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Huang R, Zheng XP, Zhao M. [Clear cell stromal tumor of the lung: report of a case]. Zhonghua Bing Li Xue Za Zhi 2024; 53:401-403. [PMID: 38556828 DOI: 10.3760/cma.j.cn112151-20231107-00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Affiliation(s)
- R Huang
- Zhejiang Chinese Medical University,Hangzhou 310053, China Hangzhou Tongchuang Medical Laboratory, Hangzhou 310006, China
| | - X P Zheng
- Hangzhou Tongchuang Medical Laboratory, Hangzhou 310006, China
| | - M Zhao
- Ningbo Clinical Pathology Diagnosis Center, Ningbo 315100, China
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Tong ZB, Huang R, Braisted J, Chu PH, Simeonov A, Gerhold DL. 3D-Suspension culture platform for high throughput screening of neurotoxic chemicals using LUHMES dopaminergic neurons. SLAS Discov 2024; 29:100143. [PMID: 38280460 PMCID: PMC11056300 DOI: 10.1016/j.slasd.2024.01.004] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 01/29/2024]
Abstract
Three-dimensional (3D) cell culture in vitro promises to improve representation of neuron physiology in vivo. This inspired development of a 3D culture platform for LUHMES (Lund Human Mesencephalic) dopaminergic neurons for high-throughput screening (HTS) of chemicals for neurotoxicity. Three culture platforms, adhesion (2D-monolayer), 3D-suspension, and 3D-shaken, were compared to monitor mRNA expression of seven neuronal marker genes, DCX, DRD2, ENO2, NEUROD4, SYN1, TH, and TUBB3. These seven marker genes reached similar maxima in all three formats, with the two 3D platforms showing similar kinetics, whereas several markers peaked earlier in 2D adhesion compared to both 3D culture platforms. The differentiated LUHMES (dLUHMES) neurons treated with ziram, methylmercury or thiram dynamically increased expression of metallothionein biomarker genes MT1G, MT1E and MT2A at 6 h. These gene expression increases were generally more dynamic in 2D adhesion cultures than in 3D cultures, but were generally comparable between 3D-suspension and 3D-u plate (low binding) platforms. Finally, we adapted 3D-suspension culture of dLUHMES and neural stem cells to 1536 well plates with a HTS cytotoxicity assay. This HTS assay revealed that cytotoxicity IC50 values were not significantly different between adhesion and 3D-suspension platforms for 31 of 34 (91%) neurotoxicants tested, whereas IC50 values were significantly different for at least two toxicants. In summary, the 3D-suspension culture platform for LUHMES dopaminergic neurons supported full differentiation and reproducible assay results, enabling quantitative HTS (qHTS) for cytotoxicity in 1536 well format with a Robust Z' score of 0.68.
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Affiliation(s)
- Zhi-Bin Tong
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - John Braisted
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - Pei-Hsuan Chu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - David L Gerhold
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States.
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Liu F, Patt A, Chen C, Huang R, Xu Y, Mathé EA, Zhu Q. Exploring NCATS in-house biomedical data for evidence-based drug repurposing. PLoS One 2024; 19:e0289518. [PMID: 38271343 PMCID: PMC10810548 DOI: 10.1371/journal.pone.0289518] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/19/2023] [Accepted: 11/08/2023] [Indexed: 01/27/2024] Open
Abstract
Drug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
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Affiliation(s)
- Fang Liu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Andrew Patt
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, United States of America
| | - Chloe Chen
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, United States of America
| | - Yanji Xu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Ewy A. Mathé
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, United States of America
| | - Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland, United States of America
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Lynch C, Sakamuru S, Ooka M, Huang R, Klumpp-Thomas C, Shinn P, Gerhold D, Rossoshek A, Michael S, Casey W, Santillo MF, Fitzpatrick S, Thomas RS, Simeonov A, Xia M. High-Throughput Screening to Advance In Vitro Toxicology: Accomplishments, Challenges, and Future Directions. Annu Rev Pharmacol Toxicol 2024; 64:191-209. [PMID: 37506331 PMCID: PMC10822017 DOI: 10.1146/annurev-pharmtox-112122-104310] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Traditionally, chemical toxicity is determined by in vivo animal studies, which are low throughput, expensive, and sometimes fail to predict compound toxicity in humans. Due to the increasing number of chemicals in use and the high rate of drug candidate failure due to toxicity, it is imperative to develop in vitro, high-throughput screening methods to determine toxicity. The Tox21 program, a unique research consortium of federal public health agencies, was established to address and identify toxicity concerns in a high-throughput, concentration-responsive manner using a battery of in vitro assays. In this article, we review the advancements in high-throughput robotic screening methodology and informatics processes to enable the generation of toxicological data, and their impact on the field; further, we discuss the future of assessing environmental toxicity utilizing efficient and scalable methods that better represent the corresponding biological and toxicodynamic processes in humans.
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Affiliation(s)
- Caitlin Lynch
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Masato Ooka
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - David Gerhold
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Anna Rossoshek
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Warren Casey
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Michael F Santillo
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Suzanne Fitzpatrick
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA; ,
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Zhuo YQ, Tu SF, Zhou X, Yang JL, Zhou LJ, Huang R, Huang YX, Li MF, Jin B, Wang B, Li SQ, Yuan ZT, Zhang LH, Liu L, Wang SB, Li YH. [Safety and efficacy of donor-derived chimeric antigen receptor T-cell therapy in patients with relapsed B-cell acute lymphoblastic leukemia after allogeneic hematopoietic stem cell transplantation]. Zhonghua Xue Ye Xue Za Zhi 2024; 45:74-81. [PMID: 38527842 DOI: 10.3760/cma.j.cn121090-20230815-00068] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Objective: To investigated the safety and efficacy of donor-derived CD19+ or sequential CD19+ CD22+ chimeric antigen receptor T-cell (CAR-T) therapy in patients with B-cell acute lymphoblastic leukemia (B-ALL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: The data of 22 patients with B-ALL who relapsed after allo-HSCT and who underwent donor-derived CAR-T therapy at the Zhujiang Hospital of Southern Medical University and the 920th Hospital of Joint Logistics Support Force of the People's Liberation Army of China from September 2015 to December 2022 were retrospectively analyzed. The primary endpoint was overall survival (OS), and the secondary endpoints were event-free survival (EFS), complete remission (CR) rate, and Grade 3-4 adverse events. Results: A total of 81.82% (n=18) of the 22 patients achieved minimal residual disease-negative CR after CAR-T infusion. The median follow-up time was 1037 (95% CI 546-1509) days, and the median OS and EFS were 287 (95% CI 132-441) days and 212 (95% CI 120-303) days, respectively. The 6-month OS and EFS rates were 67.90% (95% CI 48.30%-84.50%) and 58.70% (95% CI 37.92%-79.48%), respectively, and the 1-year OS and EFS rates were 41.10% (95% CI 19.15%-63.05%) and 34.30% (95% CI 13.92%-54.68%), respectively. Grade 1-2 cytokine release syndrome occurred in 36.36% (n=8) of the patients, and grade 3-4 occurred in 13.64% of the patients (n=3). Grade 2 and 4 graft-versus-host disease occurred in two patients. Conclusion: Donor-derived CAR-T therapy is safe and effective in patients with relapsed B-ALL after allo-HSCT.
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Affiliation(s)
- Y Q Zhuo
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - S F Tu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - X Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - J L Yang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - L J Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - R Huang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Y X Huang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - M F Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - B Jin
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - B Wang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - S Q Li
- Department of Hematology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming 650118, China
| | - Z T Yuan
- Department of Hematology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming 650118, China
| | - L H Zhang
- Department of Hematology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming 650118, China
| | - L Liu
- Department of Hematology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming 650118, China
| | - S B Wang
- Department of Hematology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming 650118, China
| | - Y H Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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Li Z, Huang R, Xia M, Patterson TA, Hong H. Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery. Biomolecules 2024; 14:72. [PMID: 38254672 PMCID: PMC10813698 DOI: 10.3390/biom14010072] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein-ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure-activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure-activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein-ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.
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Affiliation(s)
- Zoe Li
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; (Z.L.); (T.A.P.)
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA; (R.H.); (M.X.)
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA; (R.H.); (M.X.)
| | - Tucker A. Patterson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; (Z.L.); (T.A.P.)
| | - Huixiao Hong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; (Z.L.); (T.A.P.)
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Chao X, Niu M, Wang S, Ma X, Yang X, Sun H, Hu X, Wang H, Zhang L, Huang R, Xia M, Ballabio A, Jaeschke H, Ni HM, Ding WX. High-throughput screening of novel TFEB agonists in protecting against acetaminophen-induced liver injury in mice. Acta Pharm Sin B 2024; 14:190-206. [PMID: 38261809 PMCID: PMC10793101 DOI: 10.1016/j.apsb.2023.10.017] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 01/25/2024] Open
Abstract
Macroautophagy (referred to as autophagy hereafter) is a major intracellular lysosomal degradation pathway that is responsible for the degradation of misfolded/damaged proteins and organelles. Previous studies showed that autophagy protects against acetaminophen (APAP)-induced injury (AILI) via selective removal of damaged mitochondria and APAP protein adducts. The lysosome is a critical organelle sitting at the end stage of autophagy for autophagic degradation via fusion with autophagosomes. In the present study, we showed that transcription factor EB (TFEB), a master transcription factor for lysosomal biogenesis, was impaired by APAP resulting in decreased lysosomal biogenesis in mouse livers. Genetic loss-of and gain-of function of hepatic TFEB exacerbated or protected against AILI, respectively. Mechanistically, overexpression of TFEB increased clearance of APAP protein adducts and mitochondria biogenesis as well as SQSTM1/p62-dependent non-canonical nuclear factor erythroid 2-related factor 2 (NRF2) activation to protect against AILI. We also performed an unbiased cell-based imaging high-throughput chemical screening on TFEB and identified a group of TFEB agonists. Among these agonists, salinomycin, an anticoccidial and antibacterial agent, activated TFEB and protected against AILI in mice. In conclusion, genetic and pharmacological activating TFEB may be a promising approach for protecting against AILI.
