from ovarian cancer with 95% accuracy and pancreatic cancer with 90% accuracy. Plasma samples from patients with early-stage ovarian and pancreatic cancers were correctly identified by the algorithms. Conclusions: Nano-enabled DNA coated vapor sensors were able to distinguish the VOC pattern between cancer, benign and control samples in both ovarian and pancreatic cancer. We provide strong evidence that ovarian and pancreatic cancer alters the VOC pattern emanating from plasma. Our results provide optimism that a diagnostic approach based on vapor detection of ovarian and pancreatic cancer is achievable.
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Affiliation(s)
| | | | - Erica L. Carpenter
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jody Piltz-Seymour
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Janos Laszlo Tanyi
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Cindy Otto
- University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| | | | - Taylor A. Black
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Stephanie S. Yee
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
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7
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Till JE, Abdalla A, Bhagwat N, Black TA, Wang Z, Yee SS, Gherardini PF, Kitch LJ, Selinsky C, Lyman JP, LaVallee T, Fisher GA, Rahma OE, Ko AH, Wainberg ZA, Wolff RA, O'Reilly EM, Vonderheide RH, O'Hara MH, Carpenter EL. Baseline level and early on-treatment clearance of circulating mutant KRAS in metastatic pancreatic ductal adenocarcinoma treated with chemotherapy with or without immunotherapy. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.4122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4122 Background: Traditional imaging-guided therapeutic decision-making for patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) may lag and, on occasion, be misleading. The concept of liquid biopsy-based molecular response holds promise for proximate and accurate therapy monitoring and assessment of emerging resistance to therapy. Here we investigate the association between baseline (pre-treatment) level and early, on-treatment changes in plasma circulating cell-free DNA (ccfDNA) mutant KRAS (ctKRAS) with progression-free survival (PFS) and overall survival (OS) in mPDAC. Methods: 189 plasma samples were analyzed from 123 total patients with mPDAC. An initial cohort included 54 patients treated at the University of Pennsylvania who received first-line standard of care (SOC) regimens and had a baseline plasma sample. Of these, 21 also had an on-therapy sample collected at ̃8 weeks. We also analyzed an independent cohort of 69 patients enrolled in the PRINCE trial (NCT03214250) who had a baseline sample, of which 45 also had an on-treatment sample at ̃8 weeks. PRINCE trial patients received gemcitabine/nab-paclitaxel with immunotherapy (I/O) agents (APX005M and/or nivolumab). ctKRAS variant allele fraction (VAF) was quantified by droplet digital PCR on pre-amplified ccfDNA. Baseline ctKRAS was dichotomized at 5% VAF. ctKRAS clearance was defined as detectable ctKRAS at baseline followed by ctKRAS becoming undetectable in the on-treatment sample. Results: Baseline ctKRAS (above/below 5% VAF) and ctKRAS clearance were associated with PFS and OS in both cohorts (Table). Further, in a multivariate cox regression model, ctKRAS clearance associated with improved PFS (HR 3.8, 1.4-10.9 or 3.6, 1.8-7.2) in both the SOC and I/O cohorts, respectively, and OS in the SOC cohort (HR 5.5, 1.5-20.8) after adjusting for baseline VAF. Conclusions: Baseline ctKRAS is significantly associated with OS and PFS in mPDAC in both independent cohorts. Further, early on-treatment ctKRAS clearance is strongly associated with improved PFS and OS, independent of baseline ctKRAS VAF. These data strongly support further investigation of ccfDNA as a biomarker of response and resistance to therapy.[Table: see text]
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Affiliation(s)
- Jacob E. Till
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Aseel Abdalla
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Neha Bhagwat
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Taylor A. Black
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Zhuoyang Wang
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | - Stephanie S. Yee
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
| | | | - Lacey J. Kitch
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Cheryl Selinsky
- Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | | | | | | | | | - Andrew H. Ko
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | | | - Robert A. Wolff
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Mark H. O'Hara
- University of Pennsylvania Abramson Cancer Center, Philadelphia, PA
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8
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Thompson JC, Carpenter EL, Silva BA, Rosenstein J, Chien AL, Quinn K, Espenschied CR, Mak A, Kiedrowski LA, Lefterova M, Nagy RJ, Katz SI, Yee SS, Black TA, Singh AP, Ciunci CA, Bauml JM, Cohen RB, Langer CJ, Aggarwal C. Serial Monitoring of Circulating Tumor DNA by Next-Generation Gene Sequencing as a Biomarker of Response and Survival in Patients With Advanced NSCLC Receiving Pembrolizumab-Based Therapy. JCO Precis Oncol 2021; 5:PO.20.00321. [PMID: 34095713 PMCID: PMC8169078 DOI: 10.1200/po.20.00321] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 08/09/2020] [Revised: 01/07/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
Although the majority of patients with metastatic non-small-cell lung cancer (mNSCLC) lacking a detectable targetable mutation will receive pembrolizumab-based therapy in the frontline setting, predicting which patients will experience a durable clinical benefit (DCB) remains challenging. MATERIALS AND METHODS Patients with mNSCLC receiving pembrolizumab monotherapy or in combination with chemotherapy underwent a 74-gene next-generation sequencing panel on blood samples obtained at baseline and at 9 weeks. The change in circulating tumor DNA levels on-therapy (molecular response) was quantified using a ratio calculation with response defined by a > 50% decrease in mean variant allele fraction. Patient response was assessed using RECIST 1.1; DCB was defined as complete or partial response or stable disease that lasted > 6 months. Progression-free survival and overall survival were recorded. RESULTS Among 67 patients, 51 (76.1%) had > 1 variant detected at a variant allele fraction > 0.3% and thus were eligible for calculation of molecular response from paired baseline and 9-week samples. Molecular response values were significantly lower in patients with an objective radiologic response (log mean 1.25% v 27.7%, P < .001). Patients achieving a DCB had significantly lower molecular response values compared to patients with no durable benefit (log mean 3.5% v 49.4%, P < .001). Molecular responders had significantly longer progression-free survival (hazard ratio, 0.25; 95% CI, 0.13 to 0.50) and overall survival (hazard ratio, 0.27; 95% CI, 0.12 to 0.64) compared with molecular nonresponders. CONCLUSION Molecular response assessment using circulating tumor DNA may serve as a noninvasive, on-therapy predictor of response to pembrolizumab-based therapy in addition to standard of care imaging in mNSCLC. This strategy requires validation in independent prospective studies.
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Affiliation(s)
- Jeffrey C. Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Benjamin A. Silva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jamie Rosenstein
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Austin L. Chien
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | | | | | | | | | | | - Sharyn I. Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Aditi P. Singh
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Christine A. Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Joshua M. Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Roger B. Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Corey J. Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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9
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Bagley SJ, Till J, Abdalla A, Sangha HK, Yee SS, Freedman J, Black TA, Hussain J, Binder ZA, Brem S, Desai AS, O’Rourke DM, Long Q, Nabavizadeh SA, Carpenter EL. Association of plasma cell-free DNA with survival in patients with IDH wild-type glioblastoma. Neurooncol Adv 2021; 3:vdab011. [PMID: 33615225 PMCID: PMC7883768 DOI: 10.1093/noajnl/vdab011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND We aimed to determine whether plasma cell-free DNA (cfDNA) concentration is associated with survival in patients with isocitrate dehydrogenase (IDH) wild-type glioblastoma (GBM). METHODS Pre-operative and post-chemoradiotherapy blood samples were prospectively collected from patients with newly diagnosed IDH wild-type GBM. Patients underwent surgical resection or biopsy and received adjuvant radiotherapy with concomitant temozolomide. Cell-free DNA (cfDNA) was isolated from plasma and quantified using SYBR Green-based q polymerase chain reaction (qPCR). RESULTS Sixty-two patients were enrolled and categorized into high vs. low cfDNA groups relative to the pre-operative median value (25.2 ng/mL, range 5.7-153.0 ng/mL). High pre-operative cfDNA concentration was associated with inferior PFS (median progression-free survival (PFS), 3.4 vs. 7.7 months; log-rank P = .004; hazard ratio [HR], 2.19; 95% CI, 1.26-3.81) and overall survival (OS) (median OS, 8.0 vs. 13.9 months; log-rank P = .01; HR, 2.43; 95% CI, 1.19-4.95). After adjusting for risk factors, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status, pre-operative cfDNA remained independently associated with PFS (HR, 2.70; 95% CI, 1.50-4.83; P = .001) and OS (HR, 2.65; 95% CI, 1.25-5.59; P = .01). Post-hoc analysis of change in cfDNA post-chemoradiotherapy compared to pre-surgery (n = 24) showed increasing cfDNA concentration was associated with worse PFS (median, 2.7 vs. 6.0 months; log-rank P = .003; HR, 4.92; 95% CI, 1.53-15.84) and OS (median, 3.9 vs. 19.4 months; log-rank P < .001; HR, 7.77; 95% CI, 2.17-27.76). CONCLUSIONS cfDNA concentration is a promising prognostic biomarker for patients with IDH wild-type GBM. Plasma cfDNA can be obtained noninvasively and may enable more accurate estimates of survival and effective clinical trial stratification.
