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Xu J, Yu B, Wang F, Yang J. Xenograft and organoid models in developing precision medicine for gastric cancer (Review). Int J Oncol 2024; 64:41. [PMID: 38390969 PMCID: PMC10919760 DOI: 10.3892/ijo.2024.5629] [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: 10/07/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Gastric cancer (GC), a highly heterogeneous disease, has diverse histological and molecular subtypes. For precision medicine, well‑characterized models encompassing the full spectrum of subtypes are necessary. Patient‑derived tumor xenografts and organoids serve as important preclinical models in GC research. The main advantage of these models is the retention of phenotypic and genotypic heterogeneity present in parental tumor tissues. Utilizing diverse sequencing techniques and preclinical models for GC research facilitates accuracy in predicting personalized clinical responses to anti‑cancer treatments. The present review summarizes the latest advances of these two preclinical models in GC treatment and drug response assessment.
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Affiliation(s)
- Jiao Xu
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Bixin Yu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Fan Wang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Jin Yang
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Phase I Clinical Trial Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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Sally Samson J, Ramesh A, Deepa Parvathi V. Development of midbrain dopaminergic neurons and the advantage of using hiPSCs as a model system to study Parkinson's disease. Neuroscience 2024:S0306-4522(24)00138-6. [PMID: 38522661 DOI: 10.1016/j.neuroscience.2024.03.025] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
Midbrain dopaminergic (mDA) neurons are significantly impaired in patients inflicted with Parkinson's disease (PD), subsequently affecting a variety of motor functions. There are four pathways through which dopamine elicits its function, namely, nigrostriatal, mesolimbic, mesocortical and tuberoinfundibular dopamine pathways. SHH and Wnt signalling pathways in association with favourable expression of a variety of genes, promotes the development and differentiation of mDA neurons in the brain. However, there is a knowledge gap regarding the complex signalling pathways involved in development of mDA neurons. hiPSC models have been acclaimed to be effective in generating complex disease phenotypes. These models mimic the microenvironment found in vivo thus ensuring maximum reliability. Further, a variety of therapeutic compounds can be screened using hiPSCs since they can be used to generate neurons that could carry a myriad array of mutations associated with both familial and sporadic PD. Thus, culturing hiPSCs to study gene expression and dysregulation of cellular processes associated with PD can be useful in developing targeted therapies that will be a step towards halting disease progression.
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Affiliation(s)
- Jennifer Sally Samson
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 600116, India
| | - Anuradha Ramesh
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 600116, India
| | - Venkatachalam Deepa Parvathi
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 600116, India.
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Romussi S, Giunti S, Andersen N, De Rosa MJ. C. elegans: a prominent platform for modeling and drug screening in neurological disorders. Expert Opin Drug Discov 2024:1-21. [PMID: 38509691 DOI: 10.1080/17460441.2024.2329103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Human neurodevelopmental and neurodegenerative diseases (NDevDs and NDegDs, respectively) encompass a broad spectrum of disorders affecting the nervous system with an increasing incidence. In this context, the nematode C. elegans, has emerged as a benchmark model for biological research, especially in the field of neuroscience. AREAS COVERED The authors highlight the numerous advantages of this tiny worm as a model for exploring nervous system pathologies and as a platform for drug discovery. There is a particular focus given to describing the existing models of C. elegans for the study of NDevDs and NDegDs. Specifically, the authors underscore their strong applicability in preclinical drug development. Furthermore, they place particular emphasis on detailing the common techniques employed to explore the nervous system in both healthy and diseased states. EXPERT OPINION Drug discovery constitutes a long and expensive process. The incorporation of invertebrate models, such as C. elegans, stands as an exemplary strategy for mitigating costs and expediting timelines. The utilization of C. elegans as a platform to replicate nervous system pathologies and conduct high-throughput automated assays in the initial phases of drug discovery is pivotal for rendering therapeutic options more attainable and cost-effective.
