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No HJ, Guo FB, Park NJI, Kastelowitz N, Rhee JW, Clark DE, Chin ALC, Vitzthum LK, Horst KC, Moding EJ, Loo BW, Diehn M, Binkley MS. Predicting Adverse Cardiac Events After Radiotherapy for Locally Advanced Non-Small Cell Lung Cancer. JACC CardioOncol 2023; 5:775-787. [PMID: 38205000 PMCID: PMC10774791 DOI: 10.1016/j.jaccao.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 01/12/2024] Open
Abstract
Background Radiotherapy may cause grade ≥3 cardiac events, necessitating a better understanding of risk factors. The potential predictive role of imaging biomarkers with radiotherapy doses for cardiac event occurrence has not been studied. Objectives The aim of this study was to establish the associations between cardiac substructure dose and coronary artery calcium (CAC) scores and cardiac event occurrence. Methods A retrospective cohort analysis included patients with locally advanced non-small cell lung cancer treated with radiotherapy (2006-2018). Cardiac substructures, including the left anterior descending coronary artery, left main coronary artery, left circumflex coronary artery, right coronary artery, and TotalLeft (left anterior descending, left main, and left circumflex coronary arteries), were contoured. Doses were measured in 2-Gy equivalent units, and visual CAC scoring was compared with automated scoring. Grade ≥3 adverse cardiac events were recorded. Time-dependent receiver-operating characteristic modeling, the log-rank statistic, and competing-risk models were used to measure prediction performance, threshold modeling, and the cumulative incidence of cardiac events, respectively. Results Of the 233 eligible patients, 61.4% were men, with a median age of 68.1 years (range: 34.9-90.7 years). The median follow-up period was 73.7 months (range: 1.6-153.9 months). Following radiotherapy, 22.3% experienced cardiac events, within a median time of 21.5 months (range: 1.7-118.9 months). Visual CAC scoring showed significant correlation with automated scoring (r = 0.72; P < 0.001). In a competing-risk multivariable model, TotalLeft volume receiving 15 Gy (per 1 cc; HR: 1.38; 95% CI: 1.11-1.72; P = 0.004) and CAC score >5 (HR: 2.51; 95% CI: 1.08-5.86; P = 0.033) were independently associated with cardiac events. A model incorporating age, TotalLeft CAC (score >5), and volume receiving 15 Gy demonstrated a higher incidence of cardiac events for a high-risk group (28.9%) compared with a low-risk group (6.9%) (P < 0.001). Conclusions Adverse cardiac events associated with radiation occur in more than 20% of patients undergoing thoracic radiotherapy within a median time of <2 years. The present findings provide further evidence to support significant associations between TotalLeft radiotherapy dose and cardiac events and define CAC as a predictive risk factor.
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Affiliation(s)
- Hyunsoo Joshua No
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Felicia B. Guo
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Natalie Jung-In Park
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Noah Kastelowitz
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - June-Wha Rhee
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Daniel Eugene Clark
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Li-Che Chin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Lucas Kas Vitzthum
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen Claire Horst
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Everett James Moding
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Billy W. Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Sargent Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
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2
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No HJ, Park NJ, Guo FB, Kastelowitz N, Snyder JM, Rhee JW, Clark DE, Chin AL, Vitzthum L, Horst KC, Moding EJ, Loo BW, Diehn M, Binkley MS. Investigating Dosimetry and Imaging Biomarkers for Prediction of Major Adverse Cardiac Events Following Locally Advanced Non-Small Cell Lung Cancer Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:S170. [PMID: 37784425 DOI: 10.1016/j.ijrobp.2023.06.