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Affiliation(s)
- Stephen J Bagley
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jacob Till
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aseel Abdalla
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hareena K Sangha
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Stephanie S Yee
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jake Freedman
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Taylor A Black
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jasmin Hussain
- Department of Neurosurgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Zev A Binder
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurosurgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Steven Brem
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurosurgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Arati S Desai
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Donald M O’Rourke
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neurosurgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Seyed Ali Nabavizadeh
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Radiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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10
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Haas NB, LaRiviere MJ, Buckingham TH, Cherkas Y, Calara-Nielsen K, Foulk B, Patel J, Gross S, Smirnov D, Vaughn DJ, Amaravadi R, Wellen KE, Savitch SL, Majmundar KJ, Black TA, Yee SS, He M, Min EJ, Long Q, Jones JO, Pal SK, Carpenter EL. Blood-based gene expression signature associated with metastatic castrate-resistant prostate cancer patient response to abiraterone plus prednisone or enzalutamide. Prostate Cancer Prostatic Dis 2020; 24:448-456. [PMID: 33009489 DOI: 10.1038/s41391-020-00295-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Precision medicine approaches for managing patients with metastatic castrate-resistant prostate cancer (mCRPC) are lacking. Non-invasive approaches for molecular monitoring of disease are urgently needed, especially for patients suffering from bone metastases for whom tissue biopsy is challenging. Here we utilized baseline blood samples to identify mCRPC patients most likely to benefit from abiraterone plus prednisone (AAP) or enzalutamide. METHODS Baseline blood samples were collected for circulating tumor cell (CTC) enumeration and qPCR-based gene expression analysis from 51 men with mCRPC beginning treatment with abiraterone or enzalutamide. RESULTS Of 51 patients (median age 68 years [51-82]), 22 received AAP (abiraterone 1000 mg/day plus prednisone 10 mg/day) and 29 received enzalutamide (160 mg/day). The cohort was randomly divided into training (n = 37) and test (n = 14) sets. Baseline clinical variables (Gleason score, PSA, testosterone, and hemoglobin), CTC count, and qPCR-based gene expression data for 141 genes/isoforms in CTC-enriched blood were analyzed with respect to overall survival (OS). Genes with expression most associated with OS included MSLN, ARG2, FGF8, KLK3, ESRP2, NPR3, CCND1, and WNT5A. Using a Cox-elastic net model for our test set, the 8-gene expression signature had a c-index of 0.87 (95% CI [0.80, 0.94]) and was more strongly associated with OS than clinical variables or CTC count alone, or a combination of the three variables. For patients with a low-risk vs. high-risk gene expression signature, median OS was not reached vs. 18 months, respectively (HR 5.32 [1.91-14.80], p = 0.001). For the subset of 41 patients for whom progression-free survival (PFS) data was available, the median PFS for patients with a low-risk vs high-risk gene expression signature was 20 vs. 5 months, respectively (HR 2.95 [1.46-5.98], p = 0.003). CONCLUSIONS If validated in a larger prospective study, this test may predict patients most likely to benefit from second-generation antiandrogen therapy.
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Affiliation(s)
- Naomi B Haas
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael J LaRiviere
- Department of Radiation Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Thomas H Buckingham
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yauheniya Cherkas
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - Karl Calara-Nielsen
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - Brad Foulk
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - Jaymala Patel
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - Steven Gross
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - Denis Smirnov
- Janssen, Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, USA
| | - David J Vaughn
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ravi Amaravadi
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Samantha L Savitch
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Krishna J Majmundar
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Taylor A Black
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie S Yee
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Miaoling He
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Eun Jeong Min
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeremy O Jones
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Sumanta K Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Erica L Carpenter
- Division of Hematology/Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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11
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Yang Z, LaRiviere MJ, Ko J, Till JE, Christensen T, Yee SS, Black TA, Tien K, Lin A, Shen H, Bhagwat N, Herman D, Adallah A, O'Hara MH, Vollmer CM, Katona BW, Stanger BZ, Issadore D, Carpenter EL. A Multianalyte Panel Consisting of Extracellular Vesicle miRNAs and mRNAs, cfDNA, and CA19-9 Shows Utility for Diagnosis and Staging of Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2020; 26:3248-3258. [PMID: 32299821 PMCID: PMC7334066 DOI: 10.1158/1078-0432.ccr-19-3313] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 10/15/2019] [Revised: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 12/27/2022]
Abstract
PURPOSE To determine whether a multianalyte liquid biopsy can improve the detection and staging of pancreatic ductal adenocarcinoma (PDAC). EXPERIMENTAL DESIGN We analyzed plasma from 204 subjects (71 healthy, 44 non-PDAC pancreatic disease, and 89 PDAC) for the following biomarkers: tumor-associated extracellular vesicle miRNA and mRNA isolated on a nanomagnetic platform that we developed and measured by next-generation sequencing or qPCR, circulating cell-free DNA (ccfDNA) concentration measured by qPCR, ccfDNA KRAS G12D/V/R mutations detected by droplet digital PCR, and CA19-9 measured by electrochemiluminescence immunoassay. We applied machine learning to training sets and subsequently evaluated model performance in independent, user-blinded test sets. RESULTS To identify patients with PDAC versus those without, we generated a classification model using a training set of 47 subjects (20 PDAC and 27 noncancer). When applied to a blinded test set (N = 136), the model achieved an AUC of 0.95 and accuracy of 92%, superior to the best individual biomarker, CA19-9 (89%). We next used a cohort of 20 patients with PDAC to train our model for disease staging and applied it to a blinded test set of 25 patients clinically staged by imaging as metastasis-free, including 9 subsequently determined to have had occult metastasis. Our workflow achieved significantly higher accuracy for disease staging (84%) than imaging alone (accuracy = 64%; P < 0.05). CONCLUSIONS Algorithmically combining blood-based biomarkers may improve PDAC diagnostic accuracy and preoperative identification of nonmetastatic patients best suited for surgery, although larger validation studies are necessary.