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Affiliation(s)
- Stefano Romussi
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
| | - Sebastián Giunti
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Natalia Andersen
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - María José De Rosa
- Laboratorio de Neurobiología de Invertebrados, Instituto de Investigaciones Bioquímicas de Bahía Blanca (INIBIBB), UNS-CONICET, Bahía Blanca, Argentina
- Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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Shin A, Ryu JR, Kim BG, Sun W. Establishment and Validation of a Model for Fetal Neural Ischemia Using Necrotic Core-Free Human Spinal Cord Organoids. Stem Cells Transl Med 2024; 13:268-277. [PMID: 38103168 PMCID: PMC10940837 DOI: 10.1093/stcltm/szad089] [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: 06/29/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Fetal spinal cord ischemia is a serious medical condition that can result in significant neurological damage and adverse outcomes for the fetus. However, the lack of an appropriate experimental model has hindered the understanding of the pathology and the development of effective treatments. In our study, we established a system for screening drugs that affect fetal spinal cord ischemia using spinal cord organoids. Importantly, we produced necrotic core-free human spinal cord organoids (nf-hSCOs) by reducing the organoid size to avoid potential complications of spontaneous necrosis in large organoids. Exposing nf-hSCOs to CoCl2 as a hypoxia mimetic and hypoglycemic conditions resulted in significant neuronal damage, as assessed by multiple assay batteries. By utilizing this model, we tested chemicals that have been reported to exhibit beneficial effects in brain organoid-based ischemia models. Surprisingly, these chemicals did not provide sufficient benefit, and we discovered that rapamycin is a mild neuroprotective reagent for both axon degeneration and neuronal survival. We propose that nf-hSCO is suitable for large-scale screening of fetal neural ischemia due to its scalability, ease of ischemic induction, implementation of quantifiable assay batteries, and the absence of spontaneous necrosis.
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Affiliation(s)
- Aeri Shin
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Byung Gon Kim
- Department of Brain Science, A-Jou University School of Medicine, Suwon, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
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Jain N, Shashi Bhushan BL, Natarajan M, Mehta R, Saini DK, Chatterjee K. Advanced 3D In Vitro Lung Fibrosis Models: Contemporary Status, Clinical Uptake, and Prospective Outlooks. ACS Biomater Sci Eng 2024; 10:1235-1261. [PMID: 38335198 DOI: 10.1021/acsbiomaterials.3c01499] [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] [Indexed: 02/12/2024]
Abstract
Fibrosis has been characterized as a global health problem and ranks as one of the primary causes of organ dysfunction. Currently, there is no cure for pulmonary fibrosis, and limited therapeutic options are available due to an inadequate understanding of the disease pathogenesis. The absence of advanced in vitro models replicating dynamic temporal changes observed in the tissue with the progression of the disease is a significant impediment in the development of novel antifibrotic treatments, which has motivated research on tissue-mimetic three-dimensional (3D) models. In this review, we summarize emerging trends in preparing advanced lung models to recapitulate biochemical and biomechanical processes associated with lung fibrogenesis. We begin by describing the importance of in vivo studies and highlighting the often poor correlation between preclinical research and clinical outcomes and the limitations of conventional cell culture in accurately simulating the 3D tissue microenvironment. Rapid advancement in biomaterials, biofabrication, biomicrofluidics, and related bioengineering techniques are enabling the preparation of in vitro models to reproduce the epithelium structure and operate as reliable drug screening strategies for precise prediction. Improving and understanding these model systems is necessary to find the cross-talks between growing cells and the stage at which myofibroblasts differentiate. These advanced models allow us to utilize the knowledge and identify, characterize, and hand pick medicines beneficial to the human community. The challenges of the current approaches, along with the opportunities for further research with potential for translation in this field, are presented toward developing novel treatments for pulmonary fibrosis.