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Thoracic radiotherapy (RT) may confer major adverse cardiac events (MACE) following treatment. Mean heart dose positively associates with MACE and recent studies show cardiac substructure dosimetry improves MACE prediction. Use of imaging biomarkers with cardiac substructure dose has not been studied for prediction of MACE. We sought to develop an integrated model for cardiac substructure dose and baseline coronary artery calcium (CAC) scoring and establish its relationship to MACE. MATERIALS/METHODS A retrospective cohort analysis was performed of consecutive patients with locally advanced non-small cell lung cancer (NSCLC) treated with definitive RT from 2006-2018 at a single institution. Demographics, medical history, cardiac events, and treatments received were recorded. Cardiac substructures were contoured, including the left descending artery (LAD), left main coronary artery (LMCA), left circumflex (LCX), right coronary artery (RCA), TotalLeft (LAD+LMCA+LCX), and TotalCor (TotalLeft+RCA). Doses were measured in 2 Gy equivalent dose. CAC was scored by visual assessment and compared to established automated Agatston scoring. Primary endpoint was MACE incidence. Receiver operating characteristic (ROC) curves assessed dose and CAC metric model performance. Threshold modeling was conducted using the log rank statistic with 95% confidence intervals measured using bootstrap resampling with 1000 iterations. Competing risk models adjusted for death were used to measure cumulative incidence of MACE as well as in univariable and multivariable risk regression modeling. Pearson correlations were used to validate CAC scoring. P-values were two tailed and considered significant at P≤0.05. RESULTS Of 233 eligible patients, 61.4% were male with a 68.1 years (range 34.9-90.7) median age. Median follow-up was 73.7 months (range 1.6-153.9). Median overall survival was 34.8 months. Following RT, 22.3% experienced at least one cardiac event at a median time of 21.5 months (range 1.7-118.9). Visual CAC scoring showed significant correlation with automated Agatston scoring (r = 0.72, P=1e-5). While left sided coronary arteries (TotalLeft), mean heart dose (MHD) and CAC scores individually predicted for MACE (AUC = 0.56-0.59), a multivariable model of TotalLeft CAC had the highest ROC analysis performance (AUC = 0.69). On univariable and multivariable competing risk regression analyses, TotalLeft V15 Gy >2.53 cc and CAC score >5 independently associated with MACE (P<0.05). A model incorporating age, TotalLeft CAC>5 and V15>2.53cc, showed incrementally higher MACE incidences for low (9.3%), intermediate (18.4%), and high-risk groups (27.7%) (P<0.01). CONCLUSION RT-induced MACE occurs in >20% of those undergoing thoracic RT in a median time of <2 years. We validate significant associations between TotalLeft RT dose and MACE and establish CAC as a predictive risk factor. These findings may serve to inform personalized RT and future cardiac risk in locally advanced NSCLC.
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Affiliation(s)
- H J No
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - N J Park
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - F B Guo
- University of Rochester School of Medicine and Dentistry, Rochester, NY
| | - N Kastelowitz
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - J M Snyder
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - J W Rhee
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - D E Clark
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - A L Chin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - L Vitzthum
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | - K C Horst
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - E J Moding
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
| | - B W Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA; Stanford Cancer Institute, Stanford, CA
| | - M Diehn
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA; Stanford Cancer Institute, Stanford, CA
| | - M S Binkley
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA
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3
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Wu YF, Skinner L, Lewis J, Khodadoust MS, Kim YH, Kwong BY, Weng WK, Hoppe RT, Sodji Q, Hui C, Kastelowitz N, Fernandez-Pol S, Hiniker SM. Radiation Therapy for Primary Cutaneous Gamma Delta Lymphoma Prior to Stem Cell Transplantation. Cancer Invest 2023; 41:1-8. [PMID: 33899635 DOI: 10.1080/07357907.2021.1919696] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/01/2023]
Abstract
We present a patient with widespread PCGD-TCL of the bilateral arms and legs, who underwent radiotherapy with 34 Gy in 17 fractions using circumferential VMAT and 3-D printed bolus to the four extremities prior to planned stem cell transplant, who was then found to have progression in the liver, lung, and skin, followed by drastic regression of all in and out-of-field lesions on imaging 1.5 months later. The cause of regression may be related to a radiation-induced abscopal effect from the immunomodulatory effects of radiation, or related to immune reactivation in the setting of cessation of systemic immunosuppressive agents.