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Affiliation(s)
- Zijian Yang
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael J LaRiviere
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacob E Till
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Theresa Christensen
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Tien
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Lin
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hanfei Shen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Neha Bhagwat
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel Herman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Adallah
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark H O'Hara
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charles M Vollmer
- Division of General Surgery, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Bryson W Katona
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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12
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Aggarwal C, Thompson JC, Chien AL, Quinn KJ, Hwang WT, Black TA, Yee SS, Christensen TE, LaRiviere MJ, Silva BA, Banks KC, Nagy RJ, Helman E, Berman AT, Ciunci CA, Singh AP, Wasser JS, Bauml JM, Langer CJ, Cohen RB, Carpenter EL. Baseline Plasma Tumor Mutation Burden Predicts Response to Pembrolizumab-based Therapy in Patients with Metastatic Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:2354-2361. [PMID: 32102950 DOI: 10.1158/1078-0432.ccr-19-3663] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 11/21/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE The role of plasma-based tumor mutation burden (pTMB) in predicting response to pembrolizumab-based first-line standard-of-care therapy for metastatic non-small cell lung cancer (mNSCLC) has not been explored. EXPERIMENTAL DESIGN A 500-gene next-generation sequencing panel was used to assess pTMB. Sixty-six patients with newly diagnosed mNSCLC starting first-line pembrolizumab-based therapy, either alone or in combination with chemotherapy, were enrolled (Clinicaltrial.gov identifier: NCT03047616). Response was assessed using RECIST 1.1. Associations were made for patient characteristics, 6-month durable clinical benefit (DCB), progression-free survival (PFS), and overall survival (OS). RESULTS Of 66 patients, 52 (78.8%) were pTMB-evaluable. Median pTMB was 16.8 mutations per megabase (mut/Mb; range, 1.9-52.5) and was significantly higher for patients achieving DCB compared with no durable benefit (21.3 mut/Mb vs. 12.4 mut/Mb, P = 0.003). For patients with pTMB ≥ 16 mut/Mb, median PFS was 14.1 versus 4.7 months for patients with pTMB < 16 mut/Mb [HR, 0.30 (0.16-0.60); P < 0.001]. Median OS for patients with pTMB ≥ 16 was not reached versus 8.8 months for patients with pTMB < 16 mut/Mb [HR, 0.48 (0.22-1.03); P = 0.061]. Mutations in ERBB2 exon 20, STK11, KEAP1, or PTEN were more common in patients with no DCB. A combination of pTMB ≥ 16 and absence of negative predictor mutations was associated with PFS [HR, 0.24 (0.11-0.49); P < 0.001] and OS [HR, 0.31 (0.13-0.74); P = 0.009]. CONCLUSIONS pTMB ≥ 16 mut/Mb is associated with improved PFS after first-line standard-of-care pembrolizumab-based therapy in mNSCLC. STK11/KEAP1/PTEN and ERBB2 mutations may help identify pTMB-high patients unlikely to respond. These results should be validated in larger prospective studies.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Agents, Immunological/administration & dosage
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Female
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Metastasis
- Predictive Value of Tests
- Prospective Studies
- Survival Rate
- Treatment Outcome
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Affiliation(s)
- Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Jeffrey C Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Austin L Chien
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Theresa E Christensen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Michael J LaRiviere
- Division of Radiation Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Benjamin A Silva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | | | | | - Abigail T Berman
- Division of Radiation Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christine A Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Aditi P Singh
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jeffrey S Wasser
- Neag Comprehensive Cancer Center, UConn Health, University of Connecticut, Farmington, Connecticut
| | - Joshua M Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Corey J Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Roger B Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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13
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Sen M, Hahn F, Black TA, DeMarshall M, Porter W, Snowden E, Yee SS, Tong F, Ferguson M, Fleshman EN, Nakagawa H, Falk GW, Ginsberg GG, Kochman ML, Blaesius R, Rustgi AK, Carpenter EL. Correction: Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue. Oncotarget 2019; 10:5119. [PMID: 31489121 PMCID: PMC6707951 DOI: 10.18632/oncotarget.27161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Moen Sen
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,These co-first authors have contributed equally to this work
| | - Friedrich Hahn
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA.,These co-first authors have contributed equally to this work
| | - Taylor A Black
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,These co-first authors have contributed equally to this work
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Warren Porter
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Eileen Snowden
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Stephanie S Yee
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frances Tong
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Mitchell Ferguson
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Emylee N Fleshman
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hiroshi Nakagawa
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary W Falk
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory G Ginsberg
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Kochman
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rainer Blaesius
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Co-corresponding authors
| | - Erica L Carpenter
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Co-corresponding authors
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14
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Sen M, Hahn F, Black TA, DeMarshall M, Porter W, Snowden E, Yee SS, Tong F, Ferguson M, Fleshman EN, Nakagawa H, Falk GW, Ginsberg GG, Kochman ML, Blaesius R, Rustgi AK, Carpenter EL. Flow based single cell analysis of the immune landscape distinguishes Barrett's esophagus from adjacent normal tissue. Oncotarget 2019; 10:3592-3604. [PMID: 31217895 PMCID: PMC6557213 DOI: 10.18632/oncotarget.26911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/17/2019] [Accepted: 04/14/2019] [Indexed: 01/21/2023] Open
Abstract
Barrett’s esophagus (BE) is metaplasia of the squamous epithelium to a specialized columnar epithelium. BE progresses through low- and high-grade dysplasia before developing into esophageal adenocarcinoma. The BE microenvironment is not well defined. We compare 12 human clinical BE and adjacent normal squamous epithelium biopsies using single cell immunophenotyping by flow cytometry. A cassette of 19 epithelial and immune cell markers was used to detect differences between cellular compartments in normal and BE tissues. We found that the BE microenvironment has an immunological landscape distinct from adjacent normal epithelium. BE has an increased percentage of epithelial cells with a concomitant decrease in the percentage of immune cells, accompanied by a shift in the immune landscape from a predominantly T cell rich microenvironment in normal tissue to a B cell rich landscape in BE tissue. Hierarchical clustering separates BE and normal samples into two discrete groups based upon our 19-marker panel, but also reveals unexpected, shared phenotypes for three patients. Our results suggest that flow based single cell analysis may have the potential for revealing clinically relevant differences between BE and normal adjacent tissue, and that surface immunophenotypes could identify specific subpopulations from dysplastic tissue for further investigation.
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Affiliation(s)
- Moen Sen
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Friedrich Hahn
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Taylor A Black
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Warren Porter
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Eileen Snowden
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Stephanie S Yee
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frances Tong
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Mitchell Ferguson
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Emylee N Fleshman
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hiroshi Nakagawa
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gary W Falk
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory G Ginsberg
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Kochman
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rainer Blaesius
- Department of Genomic Sciences, BD Technologies and Innovation, Research Triangle Park, Durham, North Carolina, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erica L Carpenter
- Division of Hematology and Oncology, Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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15
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Lee JW, Stone ML, Porrett PM, Thomas SK, Komar CA, Li JH, Delman D, Graham K, Gladney WL, Hua X, Black TA, Chien AL, Majmundar KS, Thompson JC, Yee SS, O'Hara MH, Aggarwal C, Xin D, Shaked A, Gao M, Liu D, Borad MJ, Ramanathan RK, Carpenter EL, Ji A, de Beer MC, de Beer FC, Webb NR, Beatty GL. Hepatocytes direct the formation of a pro-metastatic niche in the liver. Nature 2019; 567:249-252. [PMID: 30842658 PMCID: PMC6430113 DOI: 10.1038/s41586-019-1004-y] [Citation(s) in RCA: 224] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/12/2019] [Indexed: 12/25/2022]
Abstract
The liver is the most common site of metastatic disease1. Although this metastatic tropism may reflect the mechanical trapping of circulating tumour cells, liver metastasis is also dependent, at least in part, on the formation of a 'pro-metastatic' niche that supports the spread of tumour cells to the liver2,3. The mechanisms that direct the formation of this niche are poorly understood. Here we show that hepatocytes coordinate myeloid cell accumulation and fibrosis within the liver and, in doing so, increase the susceptibility of the liver to metastatic seeding and outgrowth. During early pancreatic tumorigenesis in mice, hepatocytes show activation of signal transducer and activator of transcription 3 (STAT3) signalling and increased production of serum amyloid A1 and A2 (referred to collectively as SAA). Overexpression of SAA by hepatocytes also occurs in patients with pancreatic and colorectal cancers that have metastasized to the liver, and many patients with locally advanced and metastatic disease show increases in circulating SAA. Activation of STAT3 in hepatocytes and the subsequent production of SAA depend on the release of interleukin 6 (IL-6) into the circulation by non-malignant cells. Genetic ablation or blockade of components of IL-6-STAT3-SAA signalling prevents the establishment of a pro-metastatic niche and inhibits liver metastasis. Our data identify an intercellular network underpinned by hepatocytes that forms the basis of a pro-metastatic niche in the liver, and identify new therapeutic targets.
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Affiliation(s)
- Jae W Lee
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meredith L Stone
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paige M Porrett
- Division of Transplant Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stacy K Thomas
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chad A Komar
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joey H Li
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Devora Delman
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen Graham
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Whitney L Gladney
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xia Hua
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taylor A Black
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Austin L Chien
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Krishna S Majmundar
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeffrey C Thompson
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie S Yee
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark H O'Hara
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Charu Aggarwal
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dong Xin
- Division of Transplant Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abraham Shaked
- Division of Transplant Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mingming Gao
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Dexi Liu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Mitesh J Borad
- Mayo Clinic Cancer Center, Mayo Clinic, Phoenix, AZ, USA
| | - Ramesh K Ramanathan
- Mayo Clinic Cancer Center, Mayo Clinic, Phoenix, AZ, USA
- Merck Research Labs, Rahway, NJ, USA
| | - Erica L Carpenter
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ailing Ji
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Maria C de Beer
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Frederick C de Beer
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Nancy R Webb
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, USA
| | - Gregory L Beatty
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Aggarwal C, Thompson JC, Black TA, Katz SI, Fan R, Yee SS, Chien AL, Evans TL, Bauml JM, Alley EW, Ciunci CA, Berman AT, Cohen RB, Lieberman DB, Majmundar KS, Savitch SL, Morrissette JJD, Hwang WT, Elenitoba-Johnson KSJ, Langer CJ, Carpenter EL. Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non-Small Cell Lung Cancer. JAMA Oncol 2019; 5:173-180. [PMID: 30325992 PMCID: PMC6396811 DOI: 10.1001/jamaoncol.2018.4305] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [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: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 12/27/2022]
Abstract
Importance The clinical implications of adding plasma-based circulating tumor DNA next-generation sequencing (NGS) to tissue NGS for targetable mutation detection in non-small cell lung cancer (NSCLC) have not been formally assessed. Objective To determine whether plasma NGS testing was associated with improved mutation detection and enhanced delivery of personalized therapy in a real-world clinical setting. Design, Setting, and Participants This prospective cohort study enrolled 323 patients with metastatic NSCLC who had plasma testing ordered as part of routine clinical management. Plasma NGS was performed using a 73-gene commercial platform. Patients were enrolled at the Hospital of the University of Pennsylvania from April 1, 2016, through January 2, 2018. The database was locked for follow-up and analyses on January 2, 2018, with a median follow-up of 7 months (range, 1-21 months). Main Outcomes and Measures The number of patients with targetable alterations detected with plasma and tissue NGS; the association between the allele fractions (AFs) of mutations detected in tissue and plasma; and the association of response rate with the plasma AF of the targeted mutations. Results Among the 323 patients with NSCLC (60.1% female; median age, 65 years [range, 33-93 years]), therapeutically targetable mutations were detected in EGFR, ALK, MET, BRCA1, ROS1, RET, ERBB2, or BRAF for 113 (35.0%) overall. Ninety-four patients (29.1%) had plasma testing only at the discretion of the treating physician or patient preference. Among the 94 patients with plasma testing alone, 31 (33.0%) had a therapeutically targetable mutation detected, thus obviating the need for an invasive biopsy. Among the remaining 229 patients who had concurrent plasma and tissue NGS or were unable to have tissue NGS, a therapeutically targetable mutation was detected in tissue alone for 47 patients (20.5%), whereas the addition of plasma testing increased this number to 82 (35.8%). Thirty-six of 42 patients (85.7%) who received a targeted therapy based on the plasma result achieved a complete or a partial response or stable disease. The plasma-based targeted mutation AF had no correlation with depth of Response Evaluation Criteria in Solid Tumors response (r = -0.121; P = .45). Conclusions and Relevance Integration of plasma NGS testing into the routine management of stage IV NSCLC demonstrates a marked increase of the detection of therapeutically targetable mutations and improved delivery of molecularly guided therapy.