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Affiliation(s)
- Nipun Jain
- Department of Materials Engineering, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
| | - B L Shashi Bhushan
- Department of Pulmonary Medicine, Victoria Hospital, Bangalore Medical College and Research Institute, Bangalore 560002 India
| | - M Natarajan
- Department of Pathology, Victoria Hospital, Bangalore Medical College and Research Institute, Bangalore 560002 India
| | - Ravi Mehta
- Department of Pulmonology and Critical Care, Apollo Hospitals, Jayanagar, Bangalore 560011 India
| | - Deepak Kumar Saini
- Department of Developmental Biology and Genetics, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
| | - Kaushik Chatterjee
- Department of Materials Engineering, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
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Kostadinova R, Ströbel S, Chen L, Fiaschetti-Egli K, Gadient J, Pawlowska A, Petitjean L, Bieri M, Thoma E, Petitjean M. Digital pathology with artificial intelligence analysis provides insight to the efficacy of anti-fibrotic compounds in human 3D MASH model. Sci Rep 2024; 14:5885. [PMID: 38467661 PMCID: PMC10928082 DOI: 10.1038/s41598-024-55438-2] [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: 11/10/2023] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH) is a severe liver disease characterized by lipid accumulation, inflammation and fibrosis. The development of MASH therapies has been hindered by the lack of human translational models and limitations of analysis techniques for fibrosis. The MASH three-dimensional (3D) InSight™ human liver microtissue (hLiMT) model recapitulates pathophysiological features of the disease. We established an algorithm for automated phenotypic quantification of fibrosis of Sirius Red stained histology sections of MASH hLiMTs model using a digital pathology quantitative single-fiber artificial intelligence (AI) FibroNest™ image analysis platform. The FibroNest™ algorithm for MASH hLiMTs was validated using anti-fibrotic reference compounds with different therapeutic modalities-ALK5i and anti-TGF-β antibody. The phenotypic quantification of fibrosis demonstrated that both reference compounds decreased the deposition of fibrillated collagens in alignment with effects on the secretion of pro-collagen type I/III, tissue inhibitor of metalloproteinase-1 and matrix metalloproteinase-3 and pro-fibrotic gene expression. In contrast, clinical compounds, Firsocostat and Selonsertib, alone and in combination showed strong anti-fibrotic effects on the deposition of collagen fibers, however less pronounced on the secretion of pro-fibrotic biomarkers. In summary, the phenotypic quantification of fibrosis of MASH hLiMTs combined with secretion of pro-fibrotic biomarkers and transcriptomics represents a promising drug discovery tool for assessing anti-fibrotic compounds.
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Affiliation(s)
| | - Simon Ströbel
- InSphero AG, Wagistrasse 27A, Schlieren, Switzerland
| | - Li Chen
- PharmaNest, Princeton, NJ, USA
| | | | - Jana Gadient
- InSphero AG, Wagistrasse 27A, Schlieren, Switzerland
| | | | | | - Manuela Bieri
- InSphero AG, Wagistrasse 27A, Schlieren, Switzerland
| | - Eva Thoma
- InSphero AG, Wagistrasse 27A, Schlieren, Switzerland
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Liu YC, Chen P, Chang R, Liu X, Jhang JW, Enkhbat M, Chen S, Wang H, Deng C, Wang PY. Artificial tumor matrices and bioengineered tools for tumoroid generation. Biofabrication 2024; 16:022004. [PMID: 38306665 DOI: 10.1088/1758-5090/ad2534] [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: 08/10/2023] [Accepted: 02/01/2024] [Indexed: 02/04/2024]
Abstract
The tumor microenvironment (TME) is critical for tumor growth and metastasis. The TME contains cancer-associated cells, tumor matrix, and tumor secretory factors. The fabrication of artificial tumors, so-called tumoroids, is of great significance for the understanding of tumorigenesis and clinical cancer therapy. The assembly of multiple tumor cells and matrix components through interdisciplinary techniques is necessary for the preparation of various tumoroids. This article discusses current methods for constructing tumoroids (tumor tissue slices and tumor cell co-culture) for pre-clinical use. This article focuses on the artificial matrix materials (natural and synthetic materials) and biofabrication techniques (cell assembly, bioengineered tools, bioprinting, and microfluidic devices) used in tumoroids. This article also points out the shortcomings of current tumoroids and potential solutions. This article aims to promotes the next-generation tumoroids and the potential of them in basic research and clinical application.