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Affiliation(s)
- Yufan F Wu
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lawrie Skinner
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan Lewis
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Internal Medicine, Medical Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Youn H Kim
- Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bernice Y Kwong
- Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wen-Kai Weng
- Stem Cell Transplantation, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard T Hoppe
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Quaovi Sodji
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Caressa Hui
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah Kastelowitz
- Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Susan M Hiniker
- School of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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4
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Kastelowitz N, Marsh MD, McCarter M, Meguid RA, Bhardwaj NW, Mitchell JD, Weyant MJ, Scott C, Schefter T, Stumpf P, Leong S, Messersmith W, Lieu C, Leal AD, Davis SL, Purcell WT, Kane M, Wani S, Shah R, Hammad H, Edmundowicz S, Goodman KA. Impact of Radiation Dose on Postoperative Complications in Esophageal and Gastroesophageal Junction Cancers. Front Oncol 2021; 11:614640. [PMID: 33777751 PMCID: PMC7987936 DOI: 10.3389/fonc.2021.614640] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/08/2021] [Indexed: 01/03/2023] Open
Abstract
Introduction: The impact of radiation prescription dose on postoperative complications during standard of care trimodality therapy for operable stage II-III esophageal and gastroesophageal junction cancers has not been established. Methods: We retrospectively reviewed 82 patients with esophageal or gastroesophageal junction cancers treated between 2004 and 2016 with neoadjuvant chemoradiation followed by resection at a single institution. Post-operative complications within 30 days were reviewed and scored using the Comprehensive Complication Index (CCI). Results were compared between patients treated with <50 Gy and ≥ 50 Gy, as well as to published CROSS study neoadjuvant chemoradiation group data (41.4 Gy). Results: Twenty-nine patients were treated with <50 Gy (range 39.6-46.8 Gy) and 53 patients were treated with ≥ 50 Gy (range 50.0-52.5 Gy) delivered using IMRT/VMAT (41%), 3D-CRT (46%), or tomotherapy IMRT (12%). Complication rates and CCI scores between our <50 Gy and ≥ 50 Gy groups were not significantly different. Assuming a normal distribution of the CROSS data, there was no significant difference in CCI scores between the CROSS study neoadjuvant chemoradiation, <50 Gy, or ≥ 50 Gy groups. Rates of pulmonary complications were greater in the CROSS group (50%) than our <50 Gy (38%) or ≥ 50 Gy (30%) groups. Conclusions: In selected esophageal and gastroesophageal junction cancer patients, radiation doses ≥ 50 Gy do not appear to increase 30 day post-operative complication rates. These findings suggest that the use of definitive doses of radiotherapy (50-50.4 Gy) in the neoadjuvant setting may not increase post-operative complications.
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Affiliation(s)
- Noah Kastelowitz
- Stanford University School of Medicine, Stanford, CA, United States
| | - Megan D. Marsh
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Martin McCarter
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Robert A. Meguid
- University of Colorado School of Medicine, Aurora, CO, United States
| | | | - John D. Mitchell
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Michael J. Weyant
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Christopher Scott
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Tracey Schefter
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Priscilla Stumpf
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Stephen Leong
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Wells Messersmith
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Christopher Lieu
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexis D. Leal
- University of Colorado School of Medicine, Aurora, CO, United States
| | - S. Lindsey Davis
- University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Madeleine Kane
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Sachin Wani
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Raj Shah
- University of Colorado School of Medicine, Aurora, CO, United States
| | - Hazem Hammad
- University of Colorado School of Medicine, Aurora, CO, United States
| | | | - Karyn A. Goodman
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
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5
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Pollom EL, Sandhu N, Frank J, Miller JA, Obeid JP, Kastelowitz N, Panjwani N, Soltys SG, Bagshaw HP, Donaldson SS, Horst K, Beadle BM, Chang DT, Gibbs I. Continuing Medical Student Education During the Coronavirus Disease 2019 (COVID-19) Pandemic: Development of a Virtual Radiation Oncology Clerkship. Adv Radiat Oncol 2020; 5:732-736. [PMID: 32775783 PMCID: PMC7237939 DOI: 10.1016/j.adro.2020.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/05/2020] [Accepted: 05/05/2020] [Indexed: 11/04/2022] Open
Abstract
Purpose Our institution cancelled all in-person clerkships owing to the coronavirus disease 2019 pandemic. In response, we designed a virtual radiation oncology medical student clerkship. Methods and Materials We convened an advisory panel to design a virtual clerkship curriculum. We implemented clerkship activities using a cloud-based learning management system, video web conferencing systems, and a telemedicine portal. Students completed assessments pre- and postclerkship to provide data to improve future versions of the clerkship. Results The virtual clerkship spans 2 weeks and is graded pass or fail. Students attend interactive didactic sessions during the first week and participate in virtual clinic and give talks to the department during the second week. Didactic sessions include lectures, case-based discussions, treatment planning seminars, and material adapted from the Radiation Oncology Education Collaborative Study Group curriculum. Students also attend virtual departmental quality assurance rounds, cancer center seminars, and multidisciplinary tumor boards. The enrollment cap was met during the first virtual clerkship period (April 27 through May 8, 2020), with a total of 12 students enrolling. Conclusions Our virtual clerkship can increase student exposure and engagement in radiation oncology. Data on clerkship outcomes are forthcoming.