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Affiliation(s)
- Xiaojuan Chao
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Mengwei Niu
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Shaogui Wang
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xiaowen Ma
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Xiao Yang
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hua Sun
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei 230032, China
| | - Xujia Hu
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hua Wang
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei 230032, China
| | - Li Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli, Naples 80131, Italy
- Medical Genetics, Department of Translational Medicine, Federico II University, Naples 80131, Italy
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hong-Min Ni
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Internal Medicine, Division of Gastroenterology, Hepatology & Motility, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Nian Z, Zhao Q, He Y, Xie R, Liu W, Chen T, Huang S, Dong L, Huang R, Yang L. Efficacy and Safety of First-line Therapies for Advanced Unresectable Oesophageal Squamous Cell Cancer: a Systematic Review and Network Meta-analysis. Clin Oncol (R Coll Radiol) 2024; 36:30-38. [PMID: 37827946 DOI: 10.1016/j.clon.2023.09.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/27/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Abstract
AIM To compare the clinical efficacy and safety of first-line treatments for advanced unresectable oesophageal squamous cell cancer. MATERIALS AND METHODS A systematic review and network meta-analysis was carried out by retrieving and retaining relevant literature from databases. The studies were randomised controlled trials comparing first-line treatments for advanced unresectable oesophageal squamous cell cancer. A Bayesian network meta-analysis was used to assess clinical outcomes. RESULTS Nine studies including 4499 patients receiving first-line treatments were analysed. For all populations, toripalimab plus chemotherapy tended to provide the best overall survival (hazard ratio 0.58, 95% confidence intervals 0.43-0.78) and sintilimab plus chemotherapy provided the best progression-free survival (0.56, 0.46-0.68). Nivolumab plus chemotherapy presented the best objective response rate (odds ratio 2.45, 1.78-3.42) and camrelizumab plus chemotherapy (0.47, 0.29-0.74) appeared to be the safest. Sintilimab plus chemotherapy (0.55, 0.40-0.75) and nivolumab (0.54, 0.37-0.80) plus chemotherapy had the best overall survival in programmed death ligand 1 (PD-L1) tumour proportion score <1% and ≥1% subgroups. Toripalimab plus chemotherapy (0.61, 0.40-0.93) and pembrolizumab (0.57, 0.43-0.75) were the best in overall survival in combined positive score <10 and ≥10 subgroups, respectively. Toripalimab plus chemotherapy showed the best overall survival in the Asian group; pembrolizumab presented better overall survival in the Asian population than the non-Asian group. CONCLUSION Most immunotherapy combined with chemotherapy showed superior clinical benefits and sintilimab plus chemotherapy, toripalimab plus chemotherapy and tislelizumab plus chemotherapy had better comprehensive clinical efficacy. PD-L1 expression detection and ethnicity differences are still of great significance and most suitable regimens varied from each subgroup.
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Affiliation(s)
- Z Nian
- School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Q Zhao
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Y He
- School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - R Xie
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - W Liu
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - T Chen
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - S Huang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - L Dong
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - R Huang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - L Yang
- Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China.
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Ghelani GH, Zerdan MB, Jacob J, Spiess PE, Li R, Necchi A, Grivas P, Kamat A, Danziger N, Lin D, Huang R, Decker B, Sokol ES, Cheng L, Pavlick D, Ross JS, Bratslavsky G, Basnet A. HPV-positive clinically advanced squamous cell carcinoma of the urinary bladder (aBSCC): A comprehensive genomic profiling (CGP) study. Urol Oncol 2023; 41:486.e15-486.e23. [PMID: 37821306 DOI: 10.1016/j.urolonc.2023.09.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Advanced bladder squamous cell carcinoma (aBSCC) is an uncommon form of urinary bladder malignancy when compared with the much higher urothelial carcinoma incidence. We studied the genomic alteration (GA) landscape in a series of aBSCC based on the association with human papilloma virus (HPV) to determine if differences in GA would be observed between the positive and negative groups. METHODS Using a hybrid capture-based FDA-approved CGP assay, a series of 171 aBSCC were sequenced to evaluate all classes of GA. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on up to 114 loci. Programmed cell death ligand -1 (PD-L1) expression was determined by IHC (Dako 22C3) with negative expression when PD-L1 was 0, lower expression of positivity set at 1 to 49%, and higher expression set at ≥50% expression. RESULTS Overall, 11 (6.4%) of the aBSCC were found to harbor HPV sequences (10 HPV16 and 1 HPV 11). HPV+ status was identified slightly more often in women (NS) and in younger patients (P = 0.04); 2 female patients with aBSCC had a prior history of SCC including 1 anal SCC and 1 vaginal SCC. HPV+ aBSCC had fewer GA/tumor (P < 0.0001), more inactivating mutations in RB1 (P = 0.032), and fewer inactivating GA in CDKN2A (P < 0.0001), CDKN2B (P = 0.05), TERT promoter (P = 0.0004) and TP53 (P < 0.0001). GA in genes associated with urothelial carcinoma including FGFR2 and FGFR3 were similar in both HPV+ and HPV- aBSCC groups. MTAP loss (homozygous deletion) which has emerged as a biomarker for PRMT5 inhibitor-based clinical trials was not identified in any of the 11 HPV+ aBSCC cases, which was significantly lower than the 28% positive frequency of MTAP loss in the HPV- aBSCC group (P < 0.0001). MTOR and PIK3CA pathway GA were not significantly different in the 2 groups. Putative biomarkers associated with immunotherapy (IO) response, including MSI and TMB status, were also similar in the 2 groups. PD-L1 expression data was available for a subset of both HPV+ and HPV- cases and showed high frequencies of positive staining which was not different in the 2 groups. CONCLUSIONS HPV+ aBSCC tends to occur more often in younger patients. As reported in other HPV-associated squamous cell carcinomas, HPV+ aBSCC demonstrates significantly reduced frequencies of inactivating mutations in cell cycle regulatory genes with similar GA in MTOR and PIK3CA pathways. The implication of HPV in the pathogenesis of bladder cancer remains unknown but warrants further exploration and clinical validation.
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Affiliation(s)
| | | | - J Jacob
- Upstate Medical University, Syracuse, NY
| | - P E Spiess
- Department of GU Oncology, Moffitt Cancer Center, Tampa, FL
| | - R Li
- Department of GU Oncology, Moffitt Cancer Center, Tampa, FL
| | - A Necchi
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy
| | - P Grivas
- University of Washington, Seattle, WA
| | - A Kamat
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - D Lin
- Foundation Medicine, Cambridge, MA
| | - R Huang
- Foundation Medicine, Cambridge, MA
| | - B Decker
- Foundation Medicine, Cambridge, MA
| | | | - L Cheng
- Department of Pathology and Laboratory Medicine, Brown University Warren Alpert Medical School, Lifespan Academic Medical Center, and the Legorreta Cancer Center at Brown University, Providence, RI
| | | | - J S Ross
- Upstate Medical University, Syracuse, NY
| | | | - A Basnet
- Upstate Medical University, Syracuse, NY
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Huang R, Wu H, Lu X, Sun X. Clinical characteristics and prognostic factors of solitary and multiple adult gliomas: a retrospective study based on propensity score matching. Eur Rev Med Pharmacol Sci 2023; 27:10481-10498. [PMID: 37975372 DOI: 10.26355/eurrev_202311_34325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
OBJECTIVE This study aims to compare the survival and prognostic factors in patients with solitary gliomas to those with multiple to improve the understanding of multiple gliomas and investigate their heterogeneous dissemination pathways. PATIENTS AND METHODS Data on 358 patients diagnosed with adult gliomas confirmed by postoperative pathology were retrospectively collected and analyzed. The clinical characteristics, survival rates and prognosis of patients were analyzed by propensity score matching (PSM). RESULTS Between the two groups, statistically significant differences were identified in multiple general clinical characteristics, including age, pathological grade, lesion location, 1p19q co-deletion, IDH1 mutation, MGMT promoter methylation expression rate, p53 mutation and NF1 mutation (p<0.05). Before PSM, the mOS for patients with multiple gliomas was shorter than that for those with solitary (p=0.0045). Multivariate Cox regression analysis revealed that age, pathological grade IV, and absence of concurrent chemotherapy were significant risk factors affecting OS. Pathological grade IV, ki-67 expression range of 25-50%, and absence of concurrent chemotherapy were identified as risk factors for PFS. After PSM, the prognostic factors associated with OS were age and concurrent chemotherapy, while those associated with PFS were ki-67 expression range of 50-75% and lesion located in the right frontal lobe (p<0.05). CONCLUSIONS The prognosis for multiple gliomas is extremely poor, which is related to the fact that the most common pathological types are glioblastomas and the surgical procedure is challenging. Concurrent chemotherapy and radiotherapy are the strongest protective prognostic factors, and the differences in their molecular pathology expression compared to solitary gliomas remain for further investigation.
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Affiliation(s)
- R Huang
- Department of Radiation Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China.
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11
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Augier C, Barabash AS, Bellini F, Benato G, Beretta M, Bergé L, Billard J, Borovlev YA, Cardani L, Casali N, Cazes A, Celi E, Chapellier M, Chiesa D, Dafinei I, Danevich FA, De Jesus M, Dixon T, Dumoulin L, Eitel K, Ferri F, Fujikawa BK, Gascon J, Gironi L, Giuliani A, Grigorieva VD, Gros M, Helis DL, Huang HZ, Huang R, Imbert L, Johnston J, Juillard A, Khalife H, Kleifges M, Kobychev VV, Kolomensky YG, Konovalov SI, Kotila J, Loaiza P, Ma L, Makarov EP, de Marcillac P, Mariam R, Marini L, Marnieros S, Navick XF, Nones C, Norman EB, Olivieri E, Ouellet JL, Pagnanini L, Pattavina L, Paul B, Pavan M, Peng H, Pessina G, Pirro S, Poda DV, Polischuk OG, Pozzi S, Previtali E, Redon T, Rojas A, Rozov S, Sanglard V, Scarpaci JA, Schmidt B, Shen Y, Shlegel VN, Šimkovic F, Singh V, Tomei C, Tretyak VI, Umatov VI, Vagneron L, Velázquez M, Ware B, Welliver B, Winslow L, Xue M, Yakushev E, Zarytskyy M, Zolotarova AS. Measurement of the 2νββ Decay Rate and Spectral Shape of ^{100}Mo from the CUPID-Mo Experiment. Phys Rev Lett 2023; 131:162501. [PMID: 37925694 DOI: 10.1103/physrevlett.131.162501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 11/07/2023]
Abstract
Neutrinoless double beta decay (0νββ) is a yet unobserved nuclear process that would demonstrate Lepton number violation, a clear evidence of beyond standard model physics. The process two neutrino double beta decay (2νββ) is allowed by the standard model and has been measured in numerous experiments. In this Letter, we report a measurement of 2νββ decay half-life of ^{100}Mo to the ground state of ^{100}Ru of [7.07±0.02(stat)±0.11(syst)]×10^{18} yr by the CUPID-Mo experiment. With a relative precision of ±1.6% this is the most precise measurement to date of a 2νββ decay rate in ^{100}Mo. In addition, we constrain higher-order corrections to the spectral shape, which provides complementary nuclear structure information. We report a novel measurement of the shape factor ξ_{3,1}=0.45±0.03(stat)±0.05(syst) based on a constraint on the ratio of higher-order terms from theory, which can be reliably calculated. This is compared to theoretical predictions for different nuclear models. We also extract the first value for the effective axial vector coupling constant obtained from a spectral shape study of 2νββ decay.