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Affiliation(s)
- Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Jeffrey C. Thompson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Taylor A. Black
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Sharyn I. Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Ryan Fan
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Stephanie S. Yee
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Austin L. Chien
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Tracey L. Evans
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Joshua M. Bauml
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Evan W. Alley
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Christine A. Ciunci
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Abigail T. Berman
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Roger B. Cohen
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Krishna S. Majmundar
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Samantha L. Savitch
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia
| | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia
| | | | - Corey J. Langer
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Erica L. Carpenter
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia
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17
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Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma. Pigment Cell Melanoma Res 2018; 31:73-81. [PMID: 28786531 PMCID: PMC5742050 DOI: 10.1111/pcmr.12623] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 12/24/2022]
Abstract
To determine the feasibility of liquid biopsy for monitoring of patients with advanced melanoma, cell-free DNA was extracted from plasma for 25 Stage III/IV patients, most (84.0%) having received previous therapy. DNA concentrations ranged from 0.6 to 390.0 ng/ml (median = 7.8 ng/ml) and were positively correlated with tumor burden as measured by imaging (Spearman rho = 0.5435, p = .0363). Using ultra-deep sequencing for a 61-gene panel, one or more mutations were detected in 12 of 25 samples (48.0%), and this proportion did not vary significantly for patients on or off therapy at the time of blood draw (52.9% and 37.5% respectively; p = .673). Sixteen mutations were detected in eight different genes, with the most frequent mutations detected in BRAF, NRAS, and KIT. Allele fractions ranged from 1.1% to 63.2% (median = 29.1%). Among patients with tissue next-generation sequencing, nine of 11 plasma mutations were also detected in matched tissue, for a concordance of 81.8%.
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Affiliation(s)
- Tara C. Gangadhar
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Samantha L. Savitch
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Wei Xu
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Alexander C. Huang
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Institue for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Parker Institute of Immunotherapy at the University of Pennsylvania
| | - Shannon Harmon
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David B. Lieberman
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Devon Soucier
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ryan Fan
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | | | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Ravi K. Amaravadi
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lynn M. Schuchter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | - Wei-Ting Hwang
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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18
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Grant RF, Margolis HA, Barr AG, Black TA, Dunn AL, Bernier PY, Bergeron O. Changes in net ecosystem productivity of boreal black spruce stands in response to changes in temperature at diurnal and seasonal time scales. Tree Physiol 2009; 29:1-17. [PMID: 19203928 DOI: 10.1093/treephys/tpn004] [Citation(s) in RCA: 13] [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] [Indexed: 05/27/2023]
Abstract
Net ecosystem productivity (NEP) of boreal coniferous forests is believed to rise with climate warming, thereby offsetting some of the rise in atmospheric CO(2) concentration (C(a)) by which warming is caused. However, the response of conifer NEP to warming may vary seasonally, with rises in spring and declines in summer. To gain more insight into this response, we compared changes in CO(2) exchange measured by eddy covariance and simulated by the ecosystem process model ecosys under rising mean annual air temperatures (T(a)) during 2004-2006 at black spruce stands in Saskatchewan, Manitoba and Quebec. Hourly net CO(2) uptake was found to rise with warming at T(a) < 15 degrees C and to decline with warming at T(a) > 20 degrees C. As mean annual T(a) rose from 2004 to 2006, increases in net CO(2) uptake with warming at lower T(a) were greater than declines with warming at higher T(a) so that annual gross primary productivity and hence NEP increased. Increases in net CO(2) uptake measured at lower T(a) were explained in the model by earlier recovery of photosynthetic capacity in spring, and by increases in carboxylation activity, using parameters for the Arrhenius temperature functions of key carboxylation processes derived from independent experiments. Declines in net CO(2) uptake measured at higher T(a) were explained in the model by sharp declines in mid-afternoon canopy stomatal conductance (g(c)) under higher vapor pressure deficits (D). These declines were modeled from a hydraulic constraint to water uptake imposed by low axial conductivity of conifer roots and boles that forced declines in canopy water potential (psi(c)), and hence in g(c) under higher D when equilibrating water uptake with transpiration. In a model sensitivity study, the contrasting responses of net CO(2) uptake to specified rises in T(a) caused annual NEP of black spruce in the model to rise with increases in T(a) of up to 6 degrees C, but to decline with further increases at mid-continental sites with lower precipitation. However, these contrasting responses to warming also indicate that rises in NEP with climate warming would depend on the seasonality (spring versus summer) as well as the magnitude of rises in T(a).
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Affiliation(s)
- R F Grant
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2E3, Canada
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19
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Grant RF, Black TA, Humphreys ER, Morgenstern K. Changes in net ecosystem productivity with forest age following clearcutting of a coastal Douglas-fir forest: testing a mathematical model with eddy covariance measurements along a forest chronosequence. Tree Physiol 2007; 27:115-31. [PMID: 17169913 DOI: 10.1093/treephys/27.1.115] [Citation(s) in RCA: 15] [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] [Indexed: 05/13/2023]
Abstract
We hypothesized that changes in net ecosystem productivity (NEP) during aging of coastal Douglas-fir (Pseudotsuga menziesii Mirb. Franco) stands could be explained by (1) changing nutrient uptake caused by different time scales for decomposition of fine, non-woody and coarse woody litter left after harvesting, (2) declines in canopy water status with lengthening of the water uptake pathway during bole and branch growth, and (3) increases in the ratio of autotrophic respiration (R (a)) to gross primary productivity (GPP) with phytomass accumulation. These hypotheses were implemented and tested in the mathematical model ecosys against eddy covariance (EC) measurements of forest CO(2) and energy exchange in a post-clearcut Douglas-fir chronosequence. Hypothesis 1 explained how (a) an initial rise in GPP observed during the first 3 years after clearcutting could be caused by nutrient mineralization from rapid decomposition of fine, non-woody litter with lower C:N ratios (assart effect), (b) a slower rise in GPP during the next 20 years could be caused by immobilization during later decomposition of coarse woody litter, and (c) a rapid rise in GPP between 20 and 40 years after clearcutting could be caused by nutrient mineralization with further decomposition of coarse woody litter and of its decomposition products. During periods (a) and (b), heterotrophic respiration (R (h)) from decomposition of fine and coarse litter greatly exceeded net primary productivity (NPP = GPP - R (a)) so that Douglas-fir stands were large sources of CO(2). During period (c), NPP exceeded R (h) so that these stands became large sinks for CO(2). Hypothesis 2 explained how declines in NPP during later growth in period (c) could be caused by lower hydraulic conductances in taller trees that would force lower canopy water potentials and hence greater sensitivity of stomatal conductances and CO(2) uptake to vapor pressure deficits. Enhanced sensitivity to vapor pressure deficits was also apparent in the EC measurements over the post-clearcut chronosequence. Hypothesis 3 did not contribute to the explanation of forest age effects on NEP.
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Affiliation(s)
- R F Grant
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada T6G 2E3.