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Affiliation(s)
- Erqi L Pollom
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Navjot Sandhu
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Jessica Frank
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Jacob A Miller
- Stanford School of Medicine, Palo Alto, Stanford, California
| | | | | | - Neil Panjwani
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Scott G Soltys
- Stanford School of Medicine, Palo Alto, Stanford, California
| | | | | | - Kathleen Horst
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Beth M Beadle
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Daniel T Chang
- Stanford School of Medicine, Palo Alto, Stanford, California
| | - Iris Gibbs
- Stanford School of Medicine, Palo Alto, Stanford, California
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6
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Kastelowitz N, Marsh MD, McCarter M, Meguid RA, Schefter TE, Rooke DA, Stumpf P, Leong S, Messersmith WA, Lieu CH, Leal AD, Davis SL, Purcell WT, Mitchell JD, Weyant MJ, Scott C, Goodman KA. Impact of radiation dose during neoadjuvant chemoradiation on postoperative complications in esophageal (EC) and gastroesophageal junction cancers (GEJC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
119 Background: Neoadjuvant chemoradiation (nCRT) followed by resection is standard of care for operable stage II-III EC and GEJC; however, it can be associated with significant risk of postoperative complications (POC). The CROSS study group reported no increase in POC severity with nCRT using 41.4 Gy compared to surgery alone as defined by the Comprehensive Complication Index (CCI). We applied the CCI metric to evaluate the impact of nCRT radiation dose of < 50 Gy vs. ≥ 50 Gy on POC rates and compared to the CROSS rates. Methods: We retrospectively reviewed 82 pts (2004-2016) with EC or GEJC treated with nCRT followed by resection at our institution. 29 (35%) pts were treated with < 50 Gy (range 39.6-46.8 Gy) and 53 (65%) were treated with ≥ 50 Gy (range 50.0-52.5 Gy) delivered using IMRT/VMAT (41%), 3D-CRT (46%), or tomotherapy IMRT (12%). Concurrent chemotherapy were carboplatin/paclitaxel (59%), cisplatin/5-FU (17%), or other (24%). Resection was performed by Ivor Lewis esophagectomy (67%), esophagogastrectomy (14%), or trans-hiatal approach (11%). POC within 30 days were graded using the Clavien-Dindo scale and CCI scores were computed and compared between the two dose groups and with the CROSS nCRT group. Results: CCI scores and complication rates between our < 50 Gy and ≥ 50 Gy groups were not significantly different. Assuming a normal distribution of the CROSS CCI scores, there was no significant difference in CCI scores between the CROSS study nCRT, < 50 Gy, or ≥ 50 Gy groups. Rates of pulmonary complications were greater in the CROSS study. Conclusions: In highly selected EC and GEJC pts, definitive nCRT radiation doses do not appear to increase POC rates. Thus, 50 Gy can likely be delivered without increasing toxicity while also achieving a definitive dose for pts not able or willing to undergo subsequent surgery. [Table: see text]
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Affiliation(s)
| | | | | | | | | | | | | | - Stephen Leong
- University of Colorado School of Medicine, Aurora, CO
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Abstract
Nanoscale confinement has a strong effect on the phase behavior of water. Studies in the last two decades have revealed a wealth of novel crystalline and quasicrystalline structures for water confined in nanoslits. Less is known, however, about the nature of ice-liquid coexistence in extremely nanoconfined systems. Here, we use molecular simulations to investigate the ice-liquid equilibrium for water confined between two nanoscopic disks. We find that the nature of ice-liquid phase coexistence in nanoconfined water is different from coexistence in both bulk water and extended nanoslits. In highly nanoconfined systems, liquid water and ice do not coexist in space because the two-phase states are unstable. The confined ice and liquid phases coexist in time, through oscillations between all-liquid and all-crystalline states. The avoidance of spatial coexistence of ice and liquid originates on the non-negligible cost of the interface between confined ice and liquid in a small system. It is the result of the small number of water molecules between the plates and has no analogue in bulk water.