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Affiliation(s)
- C Augier
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - A S Barabash
- National Research Centre "Kurchatov Institute," Kurchatov Complex of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - F Bellini
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
| | - G Benato
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- INFN, Gran Sasso Science Institute, I-67100 L'Aquila, Italy
| | - M Beretta
- University of California, Berkeley, California 94720, USA
| | - L Bergé
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J Billard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - Yu A Borovlev
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - L Cardani
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
| | - N Casali
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
| | - A Cazes
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - E Celi
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- INFN, Gran Sasso Science Institute, I-67100 L'Aquila, Italy
| | - M Chapellier
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - D Chiesa
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - I Dafinei
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
| | - F A Danevich
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
- INFN, Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - M De Jesus
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - T Dixon
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - L Dumoulin
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - K Eitel
- Karlsruhe Institute of Technology, Institute for Astroparticle Physics, 76021 Karlsruhe, Germany
| | - F Ferri
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - B K Fujikawa
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - J Gascon
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - L Gironi
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - A Giuliani
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - V D Grigorieva
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - M Gros
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - D L Helis
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - H Z Huang
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - R Huang
- University of California, Berkeley, California 94720, USA
| | - L Imbert
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J Johnston
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A Juillard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - H Khalife
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - M Kleifges
- Karlsruhe Institute of Technology, Institute for Data Processing and Electronics, 76021 Karlsruhe, Germany
| | - V V Kobychev
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - Yu G Kolomensky
- University of California, Berkeley, California 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - S I Konovalov
- National Research Centre Kurchatov Institute, Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - J Kotila
- Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
- Finnish Institute for Educational Research, University of Jyväskylä, P.O. Box 35, FI-40014 Jyvaäskylä, Finland
- Center for Theoretical Physics, Sloane Physics Laboratory, Yale University, New Haven, Connecticut 06520-8120, USA
| | - P Loaiza
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - L Ma
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - E P Makarov
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - P de Marcillac
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - R Mariam
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - L Marini
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- University of California, Berkeley, California 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - S Marnieros
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - X-F Navick
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - C Nones
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - E B Norman
- University of California, Berkeley, California 94720, USA
| | - E Olivieri
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J L Ouellet
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - L Pagnanini
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- INFN, Gran Sasso Science Institute, I-67100 L'Aquila, Italy
| | - L Pattavina
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- Physik Department, Technische Universität München, Garching D-85748, Germany
| | - B Paul
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M Pavan
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - H Peng
- Department of Modern Physics, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - G Pessina
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - S Pirro
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
| | - D V Poda
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - O G Polischuk
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - S Pozzi
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - E Previtali
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - Th Redon
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - A Rojas
- LSM, Laboratoire Souterrain de Modane, 73500 Modane, France
| | - S Rozov
- Laboratory of Nuclear Problems, JINR, 141980 Dubna, Moscow region, Russia
| | - V Sanglard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - J A Scarpaci
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - B Schmidt
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Y Shen
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - V N Shlegel
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - F Šimkovic
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, 842 48 Bratislava, Slovakia
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, 128 00 Prague, Czech Republic
| | - V Singh
- University of California, Berkeley, California 94720, USA
| | - C Tomei
- INFN, Sezione di Roma, P.le Aldo Moro 2, I-00185 Rome, Italy
| | - V I Tretyak
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - V I Umatov
- National Research Centre Kurchatov Institute, Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - L Vagneron
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - M Velázquez
- Université Grenoble Alpes, CNRS, Grenoble INP, SIMAP, 38420 Saint Martin d'Hères, France
| | - B Ware
- John de Laeter Centre for Isotope Research, GPO Box U 1987, Curtin University, Bentley, Western Australia, Australia
| | - B Welliver
- University of California, Berkeley, California 94720, USA
| | - L Winslow
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - M Xue
- Department of Modern Physics, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - E Yakushev
- Laboratory of Nuclear Problems, JINR, 141980 Dubna, Moscow region, Russia
| | - M Zarytskyy
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - A S Zolotarova
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
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Liu C, Zou W, Huang R, Yu J, Sun B. Dissecting Systemic T Cell Responses after Stereotactic Ablative Radiotherapy in NSCLC by Single-Cell RNA and T Cell Receptor Sequencing. Int J Radiat Oncol Biol Phys 2023; 117:e246. [PMID: 37784964 DOI: 10.1016/j.ijrobp.2023.06.1182] [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) There is accumulating evidence that stereotactic ablative radiotherapy (SABR) modulates immune responses to cancer; combining SABR and immunotherapy could promote the abscopal effect, but the precise effects of SABR on patients' systemic T cells is unclear. Here, we investigated SABR-induced systemic T cell response in early-stage non-small cell lung cancer (NSCLC) by single-cell RNA and T cell receptor sequencing. MATERIALS/METHODS We performed single-cell RNA and T cell receptor sequencing on 29,439 T cells from four pairs of peripheral blood before and after SABR in early-stage NSCLC patients. Cell clustering and dimensionality reduction, SingleR, feature genes score, and TCR profiling analyses were used to investigate the heterogeneity of T cells and their changes following SABR. RESULTS We identified fourteen T cell subtypes using unsupervised graph-based clustering of uniform manifold approximation and projection. By comparing the gene set scores of CD8_TE and CD8_EM pre- and post-SABR, we found both cytotoxic and inhibitory scores were significantly elevated in CD8_TE (both P < 0.001), while cytotoxic score was significantly increased in CD8_EM (P < 0.001) after SABR. We also found that CD4_TE showed increased cytotoxic scores and decreased Treg scores (P < 0.001 and < 0.05, respectively), while Treg cells showed decreased inhibitory and Treg scores (P < 0.001 and <0.01, respectively) after SABR. The proportion of large TCR clones was higher after SABR, which was accompanied by a decrease in proportion of single clones. When we compared the transcriptomes of CD8_TE cells between the single, small and large clones post-SABR, we found high expression of GZMB and KLRC3 in cells with large clones, and GZMK, IL7R, and SELL in small and single clones. This suggested that T cells after SABR with large clones may have higher cytotoxicity than those with small and single clones. CONCLUSION Our study identified systemic T cell activation after SABR at single-cell resolution, providing unprecedented insight into the immune-modulatory role of SABR in early-stage NSCLC.
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Affiliation(s)
- C Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - W Zou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - R Huang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - J Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - B Sun
- Department of Radiation Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
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Huang R, Geng H, Zhu L, Yan J, Li C, Li Y. CT radiomics can predict disease progression within 6 months after chimeric antigen receptor-modified T-cell therapy in relapsed/refractory B-cell non-Hodgkin's lymphoma patients. Clin Radiol 2023; 78:e707-e717. [PMID: 37407367 DOI: 10.1016/j.crad.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 02/17/2023] [Revised: 05/05/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
AIM To predict progression within 6 months after chimeric antigen receptor-modified (CAR) T-cell therapy for relapsed/refractory (R/R) B-cell non-Hodgkin's lymphoma (B-NHL) patients by radiomic indexes derived from contrast-enhanced computed tomography (CECT) examinations. MATERIALS AND METHODS Seventy R/R B-NHL patients who underwent CECT before treatment with CAR T-cells were examined retrospectively. In total, 297 volumes of interest for lesions were segmented from CECT images. Patients without and with disease progression were assigned to groups 1 and 2, respectively. Radiomic and combined predictive models were constructed by three machine-learning algorithms using features from the training set, respectively. Furthermore, predictive models were constructed based on multi-lesion-based and largest-lesion-based radiomic features, respectively. RESULTS In the test set, no marked differences were observed between the areas under the curves (AUCs) of the combined and radiomic models for all three machine-learning algorithms (all p>0.05). Differences in machine-learning algorithms did not significantly affect the predictive performances of the models. Radiomics and combined models constructed with multi-lesion-based radiomic features showed better predictive performances than those applying largest-lesion-based radiomic features (all p<0.05 for comparisons between combined models). CONCLUSION CECT-based radiomic features may be applied to predict disease progression in R/R B-NHL patients within 6 months after CAR T-cell treatment, and radiomic features from multiple lesions may have better predictive efficacy. Different machine-learning algorithms may not show significant differences in prediction performance.
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Affiliation(s)
- R Huang
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China
| | - H Geng
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China
| | - L Zhu
- Department of Ultrasound, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province, 215000, PR China
| | - J Yan
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China
| | - C Li
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China; National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China
| | - Y Li
- Department of Radiology, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China; National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu province 215000, PR China; Institute of Medical Imaging, Soochow University, Suzhou City, Jiangsu province 215000, PR China.
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Wang J, He Q, Li ZR, Huang N, Huang R, Wang JY, Zhou Q, Wang XH, Han F. The Lyman Normal Tissue Complication Probability Model and Risk Prediction for Temporal Lobe Injury after Re-Irradiation in Patients with Recurrent Nasopharyngeal Carcinoma. Int J Radiat Oncol Biol Phys 2023; 117:e587. [PMID: 37785777 DOI: 10.1016/j.ijrobp.2023.06.1932] [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) The risk of temporal lobe injury (TLI) in recurrent nasopharyngeal carcinoma (rNPC) patients with intensity-modulated radiation therapy (IMRT) is high. We aimed to construct the normal tissue complication probability (NTCP) model for TLI of rNPC and establish a risk predictive model. MATERIALS/METHODS We retrospectively analyzed 103 patients with rNPC who had received two courses of IMRT in our institution. The 206 temporal lobes (TLs) of these patients were randomly divided into a training (n = 144) and validation group (n = 62). We determined the mean value of the following parameters to construct the Lyman NTCP model: TD50(1) (the dose with a 50% probability of complications to an organ when all volumes are irradiated), m [steepness of the dose-response at TD50(1)], and n (the parameter related to volume effect). The most predictive dosimetric parameter and clinical variables were integrated in Cox proportional hazards models. A nomogram was developed for predicting risk of TLs. RESULTS The parameters of the fitted NTCP model were TD50(1) = 107.84 Gy (95% confidence interval (CI), [97.15, 118.54]), m = 0.16 (95% CI, [0.14, 0.19]), and n = 0.04 (95% CI, [0.01, 0.06]). The cumulative dose delivered to 0.1 cm3 of temporal lobe volume (D0.1cc-c) was the most predictive dosimetric parameter for TLI. The Kaplan-Meier curves showed a significant difference in 2-year TLI-free survival among different risk groups according to the total score of nomograms. CONCLUSION The TD50(1) of TLI in patients with rNPC is 107.84 Gy in Lyman NTCP model. The nomogram model can accurately predict the risk of TLI for individual.