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20
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Ethier GJ, Livingston NJ, Harrison DL, Black TA, Moran JA. Low stomatal and internal conductance to CO2 versus Rubisco deactivation as determinants of the photosynthetic decline of ageing evergreen leaves. Plant Cell Environ 2006; 29:2168-84. [PMID: 17081250 DOI: 10.1111/j.1365-3040.2006.01590.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
A novel A-Ci curve (net CO2 assimilation rate of a leaf -An- as a function of its intercellular CO2 concentration -Ci) analysis method (Plant, Cell & Environment 27, 137-153, 2004) was used to estimate the CO2 transfer conductance (gi) and the maximal carboxylation (Vcmax) and electron transport (Jmax) potentials of ageing, non-senescing Pseudotsuga menziesii leaves in relation to their nitrogen (N) content and protein and pigment composition. Both gi and the stomatal conductance (gsc) of leaves were closely coupled to Vcmax, Jmax and An with all variables decreasing with increasing leaf age. Consequently, both Ci and Cc (chloroplastic CO2 concentration) remained largely conserved through successive growing seasons. The N content of leaves, as well as the amount of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and other sodium dodecyl sulfate-soluble proteins, increased during the first three growing seasons, then stabilized or decreased only slightly afterwards. Thus, the age-related photosynthetic nitrogen use efficiency (PNUE) decline of leaves was not a consequence of decreased allocation of N towards Rubisco and other proteins involved in bioenergetics and light harvesting. Rather, loss of photosynthetic capacity was the result of the decreased activation state of Rubisco and proportional down-regulation of electron transport towards the photosynthetic carbon reduction (PCR) and photorespiratory (PCO) cycles in response to a reduction of CO2 supply to the chloroplasts' stroma. This study emphasizes the regulatory potential and homeostaticity of Cc- rather than photosynthetic metabolites or Ci- in relation to the commonly observed correlation between photosynthesis and gsc.
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Affiliation(s)
- G J Ethier
- Centre for Forest Biology, Department of Biology, University of Victoria, Victoria, B.C. V8W 3 N5, Canada.
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21
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Sabatelli F, Patel R, Mann PA, Mendrick CA, Norris CC, Hare R, Loebenberg D, Black TA, McNicholas PM. In vitro activities of posaconazole, fluconazole, itraconazole, voriconazole, and amphotericin B against a large collection of clinically important molds and yeasts. Antimicrob Agents Chemother 2006; 50:2009-15. [PMID: 16723559 PMCID: PMC1479149 DOI: 10.1128/aac.00163-06] [Citation(s) in RCA: 334] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The in vitro activity of the novel triazole antifungal agent posaconazole (Noxafil; SCH 56592) was assessed in 45 laboratories against approximately 19,000 clinically important strains of yeasts and molds. The activity of posaconazole was compared with those of itraconazole, fluconazole, voriconazole, and amphotericin B against subsets of the isolates. Strains were tested utilizing Clinical and Laboratory Standards Institute broth microdilution methods using RPMI 1640 medium (except for amphotericin B, which was frequently tested in antibiotic medium 3). MICs were determined at the recommended endpoints and time intervals. Against all fungi in the database (22,850 MICs), the MIC(50) and MIC(90) values for posaconazole were 0.063 microg/ml and 1 mug/ml, respectively. MIC(90) values against all yeasts (18,351 MICs) and molds (4,499 MICs) were both 1 mug/ml. In comparative studies against subsets of the isolates, posaconazole was more active than, or within 1 dilution of, the comparator drugs itraconazole, fluconazole, voriconazole, and amphotericin B against approximately 7,000 isolates of Candida and Cryptococcus spp. Against all molds (1,702 MICs, including 1,423 MICs for Aspergillus isolates), posaconazole was more active than or equal to the comparator drugs in almost every category. Posaconazole was active against isolates of Candida and Aspergillus spp. that exhibit resistance to fluconazole, voriconazole, and amphotericin B and was much more active than the other triazoles against zygomycetes. Posaconazole exhibited potent antifungal activity against a wide variety of clinically important fungal pathogens and was frequently more active than other azoles and amphotericin B.
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Affiliation(s)
- F Sabatelli
- Schering-Plough Research Institute, Kenilworth, NJ 07033, USA
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22
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Baldocchi DD, Black TA, Curtis PS, Falge E, Fuentes JD, Granier A, Gu L, Knohl A, Pilegaard K, Schmid HP, Valentini R, Wilson K, Wofsy S, Xu L, Yamamoto S. Predicting the onset of net carbon uptake by deciduous forests with soil temperature and climate data: a synthesis of FLUXNET data. Int J Biometeorol 2005; 49:377-387. [PMID: 15688192 DOI: 10.1007/s00484-005-0256-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 10/21/2004] [Accepted: 12/30/2004] [Indexed: 05/24/2023]
Abstract
We tested the hypothesis that the date of the onset of net carbon uptake by temperate deciduous forest canopies corresponds with the time when the mean daily soil temperature equals the mean annual air temperature. The hypothesis was tested using over 30 site-years of data from 12 field sites where CO(2) exchange is being measured continuously with the eddy covariance method. The sites spanned the geographic range of Europe, North America and Asia and spanned a climate space of 16 degrees C in mean annual temperature. The tested phenology rule was robust and worked well over a 75 day range of the initiation of carbon uptake, starting as early as day 88 near Ione, California to as late as day 147 near Takayama, Japan. Overall, we observed that 64% of variance in the timing when net carbon uptake started was explained by the date when soil temperature matched the mean annual air temperature. We also observed a strong correlation between mean annual air temperature and the day that a deciduous forest starts to be a carbon sink. Consequently we are able to provide a simple phenological rule that can be implemented in regional carbon balance models and be assessed with soil and temperature outputs produced by climate and weather models.
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Affiliation(s)
- Dennis D Baldocchi
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California, 151 Hilgard Hall, Berkeley, CA 94720, USA.
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23
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Chu M, Mierzwa R, Xu L, He L, Terracciano J, Patel M, Zhao W, Black TA, Chan TM. Structure of sch 419560, a novel alpha-pyrone antibiotic produced by Pseudomonas fluorescens. J Antibiot (Tokyo) 2002; 55:215-8. [PMID: 12003005 DOI: 10.7164/antibiotics.55.215] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- M Chu
- Schering-Plough Research Institute, Kenilworth, New Jersey, USA.
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24
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Pan L, Black TA, Shi Q, Jones CA, Petrovic N, Loudon J, Kane C, Sigmund CD, Gross KW. Critical roles of a cyclic AMP responsive element and an E-box in regulation of mouse renin gene expression. J Biol Chem 2001; 276:45530-8. [PMID: 11564732 DOI: 10.1074/jbc.m103010200] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [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: 01/31/2023] Open
Abstract
Mouse As4.1 cells, obtained after transgene-targeted oncogenesis to induce neoplasia in renal renin expressing cells, express high levels of renin mRNA from their endogenous Ren-1(c) gene. We have previously identified a 242-base pair enhancer (coordinates -2866 to -2625 relative to the CAP site) upstream of the mouse Ren-1(c) gene. This enhancer, in combination with the proximal promoter (-117 to +6), activates transcription nearly 2 orders of magnitude in an orientation independent fashion. To further delimit sequences necessary for transcriptional activation, renin promoter-luciferase reporter gene constructs containing selected regions of the Ren-1(c) enhancer were analyzed after transfection into As4.1 cells. These results demonstrate that several regions are required for full enhancer activity. Sequences from -2699 to -2672, which are critical for the enhancer activity, contain a cyclic AMP responsive element (CRE) and an E-box. Electrophoretic mobility shift assays demonstrated that transcription factors CREB/CREM and USF1/USF2 in As4.1 cell nuclear extracts bind to oligonucleotides containing the Ren-1(c) CRE and E-box, respectively. These two elements are capable of synergistically activating transcription from the Ren-1(c) promoter. Moreover, mutation of either the CRE or E-box results in almost complete loss of enhancer activity, suggesting the critical roles these two elements play in regulating mouse Ren-1(c) gene expression. Although the Ren-1(c) gene contains a CRE, its expression is not induced by cAMP in As4.1 cells. This appears to reflect constitutive activation of protein kinase A in As4.1 cells since treatment with the protein kinase A inhibitor, H-89, caused a significant reduction in Ren-1(c) gene expression and this reduction is mediated through the CRE at -2699 to -2688.