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Affiliation(s)
- Noah Kastelowitz
- Department of Chemistry , The University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Valeria Molinero
- Department of Chemistry , The University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112-0850 , United States
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8
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Sammond DW, Kastelowitz N, Donohoe BS, Alahuhta M, Lunin VV, Chung D, Sarai NS, Yin H, Mittal A, Himmel ME, Guss AM, Bomble YJ. An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme. Biotechnol Biofuels 2018; 11:189. [PMID: 30002729 PMCID: PMC6036693 DOI: 10.1186/s13068-018-1178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/18/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Strategies for maximizing the microbial production of bio-based chemicals and fuels include eliminating branched points to streamline metabolic pathways. While this is often achieved by removing key enzymes, the introduction of nonnative enzymes can provide metabolic shortcuts, bypassing branched points to decrease the production of undesired side-products. Pyruvate decarboxylase (PDC) can provide such a shortcut in industrially promising thermophilic organisms; yet to date, this enzyme has not been found in any thermophilic organism. Incorporating nonnative enzymes into host organisms can be challenging in cases such as this, where the enzyme has evolved in a very different environment from that of the host. RESULTS In this study, we use computational protein design to engineer the Zymomonas mobilis PDC to resist thermal denaturation at the growth temperature of a thermophilic host. We generate thirteen PDC variants using the Rosetta protein design software. We measure thermal stability of the wild-type PDC and PDC variants using circular dichroism. We then measure and compare enzyme endurance for wild-type PDC with the PDC variants at an elevated temperature of 60 °C (thermal endurance) using differential interference contrast imaging. CONCLUSIONS We find that increases in melting temperature (Tm) do not directly correlate with increases in thermal endurance at 60 °C. We also do not find evidence that any individual mutation or design approach is the major contributor to the most thermostable PDC variant. Rather, remarkable cooperativity among sixteen thermostabilizing mutations is key to rationally designing a PDC with significantly enhanced thermal endurance. These results suggest a generalizable iterative computational protein design approach to improve thermal stability and endurance of target enzymes.
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Affiliation(s)
- Deanne W. Sammond
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Vladimir V. Lunin
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Daehwan Chung
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309 USA
| | - Ashutosh Mittal
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
| | - Adam M. Guss
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401 USA
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9
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Kastelowitz N, Tamura R, Onasoga A, Stalker TJ, White OR, Brown PN, Brodsky GL, Brass LF, Branchford BR, Di Paola J, Yin H. Peptides derived from MARCKS block coagulation complex assembly on phosphatidylserine. Sci Rep 2017; 7:4275. [PMID: 28655899 PMCID: PMC5487340 DOI: 10.1038/s41598-017-04494-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/16/2017] [Indexed: 01/27/2023] Open
Abstract
Blood coagulation involves activation of platelets and coagulation factors. At the interface of these two processes resides the lipid phosphatidylserine. Activated platelets expose phosphatidylserine on their outer membrane leaflet and activated clotting factors assemble into enzymatically active complexes on the exposed lipid, ultimately leading to the formation of fibrin. Here, we describe how small peptide and peptidomimetic probes derived from the lipid binding domain of the protein myristoylated alanine-rich C-kinase substrate (MARCKS) bind to phosphatidylserine exposed on activated platelets and thereby inhibit fibrin formation. The MARCKS peptides antagonize the binding of factor Xa to phosphatidylserine and inhibit the enzymatic activity of prothrombinase. In whole blood under flow, the MARCKS peptides colocalize with, and inhibit fibrin cross-linking, of adherent platelets. In vivo, we find that the MARCKS peptides circulate to remote injuries and bind to activated platelets in the inner core of developing thrombi.
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Affiliation(s)
- Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ryo Tamura
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Abimbola Onasoga
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Timothy J Stalker
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ormacinda R White
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Peter N Brown
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Gary L Brodsky
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lawrence F Brass
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brian R Branchford
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jorge Di Paola
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA.