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Affiliation(s)
- J Wang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Q He
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Z R Li
- Manteia Technologies Co., Ltd, Xiamen, Fujian, China
| | - N Huang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - R Huang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - J Y Wang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Q Zhou
- Manteia Technologies Co., Ltd, Xiamen, Fujian, China
| | - X H Wang
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - F Han
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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15
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Zou W, Huang R, Yue J, Liu C. Positive TIGIT and VISTA Expression Predict Worse Prognosis in Cervical Cancer Patients Treated with (Chemo)Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:S131. [PMID: 37784337 DOI: 10.1016/j.ijrobp.2023.06.481] [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) Immune checkpoint inhibitors combined with (chemo)radiotherapy could be an attractive treatment strategy for patients with cervical cancer (CC), but the expression of some immune checkpoint proteins in cervical cancer and their impact on patient survival remains largely unknown. Here, we investigated the predictive value of T cell immunoreceptor with Ig and ITIM domain (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), and lymphocyte-activation gene-3 (LAG-3) expression in pathological tissues of CC patients treated with (chemo)radiotherapy. MATERIALS/METHODS We enrolled 175 CC patients who received (chemo)radiotherapy and collected their pre-treatment tumor tissue sections for the immunohistochemical stain of TIGIT, VISTA, and LAG-3. The Kaplan-Meier method was used to calculate progression-free survival (PFS) and overall survival (OS) after (chemo)radiotherapy. Univariate and multivariate COX proportional hazards regression models were employed to analyze potential risk factors for patient survival. RESULTS Kaplan-Meier survival analyses showed that the PFS and OS of patients with positive expression of TIGIT and VISTA were significantly shorter than those patients with negative expression of the proteins (all p<0.05). However, we did not reach the same conclusion in the analysis of LAG-3 (both p>0.05). Univariate COX regression analysis showed that the positive expression of TIGIT and VISTA are related to poor PFS and OS (both HR>1.0 and p<0.05). Multivariate COX regression analysis showed that TIGIT positive and VISTA positive patients have shorter PFS and OS (both HR>1.0 and p<0.05). There is no significant correlation between LAG-3 expression and PFS or OS in these CC patients treated with (chemo)radiotherapy. CONCLUSION We revealed that positive TIGIT and VISTA expression could predict worse prognosis in cervical cancer patients treated with (chemo)radiotherapy, which may help to refine the treatment strategies of combining immune checkpoint inhibitors and radiotherapy.
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Affiliation(s)
- W Zou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - R Huang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - J Yue
- Shandong Cancer Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - C Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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Huang R, Miao J, Zhang L, Peng Y, Huang S, Han F, Wang L, Deng XW, Zhao C. Radiation-Induced Nasopharyngeal Necrosis in Locally-Recurrent Nasopharyngeal Carcinoma Patients after Re-Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e589-e590. [PMID: 37785783 DOI: 10.1016/j.ijrobp.2023.06.1938] [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) Re-radiotherapy (re-RT) is the main treatment for locally recurrent nasopharyngeal carcinoma (lrNPC) patients, and commonly led to radiation-induced nasopharyngeal (NP) necrosis, which was lethal but rare study has focused on it. The aim of this study was to evaluate the cause and impact of radiation-induced NP necrosis in lrNPC patients who received re-RT. MATERIALS/METHODS Totally 252 lrNPC patients who received re-RT between January 2013 and December 2020 were retrospectively collected. The inclusion criteria were as follows: (1) no NP necrosis before re-RT; (2) complete medical records, including treatment, clinical and dosimetric information; (3) conventional fractionated radiotherapy. All patients received intensity-modulated radiotherapy ± chemotherapy. Radiation-induced NP necrosis was diagnosed by magnetic resonance imaging and/or electronic nasopharyngoscopy. Dosimetric factors of the planning target volume of primary tumor (PTVp) were extracted from the dose-volume histogram (DVH), which was rescaled to an equivalent dose of 2 Gy per fraction (EQD 2 Gy) using a linear quadratic model. Logistic regression was used to identify the independent prognostic factors for generating the nomogram. RESULTS With a median follow-up of 44.63 months (inter-quartile range [IQR], 27.70 - 69.20 months), 47.6% of patients (120/252) occurred radiation-induced NP necrosis, which mostly happened within 1 year post re-RT (median [IQR], 5.83 [3.37 - 11.57] months). The 3-year overall survival was 83.0% vs 39.7% (P<0.001) in lrNPC patients with or without radiation-induced NP necrosis. Except for the fractionated dose, other dosimetric factors of PTVp were not significantly different between two groups, including D98 (dose to 98% of PTVp), D50, D2 and homogeneity index (Table 1). Furthermore, multivariate analysis showed that continuous variable age (HR [95% CI]: 1.04 [1.02 - 1.07], P = 0.003) and tumor volume (HR [95% CI]: 1.02 [1.01 - 1.03], P<0.001), and fractionated dose > 2.22 Gy (HR [95% CI]: 2.36 [1.32 - 4.21], P = 0.004) were independent factors in predicting radiation-induced NP necrosis, which yielded a C-index of 0.742 (95% CI, 0.682 - 0.803) for OS in the nomogram. CONCLUSION The incidence of radiation-induced NP necrosis was high in lrNPC patients who received re-RT. Patients with older age, larger tumor volume or receiving fractionated dose over 2.22 Gy were more easily to suffer NP necrosis, which need to explore novel treatment strategies to improve patients' survivals.
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Affiliation(s)
- R Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - J Miao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - L Zhang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - S Huang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - F Han
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - L Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - X W Deng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - C Zhao
- Sun Yat-sen University Cancer Center, Guangzhou, China
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Wang F, Zou W, Huang R, Yue J, Liu C. Single-Cell and Bulk RNA Sequencing Reveal the Potential Immune Suppressive Role of PODXL in Cervical Cancer Treated with Radiochemotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e265-e266. [PMID: 37785009 DOI: 10.1016/j.ijrobp.2023.06.1225] [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) Our previous study identified the tumor-promoting role of PODXL in cervical cancer (CC), but it remains largely unknown for its impact on immune response and survival in CC patients received radiochemotherapy. Here, we investigated this issue using single-cell RNA-sequencing (scRNA-seq) and Bulk RNA-sequencing data. MATERIALS/METHODS We performed scRNA-seq on 29,453 cells in five tumor tissues from CC patients, employed 141 bulk RNA-seq data from TCGA, and included a cohort of 168 CC patients treated with radiochemotherapy for immunostaining of PODXL protein. Gene Ontology (GO) and Gene set enrichment analysis (GSEA) analysis were performed for functional annotation. Immune cell infiltration analysis by single sample GSEA. Immunostaining validation was performed on tumor tissues from 168 CC patients treated with radiochemotherapy. RESULTS Single-cell analyses revealed the specific expression of PODXL on endothelial cells and divided these cells into PODXLhigh and PODXLlow cells. GO and GSEA analyses showed that PODXLhigh cells had lower levels of leukocyte cell-cell adhesion, immunoglobulin mediated immune response and cytokine production than PODXLlow cells. We further found that PODXLhigh cells could reduce macrophage recruitment through PODXL-ACKR1 and ultimately shape the immune suppressive tumor microenvironment. Analyses of bulk RNA-seq data showed that PODXL expression was negatively correlated with survival of CC patients; moreover, compared to the PODXLlow group, the infiltration of CD8+ T cells, B cells, Th1, and follicular helper T cells were lower in the PODXLhigh group (all P values < 0.05). Furthermore, in the immunostaining validation cohort, multivariate Cox analysis showed that PODXL expression was negatively correlated with the survival for CC patients who underwent radiochemotherapy (all P values < 0.05). CONCLUSION We revealed the potential immune suppressive role of PODXL in CC patients treated with radiochemotherapy, which may provide a candidate therapy target combined with radiochemotherapy.
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Affiliation(s)
- F Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - W Zou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - R Huang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - J Yue
- Shandong Cancer Hospital affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - C Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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Shin HK, Huang R, Chen M. In silico modeling-based new alternative methods to predict drug and herb-induced liver injury: A review. Food Chem Toxicol 2023; 179:113948. [PMID: 37460037 PMCID: PMC10640386 DOI: 10.1016/j.fct.2023.113948] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/19/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
New approach methods (NAMs) have been developed to predict a wide range of toxicities through innovative technologies. Liver injury is one of the most extensively studied endpoints due to its severity and frequency, occurring among populations that consume drugs or dietary supplements. In this review, we focus on recent developments of in silico modeling for liver injury prediction using deep learning and in vitro data based on adverse outcome pathways (AOPs). Despite these models being mainly developed using datasets generated from drug-like molecules, they were also applied to the prediction of hepatotoxicity caused by herbal products. As deep learning has achieved great success in many different fields, advanced machine learning algorithms have been actively applied to improve the accuracy of in silico models. Additionally, the development of liver AOPs, combined with big data in toxicology, has been valuable in developing in silico models with enhanced predictive performance and interpretability. Specifically, one approach involves developing structure-based models for predicting molecular initiating events of liver AOPs, while others use in vitro data with structure information as model inputs for making predictions. Even though liver injury remains a difficult endpoint to predict, advancements in machine learning algorithms and the expansion of in vitro databases with relevant biological knowledge have made a huge impact on improving in silico modeling for drug-induced liver injury prediction.
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Affiliation(s)
- Hyun Kil Shin
- Department of Predictive Toxicology, Korea Institute of Toxicology (KIT), 34114, Daejeon, Republic of Korea
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, 20850, USA.
| | - Minjun Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR, 72079, USA.
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Huang R, Rao HY. [Fatty liver disease's renaming impacts on drug clinical trials]. Zhonghua Gan Zang Bing Za Zhi 2023; 31:793-797. [PMID: 37723059 DOI: 10.3760/cma.j.cn501113-20230801-00026] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Fatty liver disease has undergone a major name change, with metabolic dysfunction-associated fatty liver disease (MASLD) replacing nonalcoholic fatty liver disease. The definition of MASLD no longer requires the exclusion of other co-existing liver diseases but instead associates hepatic steatosis with overweight/obesity, type 2 diabetes mellitus, or metabolic disorders and clearly defines the amount of alcohol consumption. The new definition also introduces the concepts of metabolic-related alcoholic liver disease and cryptogenic fatty liver disease. These changes will bring new challenges and opportunities for the design of clinical trials of fatty liver disease drugs and the selection of target populations.
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Affiliation(s)
- R Huang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on Non-Alcoholic Fatty Liver Disease (NAFLD) Diagnosis, Beijing 100044, China
| | - H Y Rao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing International Cooperation Base for Science and Technology on Non-Alcoholic Fatty Liver Disease (NAFLD) Diagnosis, Beijing 100044, China
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20
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Ngan DK, Xia M, Simeonov A, Huang R. In vitro profiling of pesticides within the Tox21 10K compound library for bioactivity and potential toxicity. Toxicol Appl Pharmacol 2023; 473:116600. [PMID: 37321325 PMCID: PMC10330904 DOI: 10.1016/j.taap.2023.116600] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/30/2023] [Accepted: 06/10/2023] [Indexed: 06/17/2023]
Abstract
Pesticides include a diverse class of toxic chemicals, often having numerous modes of actions when used in agriculture against targeted organisms to control insect infestation, halt unwanted vegetation, and prevent the spread of disease. In this study, the in vitro assay activity of pesticides within the Tox21 10K compound library were examined. The assays in which pesticides showed significantly more activities than non-pesticide chemicals revealed potential targets and mechanisms of action for pesticides. Furthermore, pesticides that showed promiscuous activity against many targets and cytotoxicity were identified, which warrant further toxicological evaluation. Several pesticides were shown to require metabolic activation, demonstrating the importance of introducing metabolic capacity to in vitro assays. Overall, the activity profiles of pesticides highlighted in this study can contribute to the knowledge gaps surrounding pesticide mechanisms and to the better understanding of the on- and off-target organismal effects of pesticides.