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Affiliation(s)
- L Pan
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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25
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Mann PA, Xiong L, Mankin AS, Chau AS, Mendrick CA, Najarian DJ, Cramer CA, Loebenberg D, Coates E, Murgolo NJ, Aarestrup FM, Goering RV, Black TA, Hare RS, McNicholas PM. EmtA, a rRNA methyltransferase conferring high-level evernimicin resistance. Mol Microbiol 2001; 41:1349-56. [PMID: 11580839 DOI: 10.1046/j.1365-2958.2001.02602.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [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
Enterococcus faecium strain 9631355 was isolated from animal sources on the basis of its resistance to the growth promotant avilamycin. The strain also exhibited high-level resistance to evernimicin, a drug undergoing evaluation as a therapeutic agent in humans. Ribosomes from strain 9631355 exhibited a dramatic reduction in evernimicin binding, shown by both cell-free translation assays and direct-binding assays. The resistance determinant was cloned from strain 9631355; sequence alignments suggested it was a methyltransferase and therefore it was designated emtA for evernimicin methyltransferase. Evernimicin resistance was transmissible and emtA was localized to a plasmid-borne insertion element. Purified EmtA methylated 50S subunits from an evernimicin-sensitive strain 30-fold more efficiently than those from a resistant strain. Reverse transcription identified a pause site that was unique to the 23S rRNA extracted from resistant ribosomes. The pause corresponded to methylation of residue G2470 (Escherichia coli numbering). RNA footprinting revealed that G2470 is located within the evernimicin-binding site on the ribosome, thus providing an explanation for the reduced binding of the drug to methylated ribosomes.
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MESH Headings
- Aminoglycosides
- Animals
- Anti-Bacterial Agents/metabolism
- Anti-Bacterial Agents/pharmacology
- Base Sequence
- Binding Sites
- Cloning, Molecular
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- Drug Resistance, Bacterial/genetics
- Drug Resistance, Bacterial/physiology
- Enterococcus faecium/drug effects
- Enterococcus faecium/enzymology
- Enterococcus faecium/genetics
- Genes, Bacterial
- Humans
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plasmids/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomes/metabolism
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Affiliation(s)
- P A Mann
- Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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26
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Pan L, Xie Y, Black TA, Jones CA, Pruitt SC, Gross KW. An Abd-B class HOX.PBX recognition sequence is required for expression from the mouse Ren-1c gene. J Biol Chem 2001; 276:32489-94. [PMID: 11432851 DOI: 10.1074/jbc.m011541200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [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: 11/06/2022] Open
Abstract
Expression from the mouse Ren-1(c) gene in As4.1 cells is dependent on a proximal promoter element (PPE) located at approximately -60 and a 241-base pair enhancer region located at -2625 relative to the transcription start site. The PPE (TAATAAATCAA) is identical to a consensus HOX.PBX binding sequence. Further, PBX1b has been shown to be a component of a PPE-specific binding complex present in nuclear extracts from As4.1 cells. The binding affinities of different paralog HOX members to the PPE were examined in the absence or presence of PBX1b. HOXB6, -B7, and -C8 failed to bind the PPE alone but showed weak affinity in the presence of PBX1b. In contrast, HOXD10 and to a lesser degree HOXB9 bound the PPE with high affinities regardless of whether PBX1b was present. Abd-B HOX members, including HOXD10, -A10, -A9, -B9, and -C9, are expressed in As4.1 cells. The ability of HOX and PBX1b to form a ternary complex with PREP1 on the PPE is also demonstrated both in vivo and in vitro. Point mutations in either the HOX or PBX half-site of the PPE disrupted the formation of the HOX.PBX complex and dramatically decreased transcriptional activity of the Ren-1(c) gene demonstrating that both the HOX and PBX half-sites are critical for mouse renin gene expression. These results strongly implicate Abd-B class Hox genes and their cofactors as major determinants of the sites of renin expression.
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Affiliation(s)
- L Pan
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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27
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McNicholas PM, Mann PA, Najarian DJ, Miesel L, Hare RS, Black TA. Effects of mutations in ribosomal protein L16 on susceptibility and accumulation of evernimicin. Antimicrob Agents Chemother 2001; 45:79-83. [PMID: 11120948 PMCID: PMC90243 DOI: 10.1128/aac.45.1.79-83.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [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] Open
Abstract
Chemical mutagenesis of Staphylococcus aureus RN450 generated two strains that displayed a stable reduction (30- to 60-fold) in susceptibility to evernimicin. Cell-free translation reactions demonstrated that the resistance determinant was located in the ribosomal fraction. Compared to ribosomes isolated from a wild-type strain, ribosomes from the mutant strains displayed an 8- to 10-fold reduction in affinity for [(14)C]evernimicin. In contrast, the mutants displayed no alteration in either binding affinity or in vitro susceptibility to erythromycin. Exponential cultures of the mutant strains accumulated significantly less [(14)C]evernimicin than the wild-type strain, suggesting that accumulation is dependent on the high affinity that evernimicin displays for its binding site. Sequencing rplP (encodes ribosomal protein L16) in the mutant strains revealed a single base change in each strain, which resulted in a substitution of either cysteine or histidine for arginine at residue 51. Introduction of a multicopy plasmid carrying wild-type rplP into the mutant strains restored sensitivity to evernimicin, confirming that the alterations in rplP were responsible for the change in susceptibility. Overexpression of the mutant alleles in S. aureus RN450 had no effect on susceptibility to evernimicin, demonstrating that susceptibility is dominant over resistance.
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Affiliation(s)
- P M McNicholas
- Schering Plough Research Institute, Kenilworth, New Jersey 07033, USA.
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28
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Abstract
The boreal forest, one of the world's larger biomes, is distinct from other biomes because it experiences a short growing season and extremely cold winter temperatures. Despite its size and impact on the earth's climate system, measurements of mass and energy exchange have been rare until the past five years. This paper overviews results of recent and comprehensive field studies conducted in Canada, Siberia and Scandinavia on energy exchanges between boreal forests and the atmosphere. How the boreal biosphere and atmosphere interact to affect the interception of solar energy and how solar energy is used to evaporate water and heat the air and soil is examined in detail. Specifically, we analyse the magnitudes, temporal and spatial patterns and controls of solar energy, moisture and sensible heat fluxes across the land-atmosphere interface. We interpret and synthesize field data with the aid of a soil-vegetation-atmosphere transfer model, which considers the coupling of the energy and carbon fluxes and nutrient status. Low precipitation and low temperatures limit growth of many boreal forests. These factors restrict photosynthetic capacity and lower root hydraulic conductivity and stomatal conductance of the inhabitant forests. In such circumstances, these factors interact to form a canopy that has a low leaf area index and exerts a significant resistance to evaporation. Conifer forests, growing on upland soils, for example, evaporate at rates between 25 and 75% of equilibrium evaporation and lose less than 2.5 mm day-1 of water. The open nature of many boreal conifer forest stands causes a disproportionate amount of energy exchange to occur at the soil surface. The climatic and physiological factors that yield relatively low rates of evaporation over conifer stands also cause high rates of sensible heat exchange and the diurnal development of deep planetary boundary layers. In contrast, evaporation from broad-leaved aspen stands and fen/wetlands approach equilibrium evaporation rates and lose up to 6 mm day-1 .
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Affiliation(s)
- Dennis Baldocchi
- Department of Environmental Science, Policy and Management, 151, Hilgard Hall, University of California, Berkeley, CA 94720, USA
| | | | - T A Black
- Faculty of Agricultural Sciences, University of British Columbia, 139-2357 Main Mall, Vancouver, BC, Canada V6T 1Z4
| | - Paul Jarvis
- Institute of Ecology and Resource Management, Schools of Forestry and Ecological Science, University of Edinburgh, Darwin Building, King's Buildings, Mayfield Rd, Edinburgh EH9 3JU, UK
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29
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Jones CA, Hurley MI, Black TA, Kane CM, Pan L, Pruitt SC, Gross KW. Expression of a renin/GFP transgene in mouse embryonic, extra-embryonic, and adult tissues. Physiol Genomics 2000; 4:75-81. [PMID: 11074016 DOI: 10.1152/physiolgenomics.2000.4.1.75] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [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: 11/22/2022] Open
Abstract
A reporter construct was assembled with 4-kb of renin 5'-flanking sequence fused to humanized green fluorescent protein (GFP) cDNA. Transgenic mice carrying this construct were produced and assayed for GFP expression. In the adult, expression was detected in juxtaglomerular (JG) cells of the kidney and granular convoluted tubular cells of the submandibular gland. Furthermore, treatment of mice with captopril induced GFP expression in renal vascular smooth muscle cells. During embryogenesis, GFP expression was first detected at embryonic day E13 in the adrenal gland and Wolffian duct. Expression was also seen in the developing renal vasculature as early as E14 and remained detectable through birth. Renal GFP expression became restricted to JG cells in adults. Fetal adrenal and gonadal arteries also expressed GFP. In the placenta, GFP was observed in giant cell trophoblasts, consistent with reports of renin expression in chorionic cells of both humans and mice. We conclude that 4 kb of renin 5' flank is sufficient to direct multiple known renin expression patterns. Furthermore, the renin-GFP construct characterized here will provide a useful vital reporter for renin expression.