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
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Sammond DW, Kastelowitz N, Himmel ME, Yin H, Crowley MF, Bomble YJ. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms. PLoS One 2016; 11:e0145848. [PMID: 26741367 PMCID: PMC4704809 DOI: 10.1371/journal.pone.0145848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.
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Affiliation(s)
- Deanne W Sammond
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, Colorado, 80309, United States of America
| | - Michael F Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, 80401, United States of America
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Cheng K, Gao M, Godfroy JI, Brown PN, Kastelowitz N, Yin H. Specific activation of the TLR1-TLR2 heterodimer by small-molecule agonists. Sci Adv 2015; 1:e1400139. [PMID: 26101787 PMCID: PMC4474499 DOI: 10.1126/sciadv.1400139] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Toll-like receptor (TLR) agonists activate both the innate and the adaptive immune systems. These TLR agonists have been exploited as potent vaccine adjuvants and antitumor agents. We describe the identification and characterization of a small molecule, N-methyl-4-nitro-2-(4-(4-(trifluoromethyl)phenyl)-1 H-imidazol-1-yl)aniline (CU-T12-9), that directly targets TLR1/2 to initiate downstream signaling. CU-T12-9 specifically induces TLR1/2 activation, which can be blocked by either the anti-hTLR1 or the anti-hTLR2 antibody, but not the anti-hTLR6 antibody. Using a variety of different biophysical assays, we have demonstrated the binding mode of CU-T12-9. By binding to both TLR1 and TLR2, CU-T12-9 facilitates the TLR1/2 heterodimeric complex formation, which in turn activates the downstream signaling. Fluorescence anisotropy assays revealed competitive binding to the TLR1/2 complex between CU-T12-9 and Pam3CSK4 with a half-maximal inhibitory concentration (IC50) of 54.4 nM. Finally, we showed that CU-T12-9 signals through nuclear factor κB (NF-κB) and invokes an elevation of the downstream effectors tumor necrosis factor-α (TNF-α), interleukin-10 (IL-10), and inducible nitric oxide synthase (iNOS). Thus, our studies not only provide compelling new insights into the regulation of TLR1/2 signaling transduction but also may facilitate future therapeutic developments.
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Affiliation(s)
- Kui Cheng
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Meng Gao
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - James I. Godfroy
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Peter N. Brown
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Noah Kastelowitz
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Hang Yin
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA
- Corresponding author. E-mail:
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Lupi L, Kastelowitz N, Molinero V. Vapor deposition of water on graphitic surfaces: Formation of amorphous ice, bilayer ice, ice I, and liquid water. J Chem Phys 2014; 141:18C508. [DOI: 10.1063/1.4895543] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laura Lupi
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Noah Kastelowitz
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
| | - Valeria Molinero
- Department of Chemistry, The University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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Abstract
Exosomes and microvesicles are two classes of submicroscopic vesicle released by cells into the extracellular space. Collectively referred to as extracellular vesicles, these membrane containers facilitate important cell-cell communication by carrying a diverse array of signaling molecules, including nucleic acids, proteins, and lipids. Recently, the role of extracellular vesicle signaling in cancer progression has become a topic of significant interest. Methods to detect and target exosomes and microvesicles are needed to realize applications of extracellular vesicles as biomarkers and, perhaps, therapeutic targets. Detection of exosomes and microvesicles is a complex problem as they are both submicroscopic and of heterogeneous cellular origins. In this Minireview, we highlight the basic biology of extracellular vesicles, and address available biochemical and biophysical detection methods. Detectible characteristics described here include lipid and protein composition, and physical properties such as the vesicle membrane shape and diffusion coefficient. In particular, we propose that detection of exosome and microvesicle membrane curvature with lipid chemical probes that sense membrane shape is a distinctly promising method for identifying and targeting these vesicles.
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Affiliation(s)
- Noah Kastelowitz
- Department of Chemistry & Biochemistry and the BioFrontiers Institute,
University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303 (USA)
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute,
University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80303 (USA)
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Abstract
Highly curved bilayer lipid membranes make up the shell of many intra- and extracellular compartments, including organelles and vesicles. Using all-atom molecular dynamics simulations, we show that increasing the density of lipids in the bilayer membrane can induce the membrane to form a curved shape.
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Affiliation(s)
- Armando J de Jesus
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303, USA
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