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Affiliation(s)
- Yung-Chiang Liu
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
| | - Ping Chen
- Cancer Centre, Faculty of Health Sciences, MOE Frontier Science Centre for Precision Oncology, University of Macau, Macau SAR 999078, People's Republic of China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, People's Republic of China
| | - Ray Chang
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
| | - Xingjian Liu
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
| | - Jhe-Wei Jhang
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
| | - Myagmartsend Enkhbat
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Shan Chen
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
| | - Hongxia Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Chuxia Deng
- Cancer Centre, Faculty of Health Sciences, MOE Frontier Science Centre for Precision Oncology, University of Macau, Macau SAR 999078, People's Republic of China
| | - Peng-Yuan Wang
- Oujiang Laboratory; Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, Zhejiang 325024, People's Republic of China
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Atanasova KR, Perkins CM, Ratnayake R, Jiang J, Chen QY, Schmittgen TD, Luesch H. Epigenetic small-molecule screen for inhibition and reversal of acinar ductal metaplasia in mouse pancreatic organoids. Front Pharmacol 2024; 15:1335246. [PMID: 38510657 PMCID: PMC10953826 DOI: 10.3389/fphar.2024.1335246] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Background: Acinar ductal metaplasia (ADM) is among the earliest initiating events in pancreatic ductal adenocarcinoma (PDAC) development. Methods: We developed a novel morphology-based screen using organoids from wildtype and p48Cre/+ (Cre) mice to discover epigenetic modulators that inhibit or reverse pancreatic ADM more effectively than the broad-spectrum HDAC inhibitor trichostatin A (TSA). Results: Of the 144 compounds screened, nine hits and two additional natural product HDAC inhibitors were validated by dose-response analysis. The class I HDAC inhibitors apicidin and FK228, and the histone methyltransferase inhibitor chaetocin demonstrated pronounced ADM inhibition and reversal without inducing significant cytotoxicity at 1 µM. Thioester prodrug class I HDAC inhibitor largazole attenuated ADM while its disulfide homodimer was effective in both ADM inhibition and reversal. Prioritized compounds were validated for ADM reversal in p48Cre/+; LSL-KrasG12D/+ (KC) mouse organoids using both morphological and molecular endpoints. Molecular index analysis of ADM reversal in KC mouse organoids demonstrated improved activity compared to TSA. Improved prodrug stability translated into a stronger phenotypic and molecular response. RNA-sequencing indicated that angiotensinogen was the top inhibited pathway during ADM reversal. Conclusion: Our findings demonstrate a unique epigenetic mechanism and suggest that the phenotypic screen developed here may be applied to discover potential treatments for PDAC.
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Affiliation(s)
- Kalina R. Atanasova
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Corey M. Perkins
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Ranjala Ratnayake
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Jinmai Jiang
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Qi-Yin Chen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Thomas D. Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, United States
- Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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Rotem RS, Bellavia A, Paganoni S, Weisskopf MG. Medication use and risk of amyotrophic lateral sclerosis: using machine learning for an exposome-wide screen of a large clinical database. Amyotroph Lateral Scler Frontotemporal Degener 2024:1-9. [PMID: 38426489 DOI: 10.1080/21678421.2024.2320878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Accumulating evidence suggests that non-genetic factors have important etiologic roles in amyotrophic lateral sclerosis (ALS), yet identification of specific culprit factors has been challenging. Many medications target biological pathways implicated in ALS pathogenesis, and screening large pharmacologic datasets for signals could greatly accelerate the identification of risk-modulating pharmacologic factors for ALS. METHOD We conducted a high-dimensional screening of patients' history of medication use and ALS risk using an advanced machine learning approach based on gradient-boosted decision trees coupled with Bayesian model optimization and repeated data sampling. Clinical and medication dispensing data were obtained from a large Israeli health fund for 501 ALS cases and 4,998 matched controls using a lag period of 3 or 5 years prior to ALS diagnosis for ascertaining medication exposure. RESULTS Of over 1,000 different medication classes, we identified 8 classes that were consistently associated with increased ALS risk across independently trained models, where most are indicated for control of symptoms implicated in ALS. Some suggestive protective effects were also observed, notably for vitamin E. DISCUSSION Our results indicate that use of certain medications well before the typically recognized prodromal period was associated with ALS risk. This could result because these medications increase ALS risk or could indicate that ALS symptoms can manifest well before suggested prodromal periods. The results also provide further evidence that vitamin E may be a protective factor for ALS. Targeted studies should be performed to elucidate the possible pathophysiological mechanisms while providing insights for therapeutics design.