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Affiliation(s)
- C A Jones
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo 14260, USA
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30
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Adrian PV, Mendrick C, Loebenberg D, McNicholas P, Shaw KJ, Klugman KP, Hare RS, Black TA. Evernimicin (SCH27899) inhibits a novel ribosome target site: analysis of 23S ribosomal DNA mutants. Antimicrob Agents Chemother 2000; 44:3101-6. [PMID: 11036030 PMCID: PMC101610 DOI: 10.1128/aac.44.11.3101-3106.2000] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2000] [Accepted: 08/21/2000] [Indexed: 11/20/2022] Open
Abstract
Spontaneous mutants of susceptible clinical and laboratory isolates of Streptococcus pneumoniae exhibiting reduced susceptibility to evernimicin (SCH27899; MIC, 0.5 to 4.0 mg/liter) were selected on plates containing evernimicin. Four isolates that did not harbor mutations in rplP (which encodes ribosomal protein L16) were further analyzed. Whole chromosomal DNA or PCR products of the 23S ribosomal DNA (rDNA) operons from these mutants could be used to transform the susceptible S. pneumoniae strain R6 to resistance at frequencies of 10(-5) and 10(-4), respectively, rates 10- to 100-fold lower than that for a single-allele chromosomal marker. The transformants appeared slowly (48 to 72 h) on selective medium, and primary transformants passaged on nonselective medium produced single colonies that displayed heterogeneous susceptibilities to evernimicin. A single passage on selective medium of colonies derived from a single primary transformant homogenized the resistance phenotype. Sequence analysis of the 23S rDNA and rRNA from the resistant mutants revealed single, unique mutations in each isolate at the equivalent Escherichia coli positions 2469 (A --> C), 2480 (C --> T), 2535 (G --> A), and 2536 (G --> C). The mutations map within two different stems of the peptidyltransferase region of domain V. Because multiple copies of rDNA are present in the chromosome, gene conversion between mutant and wild-type 23S rDNA alleles may be necessary for stable resistance. Additionally, none of the characterized mutants showed cross-resistance to any of a spectrum of protein synthesis inhibitors, suggesting that the target site of evernimicin may be unique.
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MESH Headings
- Alleles
- Aminoglycosides
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Base Sequence
- DNA, Bacterial/genetics
- Drug Resistance, Microbial
- Humans
- Microbial Sensitivity Tests
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/drug effects
- RNA, Ribosomal, 23S/genetics
- Streptococcus pneumoniae/drug effects
- Streptococcus pneumoniae/genetics
- Transformation, Bacterial
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Affiliation(s)
- P V Adrian
- Pneumococcal Diseases Research Unit, South African Institute for Medical Research, University of the Witwatersrand, and the Medical Research Council, Johannesburg, South Africa.
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31
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Abstract
The renin-producing and -secreting juxtaglomerular (JG) cells are thought to function as the baroreceptor of the kidney. The mechanism by which changes in pressure, or mechanical force, regulate renin at the molecular level has not been elucidated. The renin gene-expressing and -secreting clonal cell line As4.1 was derived from transgene-targeted oncogenesis in mice and was used as a cellular model for JG cells. As4.1 cells subjected to cyclic mechanical distension for a period of 24 h at various frequencies (0. 05 or 0.5 Hz) and magnitudes (12 or 24% elongation) were analyzed via Northern analysis for renin mRNA levels. Results indicate that renin gene expression is decreased by 50-85% and returns to basal levels after a 24-h recovery period. Renin gene expression was attenuated independently of elevated cell growth or changes in renin message decay, suggesting that renin gene transcription is directly modulated by mechanical distension. Transient transfection of As4.1 cells with renin 5' flanking sequence-luciferase reporter gene constructs confirmed the role of mechanical stimulation in regulating renin gene transcription. A 43% inhibition of luciferase activity, by stretch, was observed in cells transfected with a 4,000 base pair 5' flanking sequence to the renin proximal promoter. These results demonstrate for the first time that changes in mechanical force can result in the regulation of renin gene transcription and thus provide further insight into the baroreceptor properties of renin-expressing cells.
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Affiliation(s)
- M J Ryan
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo 14214, USA
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32
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Baumann H, Wang Y, Richards CD, Jones CA, Black TA, Gross KW. Endotoxin-induced renal inflammatory response. Oncostatin M as a major mediator of suppressed renin expression. J Biol Chem 2000; 275:22014-9. [PMID: 10806209 DOI: 10.1074/jbc.m002830200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [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: 11/06/2022] Open
Abstract
The systemic response to endotoxin is characterized by hypotension and severe reductions in blood pressure, leading to cardiovascular collapse that can accompany septicemia. The renin/angiotensin system would normally be expected to respond to hypotensive challenge; however, inflammation appears to modify this response. This study identifies a strong acute phase response of the kidney that is characterized by enhanced expression of serum amyloid A, haptoglobin and tissue inhibitor for metalloproteinase-1 and a reduced expression of renin. Equivalent regulatory effects were observed for the immortalized As4.1 kidney cell line that models certain features of juxtaglomerular cells. Oncostatin M, a known endotoxin-responsive proinflammatory cytokine, proved to be an effective inhibitor of renin gene expression. Suppression by oncostatin M involves activated STAT5 and requires an inhibitory element in the renin promoter that functions separately from cell type-specific enhancer elements. The renal acute phase reaction, unlike the liver acute phase reaction, is more strongly dependent on locally produced inflammatory factors.
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Affiliation(s)
- H Baumann
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.
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33
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McNicholas PM, Najarian DJ, Mann PA, Hesk D, Hare RS, Shaw KJ, Black TA. Evernimicin binds exclusively to the 50S ribosomal subunit and inhibits translation in cell-free systems derived from both gram-positive and gram-negative bacteria. Antimicrob Agents Chemother 2000; 44:1121-6. [PMID: 10770739 PMCID: PMC89832 DOI: 10.1128/aac.44.5.1121-1126.2000] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [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] Open
Abstract
Evernimicin (SCH 27899) is a new antibiotic with activity against a wide spectrum of gram-positive bacteria and activity against some gram-negative bacteria. Previous metabolic labeling studies indicated that evernimicin specifically inhibited protein synthesis in Staphylococcus aureus. Using a susceptible Escherichia coli strain, we demonstrated that evernimicin also inhibited protein synthesis in E. coli. In cell-free translation assays with extracts from either E. coli or S. aureus, evernimicin had a 50% inhibitory concentration of approximately 125 nM. In contrast, cell-free systems derived from wheat germ and rabbit reticulocytes were inhibited only by very high levels of evernimicin. Evernimicin did not promote transcript misreading. [(14)C]evernimicin specifically bound to the 50S subunit from E. coli. Nonlinear regression analysis of binding data generated with 70S ribosomes from E. coli and S. aureus and 50S subunits from E. coli returned dissociation constants of 84, 86, and 160 nM, respectively. In binding experiments, performed in the presence of excess quantities of a selection of antibiotics known to bind to the 50S subunit, only the structurally similar drug avilamycin blocked binding of [(14)C]evernimicin to ribosomes.
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Affiliation(s)
- P M McNicholas
- Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA.
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34
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Adrian PV, Zhao W, Black TA, Shaw KJ, Hare RS, Klugman KP. Mutations in ribosomal protein L16 conferring reduced susceptibility to evernimicin (SCH27899): implications for mechanism of action. Antimicrob Agents Chemother 2000; 44:732-8. [PMID: 10681347 PMCID: PMC89755 DOI: 10.1128/aac.44.3.732-738.2000] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [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] Open
Abstract
A clinical isolate of Streptococcus pneumoniae (SP#5) that showed decreased susceptibility to evernimicin (MIC, 1.5 microgram/ml) was investigated. A 4,255-bp EcoRI fragment cloned from SP#5 was identified by its ability to transform evernimicin-susceptible S. pneumoniae R6 (MIC, 0.03 microgram/ml) such that the evernimicin MIC was 1.5 microgram/ml. Nucleotide sequence analysis of this fragment revealed that it contained portions of the S10-spc ribosomal protein operons. The nucleotide sequences of resistant and susceptible isolates were compared, and a point mutation (thymine to guanine) that causes an Ile52-Ser substitution in ribosomal protein L16 was identified. The role of this mutation in decreasing susceptibility to evernimicin was confirmed by direct transformation of the altered L16 gene. The presence of the L16 mutation in the resistant strain suggests that evernimicin is an inhibitor of protein synthesis. This was confirmed by inhibition studies using radiolabeled substrates, which showed that the addition of evernimicin at sub-MIC levels resulted in a rapid decrease in the incorporation of radiolabeled isoleucine in a susceptible isolate (SP#3) but was much less effective against SP#5. The incorporation of isoleucine showed a linear response to the dose level of evernimicin. The incorporation of other classes of labeled substrates was unaffected or much delayed, indicating that these were secondary effects.