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Affiliation(s)
- Deborah K Ngan
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA.
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21
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Wang YX, Luo JM, Huang R, Xiao Y. [Continuous positive airway pressure therapy affects the recurrence of atrial fibrillation in patients with obstructive sleep apnea: a systematic review and meta-analysis]. Zhonghua Jie He He Hu Xi Za Zhi 2023; 46:751-759. [PMID: 37536985 DOI: 10.3760/cma.j.cn112147-20230213-00064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Objective: A higher incidence of atrial fibrillation is associated with obstructive sleep apnea. The effects of continuous positive airway pressure on atrial fibrillation have been studied in observational studies and randomized controlled trials. We therefore conducted this meta-analysis to assess the effect of continuous positive airway pressure on the recurrence of atrial fibrillation after radiofrequency ablation. Methods: A comprehensive search was conducted in Pubmed, Embase, Cochrane, Web of Science, Wanfang Data and CNKI databases from inception to October 2022. We included cohort studies and randomized controlled trials containing atrial fibrillation situation after catheter ablation with and without continuous positive airway pressure therapy. The random effects model was used to assess odds ratios (OR) and confidence intervals (CI). I2 was used to assess the heterogeneity. Results: Eight studies with a total of 1 395 patients with obstructive sleep apnea met the inclusion criteria. Continuous positive airway pressure therapy decreased atrial fibrillation recurrence by 61% (OR=0.392, 95%CI: 0.267-0.576, I2=37.6%). Subgroup analysis showed that the protective effect was more significant in groups with more hypertension patients (OR=0.272 vs. 0.550, 95%CI: 0.165-0.449 vs. 0.329-0.922). Conclusions: Continuous positive airway pressure therapy reduces the recurrence rate of atrial fibrillation. Patients with hypertension are more likely to benefit from it.
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Affiliation(s)
- Y X Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - J M Luo
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - R Huang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Y Xiao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
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22
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Yan W, Zhong Y, Hu X, Xu T, Zhang Y, Kales S, Qu Y, Talley DC, Baljinnyam B, LeClair CA, Simeonov A, Polster BM, Huang R, Ye Y, Rai G, Henderson MJ, Tao D, Fang S. Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes. Nat Commun 2023; 14:4798. [PMID: 37558718 PMCID: PMC10412574 DOI: 10.1038/s41467-023-40537-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/11/2023] Open
Abstract
UBA1 is the primary E1 ubiquitin-activating enzyme responsible for generation of activated ubiquitin required for ubiquitination, a process that regulates stability and function of numerous proteins. Decreased or insufficient ubiquitination can cause or drive aging and many diseases. Therefore, a small-molecule enhancing UBA1 activity could have broad therapeutic potential. Here we report that auranofin, a drug approved for the treatment of rheumatoid arthritis, is a potent UBA1 activity enhancer. Auranofin binds to the UBA1's ubiquitin fold domain and conjugates to Cys1039 residue. The binding enhances UBA1 interactions with at least 20 different E2 ubiquitin-conjugating enzymes, facilitating ubiquitin charging to E2 and increasing the activities of seven representative E3s in vitro. Auranofin promotes ubiquitination and degradation of misfolded ER proteins during ER-associated degradation in cells at low nanomolar concentrations. It also facilitates outer mitochondrial membrane-associated degradation. These findings suggest that auranofin can serve as a much-needed tool for UBA1 research and therapeutic exploration.
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Affiliation(s)
- Wenjing Yan
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yongwang Zhong
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Tuan Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yinghua Zhang
- Center for Innovative Biomedical Resources, Biosensor Core, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Stephen Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yanyan Qu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Daniel C Talley
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Oncology, UM Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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23
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Borghese MM, Huang R, MacPherson S, Gaudreau E, Gagné S, Ashley-Martin J, Fisher M, Booij L, Bouchard MF, Arbuckle TE. A descriptive analysis of first trimester urinary concentrations of 14 bisphenol analogues in the MIREC Canadian pregnancy cohort. Int J Hyg Environ Health 2023; 253:114225. [PMID: 37542835 DOI: 10.1016/j.ijheh.2023.114225] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND Concern over the health effects of BPA, particularly for the developing fetus, has led to an increasing use of bisphenol analogues in industrial and consumer products, which may be as hormonally active as BPA. Biomonitoring data for many bisphenol analogues, especially in pregnant populations, are limited. METHODS We measured concentrations of 14 bisphenol analogues in 1st trimester urine samples (n = 1851) from the Maternal-Infant Research on Environmental Chemicals (MIREC) Canadian pregnancy cohort (2008-2011). We examined patterns of exposure according to sociodemographic and sampling characteristics as well as occupation and frequency of consumption of canned fish within the previous 3 months. RESULTS BPA was detected in 89% of participants with a specific gravity standardized geometric mean concentration of 0.990 μg/L. Biphenol 4,4' (BP 4,4'), 4,4'-dihydroxydiphenyl ether (DHDPE), and bisphenol E (BPE) were detected in >97% of participants. Bisphenol F (BPF) and bisphenol S (BPS) were detected in >60% of participants. Specific gravity standardized geometric mean concentrations of these 5 compounds ranged from 0.024 to 0.564 μg/L. Nine bisphenol analogues were detected in <9% of participants. Concentrations of BP 4,4', DHDPE, and BPE were higher in younger women and those with higher pre-pregnancy BMI, lower household income, lower education, and among smokers. We found a similar pattern of differences in BPF for age, education, and smoking status while BPS similarly differed across categories of pre-pregnancy BMI. Participants who were unemployed or working in the service industry had higher molar sum of 7 bisphenol analogues than those working in healthcare, education, or an office setting. Canned fish consumption was not related to bisphenol analogue concentrations. CONCLUSION BP 4,4', DHDPE, BPE, BPF, and BPS were highly detected in 1st trimester urine samples in this large pan-Canadian pregnancy cohort. This suggests widespread exposure to these analogues around 2008-2011 and warrants further investigation into associations with health outcomes.
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Affiliation(s)
- M M Borghese
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | - R Huang
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | - S MacPherson
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | - E Gaudreau
- Centre du Toxicologie du Québec (CTQ), Institut national de santé publique du Québec (INSPQ), Quebec, Canada.
| | - S Gagné
- Centre du Toxicologie du Québec (CTQ), Institut national de santé publique du Québec (INSPQ), Quebec, Canada.
| | - J Ashley-Martin
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | - M Fisher
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | - L Booij
- Department of Psychiatry, McGill University, Montréal, Québec, Canada; Sainte-Justine University Hospital Research Center, Montréal, Québec, Canada; Department of Environmental and Occupational Health, School of Public Health of the University of Montreal, Montréal, Québec, Canada.
| | - M F Bouchard
- Department of Environmental and Occupational Health, School of Public Health of the University of Montreal, Montréal, Québec, Canada.
| | - T E Arbuckle
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
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Liu F, Patt A, Chen C, Huang R, Xu Y, Mathé EA, Zhu Q. Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing. bioRxiv 2023:2023.07.21.550045. [PMID: 37546930 PMCID: PMC10401966 DOI: 10.1101/2023.07.21.550045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Drug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
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Affiliation(s)
- Fang Liu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Andrew Patt
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Chloe Chen
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Yanji Xu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Ewy A Mathé
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
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Yasgar A, Bougie D, Eastman RT, Huang R, Itkin M, Kouznetsova J, Lynch C, McKnight C, Miller M, Ngan DK, Peryea T, Shah P, Shinn P, Xia M, Xu X, Zakharov AV, Simeonov A. Quantitative Bioactivity Signatures of Dietary Supplements and Natural Products. ACS Pharmacol Transl Sci 2023; 6:683-701. [PMID: 37200814 PMCID: PMC10186358 DOI: 10.1021/acsptsci.2c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Indexed: 05/20/2023]
Abstract
Dietary supplements and natural products are often marketed as safe and effective alternatives to conventional drugs, but their safety and efficacy are not well regulated. To address the lack of scientific data in these areas, we assembled a collection of Dietary Supplements and Natural Products (DSNP), as well as Traditional Chinese Medicinal (TCM) plant extracts. These collections were then profiled in a series of in vitro high-throughput screening assays, including a liver cytochrome p450 enzyme panel, CAR/PXR signaling pathways, and P-glycoprotein (P-gp) transporter assay activities. This pipeline facilitated the interrogation of natural product-drug interaction (NaPDI) through prominent metabolizing pathways. In addition, we compared the activity profiles of the DSNP/TCM substances with those of an approved drug collection (the NCATS Pharmaceutical Collection or NPC). Many of the approved drugs have well-annotated mechanisms of action (MOAs), while the MOAs for most of the DSNP and TCM samples remain unknown. Based on the premise that compounds with similar activity profiles tend to share similar targets or MOA, we clustered the library activity profiles to identify overlap with the NPC to predict the MOAs of the DSNP/TCM substances. Our results suggest that many of these substances may have significant bioactivity and potential toxicity, and they provide a starting point for further research on their clinical relevance.
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Affiliation(s)
- Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Danielle Bougie
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Misha Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Caitlin Lynch
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Crystal McKnight
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Mitch Miller
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Deborah K Ngan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Tyler Peryea
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
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26
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Patlewicz G, Paul-Friedman K, Houck K, Zhang L, Huang R, Xia M, Brown J, Simmons SO. Evaluating the utility of a high throughput thiol-containing fluorescent probe to screen for reactivity: A case study with the Tox21 library. Comput Toxicol 2023; 26:10.1016/j.comtox.2023.100271. [PMID: 37388277 PMCID: PMC10304587 DOI: 10.1016/j.comtox.2023.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
High-throughput screening (HTS) assays for bioactivity in the Tox21 program aim to evaluate an array of different biological targets and pathways, but a significant barrier to interpretation of these data is the lack of high-throughput screening (HTS) assays intended to identify non-specific reactive chemicals. This is an important aspect for prioritising chemicals to test in specific assays, identifying promiscuous chemicals based on their reactivity, as well as addressing hazards such as skin sensitisation which are not necessarily initiated by a receptor-mediated effect but act through a non-specific mechanism. Herein, a fluorescence-based HTS assay that allows the identification of thiol-reactive compounds was used to screen 7,872 unique chemicals in the Tox21 10K chemical library. Active chemicals were compared with profiling outcomes using structural alerts encoding electrophilic information. Random Forest classification models based on chemical fingerprints were developed to predict assay outcomes and evaluated through 10-fold stratified cross validation (CV). The mean CV Balanced Accuracy of the validation set was 0.648. The model developed shows promise as a tool to screen untested chemicals for their potential electrophilic reactivity based solely on chemical structural features.
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Affiliation(s)
- Grace Patlewicz
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Katie Paul-Friedman
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Keith Houck
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Li Zhang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Brown
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Steven O. Simmons
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
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Xu T, Li S, Li AJ, Zhao J, Sakamuru S, Huang W, Xia M, Huang R. Identification of Potent and Selective Acetylcholinesterase/Butyrylcholinesterase Inhibitors by Virtual Screening. J Chem Inf Model 2023; 63:2321-2330. [PMID: 37011147 PMCID: PMC10688023 DOI: 10.1021/acs.jcim.3c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 04/05/2023]
Abstract
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) play important roles in human neurodegenerative disorders such as Alzheimer's disease. In this study, machine learning methods were applied to develop quantitative structure-activity relationship models for the prediction of novel AChE and BChE inhibitors based on data from quantitative high-throughput screening assays. The models were used to virtually screen an in-house collection of ∼360K compounds. The optimal models achieved good performance with area under the receiver operating characteristic curve values ranging from 0.83 ± 0.03 to 0.87 ± 0.01 for the prediction of AChE/BChE inhibition activity and selectivity. Experimental validation showed that the best-performing models increased the assay hit rate by several folds. We identified 88 novel AChE and 126 novel BChE inhibitors, 25% (AChE) and 53% (BChE) of which showed potent inhibitory effects (IC50 < 5 μM). In addition, structure-activity relationship analysis of the BChE inhibitors revealed scaffolds for chemistry design and optimization. In conclusion, machine learning models were shown to efficiently identify potent and selective inhibitors against AChE and BChE and novel structural series for further design and development of potential therapeutics against neurodegenerative disorders.
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Affiliation(s)
- Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Shuaizhang Li
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Andrew J. Li
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Jinghua Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wenwei Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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28
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Li Z, Liu J, Dong F, Chang N, Huang R, Xia M, Patterson TA, Hong H. Three-Dimensional Structural Insights Have Revealed the Distinct Binding Interactions of Agonists, Partial Agonists, and Antagonists with the µ Opioid Receptor. Int J Mol Sci 2023; 24:ijms24087042. [PMID: 37108204 PMCID: PMC10138646 DOI: 10.3390/ijms24087042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/14/2023] [Revised: 04/09/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
The United States is experiencing the most profound and devastating opioid crisis in history, with the number of deaths involving opioids, including prescription and illegal opioids, continuing to climb over the past two decades. This severe public health issue is difficult to combat as opioids remain a crucial treatment for pain, and at the same time, they are also highly addictive. Opioids act on the opioid receptor, which in turn activates its downstream signaling pathway that eventually leads to an analgesic effect. Among the four types of opioid receptors, the µ subtype is primarily responsible for the analgesic cascade. This review describes available 3D structures of the µ opioid receptor in the protein data bank and provides structural insights for the binding of agonists and antagonists to the receptor. Comparative analysis on the atomic details of the binding site in these structures was conducted and distinct binding interactions for agonists, partial agonists, and antagonists were observed. The findings in this article deepen our understanding of the ligand binding activity and shed some light on the development of novel opioid analgesics which may improve the risk benefit balance of existing opioids.
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Affiliation(s)
- Zoe Li
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Jie Liu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Fan Dong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Nancy Chang
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tucker A Patterson
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
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29
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Mizrahi I, Shah P, Huang R, Nagamine T, Gozun M, Lee D, Shimabuku L, Khan Z, Lum C, Brodsky M. Echocardiographic Findings in Patients with Methamphetamine Cardiomyopathy. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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30
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Romero P, Huang R, Jiménez E, Palma-Hidalgo JM, Ungerfeld EM, Popova M, Morgavi DP, Belanche A, Yáñez-Ruiz DR. Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 2. Dairy goats. Animal 2023; 17:100789. [PMID: 37087998 DOI: 10.1016/j.animal.2023.100789] [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] [Received: 05/11/2022] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Most mitigation strategies to reduce enteric methane (CH4) production in the rumen induce an excess of rumen dihydrogen (H2) that is expelled and consequently not redirected to the synthesis of metabolites that can be utilised by the ruminant. We hypothesised that phenolic compounds can be potential H2 acceptors when added to the diet, as they can be degraded to compounds that may be beneficial for the animal, using part of the H2 available when ruminal methanogenesis is inhibited. We performed four in vitro incubation experiments using rumen inoculum from Murciano-Granadina adult goats: Experiment 1 examined the inhibitory potential of Asparagopsis taxiformis (AT) at different concentrations (0, 1, 2, 3, 4 and 5% of the substrate on a DM basis) in 24 h incubations; Experiment 2 investigated the effect of a wide range of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, gallic acid and formic acid) at different doses (0, 2, 4, and 6 mM) on rumen fermentation for 24 h; Experiment 3 evaluated the combined effect of each phenolic compound at 6 mM with AT at 2% DM in sequential batch cultures for 5 days; and Experiment 4 examined the dose-response effect of phloroglucinol at different concentrations (0, 6, 16, 26 and 36 mM) combined with AT in sequential batch cultures for 5 days. Results from Experiment 1 confirmed that AT at 2% DM substantially inhibited CH4 production while significantly increasing H2 accumulation and decreasing the acetate:propionate ratio. Results from Experiment 2 showed that phenolic compounds did not negatively affect rumen fermentation at any dose. In Experiment 3, each phenolic compound at 6 mM combined with AT at 2% DM inhibited CH4 production. Phloroglucinol numerically decreased H2 accumulation and significantly increased total gas production (TGP), volatile fatty acid (VFA) production and the acetate:propionate ratio. In Experiment 4, phloroglucinol at increasing doses supplemented with AT at 2% DM significantly decreased H2 accumulation and the abundances of archaea, protozoa and fungi abundances, and increased TGP, total VFA production and the acetate:propionate ratio in a dose-dependent way. In conclusion, combined treatment with AT and phloroglucinol was successful to mitigate CH4 production while preventing the accumulation of H2, leading to an increase in acetate and total VFA production and therefore an improvement in rumen fermentation in goats.
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Affiliation(s)
- P Romero
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - R Huang
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - E Jiménez
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - J M Palma-Hidalgo
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain
| | - E M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco 4880000, Chile
| | - M Popova
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - D P Morgavi
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - A Belanche
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain; Departamento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, Miguel Servet 177, 50013 Zaragoza, Spain
| | - D R Yáñez-Ruiz
- Estación Experimental del Zaidín (CSIC), Profesor Albareda, 1, 18008 Granada, Spain.
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31
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Tapan U, Raskina K, Huang R, Schrock A, Sands J, Oxnard G, Tukachinsky H. PPD02.01 Comprehensive Genomic Profiling (CGP) for Diagnostic Clarity in Pulmonary Large-Cell Neuroendocrine Carcinoma (LCNEC). J Thorac Oncol 2023. [DOI: 10.1016/j.jtho.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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32
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Huang R, Romero P, Belanche A, Ungerfeld E, Yanez-Ruiz D, Morgavi D, Popova M. Evaluating the effect of phenolic compounds as hydrogen acceptors when ruminal methanogenesis is inhibited in vitro – Part 1. Dairy cows. Animal 2023; 17:100788. [PMID: 37087996 DOI: 10.1016/j.animal.2023.100788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Some antimethanogenic feed additives for ruminants promote rumen dihydrogen (H2) accumulation potentially affecting the optimal fermentation of diets. We hypothesised that combining an H2 acceptor with a methanogenesis inhibitor can decrease rumen H2 build-up and improve the production of metabolites that can be useful for the host ruminant. We performed three in vitro incubation experiments using rumen fluid from lactating Holstein cows: Experiment 1 examined the effect of phenolic compounds (phenol, catechol, resorcinol, hydroquinone, pyrogallol, phloroglucinol, and gallic acid) at 0, 2, 4, and 6 mM on ruminal fermentation for 24 h; Experiment 2 examined the combined effect of each phenolic compound from Experiment 1 at 6 mM with two different methanogenesis inhibitors (Asparagopsis taxiformis or 2-bromoethanesulfonate (BES)) for 24 h incubation; Experiment 3 examined the effect of a selected phenolic compound, phloroglucinol, with or without BES over a longer term using sequential incubations for seven days. Results from Experiment 1 showed that phenolic compounds, independently of the dose, did not negatively affect rumen fermentation, whereas results from Experiment 2 showed that phenolic compounds did not decrease H2 accumulation or modify CH4 production when methanogenesis was decreased by up to 75% by inhibitors. In Experiment 3, after three sequential incubations, phloroglucinol combined with BES decreased H2 accumulation by 72% and further inhibited CH4 production, compared to BES alone. Interestingly, supplementation with phloroglucinol (alone or in combination with the CH4 inhibitor) decreased CH4 production by 99% and the abundance of methanogenic archaea, with just a nominal increase in H2 accumulation. Supplementation of phloroglucinol also increased total volatile fatty acid (VFA), acetate, butyrate, and total gas production, and decreased ammonia concentration. This study indicates that some phenolic compounds, particularly phloroglucinol, which are naturally found in plants, could improve VFA production, decrease H2 accumulation and synergistically decrease CH4 production in the presence of antimethanogenic compounds.
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Dranchak PK, Oliphant E, Queme B, Lamy L, Wang Y, Huang R, Xia M, Tao D, Inglese J. In vivo quantitative high-throughput screening for drug discovery and comparative toxicology. Dis Model Mech 2023; 16:287027. [PMID: 36786055 PMCID: PMC10067442 DOI: 10.1242/dmm.049863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Quantitative high-throughput screening (qHTS) pharmacologically evaluates chemical libraries for therapeutic uses, toxicological risk and, increasingly, for academic probe discovery. Phenotypic high-throughput screening assays interrogate molecular pathways, often relying on cell culture systems, historically less focused on multicellular organisms. Caenorhabditis elegans has served as a eukaryotic model organism for human biology by virtue of genetic conservation and experimental tractability. Here, a paradigm enabling C. elegans qHTS using 384-well microtiter plate laser-scanning cytometry is described, in which GFP-expressing organisms revealing phenotype-modifying structure-activity relationships guide subsequent life-stage and proteomic analyses, and Escherichia coli bacterial ghosts, a non-replicating nutrient source, allow compound exposures over two life cycles, mitigating bacterial overgrowth complications. We demonstrate the method with libraries of anti-infective agents, or substances of toxicological concern. Each was tested in seven-point titration to assess the feasibility of nematode-based in vivo qHTS, and examples of follow-up strategies were provided to study organism-based chemotype selectivity and subsequent network perturbations with a physiological impact. We anticipate that this qHTS approach will enable analysis of C. elegans orthologous phenotypes of human pathologies to facilitate drug library profiling for a range of therapeutic indications.