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Affiliation(s)
- P V Adrian
- Pneumococcal Diseases Research Unit of the South African Institute for Medical Research, University of the Witwatersrand and the Medical Research Council, Johannesburg, South Africa.
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35
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Abstract
A distal transcriptional enhancer has been previously reported upstream of the mouse renin gene. A homologous sequence is also present upstream of the human renin gene, but the mouse and human renin enhancers differ markedly in their ability to activate transcription of a renin promoter. Although the 2 enhancers share high homology in their 202-bp promoter distal portions, their 40-bp proximal portions are heterogeneous. Chimeric enhancers were used to test the role of the 40-bp segment (m40) of the enhancer by using transient transfection analysis in mouse kidney renin-expressing As4. 1 cells. Deletion of m40 from the mouse renin enhancer or its addition to the human renin enhancer did not significantly change transcriptional activity when placed close to a mouse or human renin promoter. However, when placed further upstream of a renin promoter, the same deletion and substitution markedly altered enhancer activity. Electrophoretic gel mobility shift analysis identified 2 elements, a and b, in m40 that specifically bound nuclear proteins from As4.1 cells. Mutagenesis and transient transfection analysis revealed that element b accounts for the function of m40 and that element a antagonizes the positive influence of element b. Gel competition and supershift analysis revealed that nuclear factor-Y, a ubiquitous CAAT-box binding protein, binds to element a. Sequence analysis revealed that the human renin enhancer has a natural loss-of-function mutation in element b that affects its ability to transactivate when placed far upstream of a promoter. Reversion of the human renin element b to match the mouse sequence restored transactivation of the enhancer in mouse As4.1 cells. These data suggest that element b cooperates with the rest of the enhancer to maintain full enhancer activity, whereas element a may regulate enhancer activity. Sequence differences in these elements may explain the functional differences in the mouse and human renin enhancer sequences.
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Affiliation(s)
- Q Shi
- Departments of Internal Medicine and Physiology & Biophysics, University of Iowa College of Medicine, Iowa City, Iowa 52242, USA
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36
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Abstract
Salt-induced genes in the cyanobacterium Anabaena sp. strain PCC 7120 were identified by use of a Tn5-based transposon bearing luxAB as a reporter. The genomic sequence adjacent to one site of insertion of the transposon was identical in part to the sequence of the lti2 gene, which was previously identified in a differential screen for cold-induced transcripts in Anabaena variabilis. The lti2-like gene was induced by sucrose and other osmotica and by low temperature, in addition to salt. Regulatory components necessary for the induction of this gene by osmotica were sought by a further round of transposon mutagenesis. One mutant that displayed reduced transcriptional activity of the lti2-like gene in response to exposure to osmotica had an insertion in an open reading frame, which was denoted orrA, whose predicted product showed sequence similarity to response regulators from two-component regulatory systems. The corresponding mutation was reconstructed and was shown, like the second-site transposon mutation, to result in reduced response to osmotic stress. Induction of the lux reporter gene by osmotica was restored by complementation with a genomic fragment containing the entire open reading frame for the presumptive response regulator, whereas a fragment containing a truncated copy of the open reading frame for the response regulator did not complement the mutation.
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Affiliation(s)
- S H Schwartz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
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37
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Petrovic N, Black TA, Fabian JR, Kane C, Jones CA, Loudon JA, Abonia JP, Sigmund CD, Gross KW. Role of proximal promoter elements in regulation of renin gene transcription. J Biol Chem 1996; 271:22499-505. [PMID: 8798416 DOI: 10.1074/jbc.271.37.22499] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [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: 02/02/2023] Open
Abstract
Mouse As4.1 cells, obtained after transgene-targeted oncogenesis to induce neoplasia in renal renin-expressing cells, express high levels of renin mRNA from the endogenous Ren-1(c) gene. We have used these cells to characterize the role of the Ren-1(c) proximal promoter (+6 to -117) in the regulation of renin gene transcription. It was found that 4.1 kilobases (kb) of Ren-1(c) 5'-flanking sequence, in combination with the proximal promoter, are required for strong activation (approximately 2 orders of magnitude over the basal level of the promoter alone) of the chloramphenicol acetyltransferase reporter in transfection assays. Within the 4.1-kb fragment, a 241-base pair region was identified that retains full activity in an orientation-independent manner in combination with the promoter. The resulting transcripts initiate at the normal renin start site. Electrophoretic mobility shift assays identified a sequence at approximately position -60 in the promoter region that binds nuclear proteins specific for renin-expressing As4.1 cells. Mutations in this sequence, which disrupt binding of nuclear protein(s), completely abolish activation of transcription by the 4. 1-kb fragment. Activation of transcription by the 241-base pair enhancer was still observed, although it was diminished in magnitude (60-fold over the mutated promoter alone). We present a model derived from the current data that suggests that regulation of renin expression is achieved through cooperation of transcription factors binding at the proximal promoter element and a distal enhancer element to abrogate or override the effects of an intervening negative regulatory region.
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Affiliation(s)
- N Petrovic
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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38
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Black TA, Wolk CP. Analysis of a Het- mutation in Anabaena sp. strain PCC 7120 implicates a secondary metabolite in the regulation of heterocyst spacing. J Bacteriol 1994; 176:2282-92. [PMID: 8157596 PMCID: PMC205350 DOI: 10.1128/jb.176.8.2282-2292.1994] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.7] [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: 01/29/2023] Open
Abstract
Transposon-generated mutant N10 of Anabaena sp. strain PCC 7120 has a Het- phenotype (A. Ernst, T. Black, Y. Cai, J.-M. Panoff, D. N. Tiwari, and C. P. Wolk, J. Bacteriol. 174:6025-6032, 1992). Reconstruction of the transposon mutation reproduced a Het- phenotype, but reconstructions with other insertions at the position of the transposon produced strains that form multiple contiguous heterocysts. Sequence analysis around the site of insertion of the transposon showed that the insertion lies within the 5' end of an 861-bp open reading frame (ORF) (hetN). The product of translation of hetN (HetN) shows extensive similarity to NAD(P)H-dependent oxidoreductases that are involved in biosyntheses of fatty acids, poly-beta-hydroxybutyrate, nod factor, and polyketides. A second, 1,518-bp ORF (hetM) that ends 556 bp 5' from the start of hetN appears to encode a protein that has at least two functional domains: its amino terminus is similar to an acyl carrier protein, while its central portion is similar to domains of proteins that perform reductive reactions. A third, 711-bp ORF (hetI) encoded on the opposite strand ends 42 bp away from the 3' end of hetN. The protein encoded by hetI, HetI, is similar to Sfp from Bacillus subtilis and EntD from Escherichia coli, proteins that are required for the biosynthesis or export of cyclic peptides. Clones from a lambda-EMBL3 library that contain the wild-type DNA for hetN do not complement the hetN::Tn5-1063 mutation in N10. The presence of hetN, as the only ORF, on a replicating plasmid suppresses heterocyst formation in wild-type cells, whereas the additional presence of hetI alleviates this effect.
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Affiliation(s)
- T A Black
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824
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39
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Abstract
The spatially patterned differentiation of heterocysts in the filamentous cyanobacterium Anabaena requires a functional hetR gene. Transcriptional fusions to luxAB show that hetR is transcribed at a low level throughout the filament when Anabaena is grown with combined nitrogen, and that induction of the gene begins within 2 h following nitrogen deprivation. By 3.5 h, induction is localized to spaced foci. By 6 h, there is an overall induction of at least threefold in whole cultures, reflecting at least a 20-fold increase within spatially separated cells. The induction requires the presence of a functional hetR gene, indicating that hetR is autoregulatory. Full induction of a heterocyst structural gene, hepA, also requires a functional hetR locus.
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Affiliation(s)
- T A Black
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824
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40
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Abstract
A physical map of the Anabaena genome permitted the localization of its genes to chromosomal fragments generated by rarely cutting restriction endonucleases and separated by pulsed-field gel electrophoresis. We introduce a novel means of mapping more precisely to c. 20 kb by use of rare restriction sites within vectors bearing cloned sequences that undergo homologous recombination with the genome. We thereby localize and orient genes encoding principal photosynthetic pigments. The relative spacing of loci within a single restriction fragment was determined with even higher resolution, as illustrated for genes required for heterocyst development and nitrogen fixation that were marked with transposons. Small, newly visualized restriction fragments of the chromosome were also mapped.
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Affiliation(s)
- T Kuritz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing 48824
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