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Affiliation(s)
- Patricia K Dranchak
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Erin Oliphant
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Bryan Queme
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Laurence Lamy
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Yuhong Wang
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Ruili Huang
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Menghang Xia
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Dingyin Tao
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - James Inglese
- Department of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
- Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20817, USA
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Huang R, He WJ, Zhang PP, Wang DQ. [Exploring the treatment of sepsis-associated acute lung injury with Liangge Powder via ERK1/2 and PI3K/AKT pathways: based on network pharmacology and whole animal experimentation]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2023; 41:94-103. [PMID: 36882272 DOI: 10.3760/cma.j.cn121094-20220408-00188] [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] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Objective: To investigate the therapeutic effect and mechanism of Liangge Powder against sepsis-induced acute lung injury (ALI) . Methods: From April to December 2021, the key components of Liangge Powder and its targets against sepsis-induced ALI were analyzed by network pharmacology, and to enrich for relevant signaling pathways. A total of 90 male Sprague-Dawley rats were randomly assigned to sham-operated group, sepsis-induced ALI model group (model group), Liangge Powder low, medium and high dose group, ten rats in the sham-operated group and 20 rats in each of the remaining four groups. Sepsis-induced ALI model was established by cecal ligation and puncture. Sham-operated group: gavage with 2 ml saline and no surgical treatment. Model group: surgery was performed and 2 ml saline was gavaged. Liangge Powder low, medium and high dose groups: surgery and gavage of Liangge Powder 3.9, 7.8 and 15.6 g/kg, respectively. To measure the wet/dry mass ratio of rats lung tissue and evaluate the permeability of alveolar capillary barrier. Lung tissue were stained with hematoxylin and eosin for histomorphological analysis. The levels of tumor necrosis factor-alpha (TNF-α), interleukin (IL) -6 and IL-1β in bronchoalveolar lavage fluid (BALF) were measured by enzyme-linked immunosorbent assay. The relative protein expression levels of p-phosphatidylinositol 3-kinase (PI3K), p-protein kinase B (AKT), and p-ertracellular regulated protein kinases (ERK) were detected via Western blot analysis. Results: Network pharmacology analysis indicated that 177 active compounds of Liangge Powder were selected. A total of 88 potential targets of Liangge Powder on sepsis-induced ALI were identified. 354 GO terms of Liangge Powder on sepsis-induced ALI and 108 pathways were identified using GO and KEGG analysis. PI3K/AKT signaling pathway was recognized to play an important role for Liangge Powder against sepsis-induced ALI. Compared with the sham-operated group, the lung tissue wet/dry weight ratio of rats in the model group (6.35±0.95) was increased (P<0.001). HE staining showed the destruction of normal structure of lung tissue. The levels of IL-6 [ (392.36±66.83) pg/ml], IL-1β [ (137.11±26.83) pg/ml] and TNF-α [ (238.34±59.36) pg/ml] were increased in the BALF (P<0.001, =0.001, <0.001), and the expression levels of p-PI3K, p-AKT and p-ERK1/2 proteins (1.04±0.15, 0.51±0.04, 2.31±0.41) were increased in lung tissue (P=0.002, 0.003, 0.005). The lung histopathological changes were reduced in each dose group of Liangge Powder compared with the model group. Compared with the model group, the wet/dry weight ratio of lung tissue (4.29±1.26) was reduced in the Liangge Powder medium dose group (P=0.019). TNF-α level [ (147.85±39.05) pg/ml] was reduced (P=0.022), and the relative protein expression levels of p-PI3K (0.37±0.18) and p-ERK1/2 (1.36±0.07) were reduced (P=0.008, 0.017). The wet/dry weight ratio of lung tissue (4.16±0.66) was reduced in the high-dose group (P=0.003). Levels of IL-6, IL-1β and TNF-α[ (187.98±53.28) pg/ml, (92.45±25.39) pg/ml, (129.77±55.94) pg/ml] were reduced (P=0.001, 0.027, 0.018), and relative protein expression levels of p-PI3K, p-AKT and p-ERK1/2 (0.65±0.05, 0.31±0.08, 1.30±0.12) were reduced (P=0.013, 0.018, 0.015) . Conclusion: Liangge Powder has therapeutic effects in rats with sepsis-induced ALI, and the mechanism may be related to the inhibition of ERK1/2 and PI3K/AKT pathway activation in lung tissue.
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Affiliation(s)
- R Huang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - W J He
- Department of Integration of Traditional Chinese and Western Medicine, Tianjin First Central Hospital, the First Central Hospital Affiliated to Nankai University, Tianjin 300192, China
| | - P P Zhang
- Department of Integration of Traditional Chinese and Western Medicine, Tianjin First Central Hospital, the First Central Hospital Affiliated to Nankai University, Tianjin 300192, China
| | - D Q Wang
- Department of Integration of Traditional Chinese and Western Medicine, Tianjin First Central Hospital, the First Central Hospital Affiliated to Nankai University, Tianjin 300192, China
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35
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Xu T, Kabir M, Sakamuru S, Shah P, Padilha E, Ngan DK, Xia M, Xu X, Simeonov A, Huang R. Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates. J Chem Inf Model 2023; 63:846-855. [PMID: 36719788 PMCID: PMC10664139 DOI: 10.1021/acs.jcim.2c01516] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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] [Indexed: 02/01/2023]
Abstract
Inappropriate use of prescription drugs is potentially more harmful in fetuses/neonates than in adults. Cytochrome P450 (CYP) 3A subfamily undergoes developmental changes in expression, such as a transition from CYP3A7 to CYP3A4 shortly after birth, which provides a potential way to distinguish medication effects on fetuses/neonates and adults. The purpose of this study was to build first-in-class predictive models for both inhibitors and substrates of CYP3A7/CYP3A4 using chemical structure analysis. Three metrics were used to evaluate model performance: area under the receiver operating characteristic curve (AUC-ROC), balanced accuracy (BA), and Matthews correlation coefficient (MCC). The performance varied for each CYP3A7/CYP3A4 inhibitor/substrate model depending on the data set type, model type, rebalancing method, and specific feature set. For the active inhibitor/substrate data set, the optimal models achieved AUC-ROC values ranging from 0.77 ± 0.01 to 0.84 ± 0.01. For the selective inhibitor/substrate data set, the optimal models achieved AUC-ROC values ranging from 0.72 ± 0.02 to 0.79 ± 0.04. The predictive power of the optimal models was validated by compounds with known potencies as CYP3A7/CYP3A4 inhibitors or substrates. In addition, we identified structural features significant for CYP3A7/CYP3A4 selective or common inhibitors and substrates. In summary, the top performing models can be further applied as a tool to rapidly evaluate the safety and efficacy of new drugs separately for fetuses/neonates and adults. The significant structural features could guide the design of new therapeutic drugs as well as aid in the optimization of existing medicine for fetuses/neonates.
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Affiliation(s)
- Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Md Kabir
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
- The Graduate School of Biomedical Sciences, Departments of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Pranav Shah
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Elias Padilha
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Deborah K. Ngan
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Xin Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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36
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Tamalunas A, Wendt A, Springer F, Vigodski V, Huang R, Wang R, Liu Y, Rutz B, Ciotkowska A, Magistro G, Stief C, Hennenberg M. Hexane-extracted saw palmetto (Permixon®) inhibits prostate stromal cell proliferation and growth, and disrupts actin formation. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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37
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Wang R, Huang R, Liu Y, Tamalunas A, Stief C, Hennenberg M. Dihydrotestosterone reduces cholinergic contractions of bladder smooth muscle cells: Novel concepts in the pathogenesis of mixed symptoms in mixed LUTS? Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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38
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Liu Y, Wang R, Huang R, Tamalunas A, Waidelich R, Strittmatter F, Stief C, Hennenberg M. NUAK1 and -2 promote contraction, proliferation and suppression of cell death in human prostate stromal cells: Evidence from isoform-specific silencing. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00096-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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39
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Necchi A, Li R, Rose K, Davaro F, Davaro E, Spiess P, Petros G, Bratslavsky G, Jacob J, Pavlick D, Ross J, Huang R, Lin D, Danziger N, Graf R. CDH1-mutated clinically advanced urothelial bladder cancer (UBC): A genomic landscape and real-world clinical outcome study (RWCOS). Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00588-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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40
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Tamalunas A, Wendt A, Huang R, Wang R, Liu Y, Rutz B, Ciotkowska A, Magistro G, Stief C, Hennenberg M. Arf1 gef inhibitor golgicide a inhibits adrenergic and non-adrenergic prostate smooth muscle contraction. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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41
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Shi Q, Zhou YJ, Fang JG, Zhong X, Chen LZ, Hou HZ, Ma L, Feng SZ, He JW, Huang R, Wang YF, Yang Y. [Role of preoperative ultrasound-guided inferior parathyroid gland localization and new classification to assist intraoperative search and protection of parathyroid glands]. Zhonghua Yi Xue Za Zhi 2022; 102:3842-3848. [PMID: 36540921 DOI: 10.3760/cma.j.cn112137-20220616-01325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Objective: To investigate the role and significance of ultrasound-guided inferior parathyroid gland (IPTG) localization in searching and protecting parathyroid glands before thyroid surgery. Methods: A randomized controlled trial study was conducted. A total of 306 patients (433 cases of lateral parathyroidectomy) who underwent primary thyroidectomy and central lymph node dissection in Beijing Tongren Hosipital from March to October 2021 were enrolled. In order to locate IPTG more quickly and effectively, new IPTG classification and the definition of quadrant position were carried out. The patients were divided into the study group (n=228) and the control group (n=205). The study group underwent ultrasound-guided IPTG examination before operation and measured the distance between the IPTG and the lower pole of the thyroid and the midline of the trachea. During the operation, the IPTG was found and protected depending on the localization. The control group did not use any auxiliary preoperative positioning method. The distribution ratio of IPTG and the coincidence rate between intraoperative validation and ultrasound localization were calculated. Results: There were 306 patients enrolled in the final analysis (95 males and 211 females), with a median age of 41 years old (18-70). Type Ⅱ and Ⅲ IPTG accounted for 77.2% (176/228) of the total cases. The total coincidence rate ranged from 72.8% to 79.4% in different IPTG groups. Type Ⅲ and quadrant 2 IPTG had the highest coincidence rate [92.4% (73/79) and 92.9% (79/85), respectively]. The study group had better in situ retention rate [82.0% (187/228) vs 73.2% (150/205), χ2=4.896, P=0.027] and less implantation rate [8.8% (20/228) vs 16.1% (33/205), χ2=5.393, P=0.020] than those of the control group. The in situ retention rate were better in type Ⅲ IPTG group, compared with those of the control group [94.9% (74/78) vs 77.4% (48/62), χ2=7.898, P=0.005]. There was no permanent hypoparathyroidism in two groups and the temporary hypoparathyroidism rate was 32.0% (24/75) and 34.6% (18/52), respectively (χ2=0.095, P=0.758). Conclusion: Ultrasound-guided IPTG localization examination has important implications for searching and protecting IPTG during operation, which can significantly increase in situ retention rate of IPTG and decrease the implantation rate.
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Affiliation(s)
- Q Shi
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Y J Zhou
- Department of Ultrasound, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - J G Fang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - X Zhong
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - L Z Chen
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - H Z Hou
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - L Ma
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - S Z Feng
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - J W He
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - R Huang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Y F Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yifan Yang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
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42
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Ye L, Ngan DK, Xu T, Liu Z, Zhao J, Sakamuru S, Zhang L, Zhao T, Xia M, Simeonov A, Huang R. Prediction of drug-induced liver injury and cardiotoxicity using chemical structure and in vitro assay data. Toxicol Appl Pharmacol 2022; 454:116250. [PMID: 36150479 PMCID: PMC9561045 DOI: 10.1016/j.taap.2022.116250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/26/2022] [Revised: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
Drug-induced liver injury (DILI) and cardiotoxicity (DICT) are major adverse effects triggered by many clinically important drugs. To provide an alternative to in vivo toxicity testing, the U.S. Tox21 consortium has screened a collection of ∼10K compounds, including drugs in clinical use, against >70 cell-based assays in a quantitative high-throughput screening (qHTS) format. In this study, we compiled reference compound lists for DILI and DICT and compared the potential of Tox21 assay data with chemical structure information in building prediction models for human in vivo hepatotoxicity and cardiotoxicity. Models were built with four different machine learning algorithms (e.g., Random Forest, Naïve Bayes, eXtreme Gradient Boosting, and Support Vector Machine) and model performance was evaluated by calculating the area under the receiver operating characteristic curve (AUC-ROC). Chemical structure-based models showed reasonable predictive power for DILI (best AUC-ROC = 0.75 ± 0.03) and DICT (best AUC-ROC = 0.83 ± 0.03), while Tox21 assay data alone only showed better than random performance. DILI and DICT prediction models built using a combination of assay data and chemical structure information did not have a positive impact on model performance. The suboptimal predictive performance of the assay data is likely due to insufficient coverage of an adequately predictive number of toxicity mechanisms. The Tox21 consortium is currently expanding coverage of biological response space with additional assays that probe toxicologically important targets and under-represented pathways that may improve the prediction of in vivo toxicity such as DILI and DICT.
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Affiliation(s)
- Lin Ye
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Deborah K Ngan
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR 72079, USA
| | - Jinghua Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Li Zhang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Tongan Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA.
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43
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Zhu H, Xie D, Yang Y, Wang Y, Huang R, Chen X, Wang B, Peng Y, Wang J, Xiao D, Wu D, Qian C, Deng X. The Immune Response and Intestinal Injury after X-Ray FLASH Irradiation in Murine Breast Cancer Transplanted Models. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Bardawil E, Murarka S, Ross W, Huang R, Chohan L, Nijjar J. 8465 Same-Day Discharge (SDD) after Total Laparoscopic Hysterectomy (TLH) in a High-Risk Patient Population. J Minim Invasive Gynecol 2022. [DOI: 10.1016/j.jmig.2022.09.416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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45
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Cameo T, Jenkins J, Okuagu C, Huang R, Biest S, Ross W, Bardawil E. Transition to Universal Same Day Discharge (SDD) in Times of Corona Virus Disease-19 (COVID): A Success Story. J Minim Invasive Gynecol 2022. [DOI: 10.1016/j.jmig.2022.09.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Sun FF, Huang R, Meng JL, Yan J, Tang B, Wu GF. [Preliminary clinical effect evaluation of digital head and neck radiotherapy oral positioning stents]. Zhonghua Kou Qiang Yi Xue Za Zhi 2022; 57:1022-1028. [PMID: 36266075 DOI: 10.3760/cma.j.cn112144-20220701-00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Objective: To develop a designing software of digital oral positioning stent for radiotherapy of head and neck, and to compare its clinical effect with traditional oral positioning stents made by lost wax process. Methods: Thirty patients with nasopharyngeal cancer who received oral examination before radiotherapy in the prosthodontics department from July to December, 2021, were selected and divided into three groups according to the patients' wishes, 10 per group: one group without radiotherapy oral positioning stents, one group with traditional oral positioning stents (traditional stents group), and the third group with digital oral positioning stents (digital stents group). Patients' ages range from 20 years old to 71 years old. There were 15 males and 15 females involved in this study. The manufacturing time and comfort of the two positioning stents were evaluated, and the radiation doses of the radiotherapy target areas and surrounding healthy tissues were statistically analyzed at the end of radiotherapy. Results: The manufacturing time of digital stents group [(209±7) min] was much less than that of traditional stents group [(490±10) min] (t=69.85, P<0.001). The comfort of patients' wearing of digital stents [first wearing: 5 (3, 6) score; at the end of radiotherapy: 4 (3, 5) score] was better than that of traditional ones [first wearing: 7 (3, 7) score; at the end of radiotherapy: 7 (3, 7) score] (U=22.00, P=0.033; U=20.50, P=0.023). There was no significant differences in the target radiation doses among the three groups, and the radiation doses of tongue [traditional stents group: (36.74±5.45) Gy; digital stents group: (35.96±4.98) Gy] and mandible [traditional stents group: (35.46±4.19) Gy; digital stents group: (35.34±3.98) Gy] were significantly lower in the patients wearing oral positioning stents than in the patients without oral positioning stents [tongue: (41.49±4.46) Gy; madible: (39.32±3.52) Gy] (P<0.05). Conclusions: Oral positioning stents for nasopharyngeal carcinoma radiotherapy could greatly reduce the exposure doses of tongue and madible of patients. Digital oral positioning stents designed and manufactured by independently developed software had higher production efficiency than the traditional method, and patients' evaluation of comfort was better.
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Affiliation(s)
- F F Sun
- Department of Prosthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - R Huang
- Department of Prosthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - J L Meng
- Department of Prosthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
| | - J Yan
- Department of Oncology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - B Tang
- Nanjing Profeta Intelligent Technology Corperation, Nanjing 211112, China
| | - G F Wu
- Department of Prosthodontics, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing 210008, China
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47
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Lu X, Luo Z, Huang R, Lo DC, Huang W. High-Throughput Platform for Novel Reaction Discovery. Chemistry 2022; 28:e202201421. [PMID: 35766989 PMCID: PMC11033702 DOI: 10.1002/chem.202201421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Indexed: 11/10/2022]
Abstract
Detecting the formation of new chemical bonds in high-throughput synthesis is limited by the efficiency and scalability of reaction product detection, as conventional methods for isolating product from reaction mixtures are time consuming and labor intensive. Here, we report a miniaturizable purification method that enables the rapid, high-throughput isolation of quaternary ammonium-tagged products from reaction mixtures with excellent purity using inexpensive equipment that easily can be set up in a typical organic chemistry laboratory. This novel purification technique enabled us to establish a high-throughput reaction discovery platform. We validated this platform in a screen of 1536 reactions, and one previously unreported transformation was identified.
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Affiliation(s)
- Xiao Lu
- Therapeutic Development Branch, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Zhiji Luo
- Therapeutic Development Branch, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ruili Huang
- Chemical Genomics Branch, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Donald C. Lo
- Therapeutic Development Branch, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Wenwei Huang
- Therapeutic Development Branch, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
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48
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Lu X, Luo Z, Huang R, Lo DC, Huang W. Cover Feature: High‐Throughput Platform for Novel Reaction Discovery (Chem. Eur. J. 50/2022). Chemistry 2022. [DOI: 10.1002/chem.202202351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xiao Lu
- Therapeutic Development Branch National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville MD-20850 USA
| | - Zhiji Luo
- Therapeutic Development Branch National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville MD-20850 USA
| | - Ruili Huang
- Chemical Genomics Branch National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville MD-20850 USA
| | - Donald C. Lo
- Therapeutic Development Branch National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville MD-20850 USA
| | - Wenwei Huang
- Therapeutic Development Branch National Center for Advancing Translational Sciences (NCATS) National Institutes of Health (NIH) Rockville MD-20850 USA
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49
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Slavov S, Zhao J, Huang R, Xia M, Beger R. Prediction and Experimental Evaluation of the hERG Blocking Potential of Drugs Showing Clinical Signs of Cardiotoxicity. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220804110706] [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: 11/22/2022]
Abstract
Background:
A large scale experimental validation conducted at the National Center for Advancing Translational Sciences (NCATS/NIH, USA) confirmed the predictions of our 3D-SDAR model of hERG blockage and phospholipidosis induction. It was demonstrated that both hERG blockage and phospholipidosis induction are driven by a common three-center toxicophore composed of two aromatic rings and an amino group. This work extends our earlier efforts by predicting the hERG blocking potential of pharmaceuticals from two additional datasets: i) one comprised of 106 drugs with reported clinical signs of cardiotoxicity from the AZCERT database and ii) a dataset of 54 FDA-approved tyrosine kinase inhibitors (TKIs).
Methods:
A bagging-like 3D-SDAR algorithm aggregating predictions from 100 randomized models was used to predict the hERG blocking potential of all 160 drugs. All 106 drugs from the AZCERT dataset were furter evaluated for their hERG inhibition at NCATS using a thallium flux assay.
Results:
Comparison of the predicted hERG class against the results from the thallium flux qHTS assay resulted in an overall predictive accuracy of 0.736 and the area under the ROC curve of 0.780. Factors such as the generation of false negatives by the thallium flux assay, proximity to the cut-off, use of conformations that may differ from the biologically relevant ones, and the lack of structurally similar compounds in the modeling set could explain the somewhat reduced predictive performance compared to that of the original model. The original 3D-SDAR model was also used to evaluate the TKIs ability to block hERG. Comparing our predictions to class assignemts based on IC50 values with a 30 μM cut-off, an accuracy of 0.850, sensitivity of 0.906, and specificity of 0.625 were achieved.
Conclusion:
3D-SDAR provides a reliable platform for prediction of hERG blockage. Particular attention should be paid to all investigational new drugs containing our three-center hERG toxicophore, especially those having highly flexible molecules. Particular scrutiny should be given to the tyrosine kinase inhibitors, which represent a therapeutic class possessing all structural characteristics previously associated with an increased potential to block hERG.
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Affiliation(s)
- Svetoslav Slavov
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Richard Beger
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
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50
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Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H. Corrigendum to "An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication" [Genomics Proteomics Bioinformatics19 (1) (2021) 108-122]. Genomics Proteomics Bioinformatics 2022; 20:808-809. [PMID: 36669818 PMCID: PMC9880883 DOI: 10.1016/j.gpb.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guang Song
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily M. Lee
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hee-Sool Rho
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yichen Cheng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nadia Whitt
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cedric Moore
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ki-Jun Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly M. Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA,Corresponding authors.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Heng Zhu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
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