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Affiliation(s)
- Ran S Rotem
- Department of Environmental Health, Harvard University T H Chan School of Public Health, Boston, MA, USA
- KSM Research and Innovation Institute, Maccabi Healthcare Services, Israel
| | - Andrea Bellavia
- Department of Environmental Health, Harvard University T H Chan School of Public Health, Boston, MA, USA
| | - Sabrina Paganoni
- Sean M. Healey and AMG Center for ALS, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Boston, MA, USA, and
| | - Marc G Weisskopf
- Department of Environmental Health, Harvard University T H Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard University T H Chan School of Public Health, Boston, MA, USA
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Beyer GV, Hueser S, Li R, Manika D, Lee M, Chan CHF, Howe JR, Ear PH. Gastroenteropancreatic neuroendocrine carcinoma tumor spheroid drug screen reveals vulnerability to tyrosyl-DNA phosphodiesterase 1 inhibitors. Surgery 2024; 175:605-612. [PMID: 37914572 PMCID: PMC10872605 DOI: 10.1016/j.surg.2023.08.044] [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: 05/16/2023] [Revised: 07/26/2023] [Accepted: 08/08/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Gastroenteropancreatic neuroendocrine carcinomas are rare neoplasms with no effective treatments and poor prognosis. Few reliable preclinical models exist for the study of gastroenteropancreatic neuroendocrine carcinomas, limiting investigation of novel treatments. We used tumor spheroids from our recently established gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models to systematically screen for compounds with diverse structures to identify potential new categories of therapeutic agents that can target gastroenteropancreatic neuroendocrine carcinomas. METHODS Tumor spheroids were derived from our NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models. Gastroenteropancreatic neuroendocrine carcinoma spheroids were screened against a library of 885 compounds from the National Cancer Institute Diversity Set VII collection. Cell viability was measured via AlamarBlue assay. After identification of potential therapeutic compounds, synergy screening of a selected group with temozolomide and doxorubicin was performed, and these combinations were further analyzed for γH2AX and phosphorylated-ERK proteins. RESULTS We identified 16 compounds that inhibit over 75% of gastroenteropancreatic neuroendocrine carcinoma spheroid survival. Seven are inhibitors of tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme working closely with the topoisomerase I complex. When combined with temozolomide or doxorubicin, the tyrosyl-DNA phosphodiesterase 1 inhibitor cytarabine increased the cytotoxic effects of these drugs on NEC1452 cells which was further evidenced by increasing γH2AX and decreasing phosphorylated-ERK in combination treatment compared to temozolomide alone. CONCLUSION Both NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma spheroid lines are useful preclinical models for drug testing. Our library screen revealed these gastroenteropancreatic neuroendocrine carcinoma spheroids are highly sensitive to a novel class of anti-cancer drugs that target nuclear genome stability.
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Affiliation(s)
- Gabriella V Beyer
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Sophia Hueser
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Rachel Li
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Deeraj Manika
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Minhyuk Lee
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Carlos H F Chan
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA
| | - James R Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA
| | - Po Hien Ear
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA.
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Erbacher C, Athmer M, Kröger E, Dahrendorf L, Imberg L, Kalinin DV, Karst U. An automated analysis method enabling the screening of covalent thrombin and factor XIIa inhibitors via liquid chromatography-mass spectrometry. Drug Test Anal 2024; 16:314-322. [PMID: 37482900 DOI: 10.1002/dta.3549] [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: 06/11/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023]
Abstract
An automated sample preparation and separation method for the analysis of various enzyme-inhibitor combinations using liquid chromatography (LC) coupled to mass spectrometry (MS) is presented. As conventional anticoagulants have several drawbacks, the most severe being the elevated risk of internal bleedings, it is necessary to develop new-generation anticoagulants with reduced side effects. Therefore, the screening of potential inhibitors against anticoagulation targets like thrombin and FXIIa is important to design a potent and selective inhibitor. To facilitate the analysis of numerous enzyme-inhibitor covalent complexes, automation of the analysis using an LC system with a user-defined injection sequence is helpful. The developed method ensures comparable reaction conditions like reaction time and temperature for all enzyme-inhibitor complexes. Furthermore, it prevents time-consuming manual sample preparation and potential manual errors. To achieve good reproducibility with relative standard deviation of approximately 3% for three-fold determination, multiple cleaning steps were added to the automated sample preparation. Subsequently, this method was applied to screen a variety of 15 aminopyrazole- and aminotriazole-based inhibitors with a covalent mechanism of action against thrombin and to test two covalent inhibitors for FXIIa. Successful complex formation and acylation of the catalytic center of the enzymes was monitored using deconvoluted mass spectra and the matching mass shifts of the acyl moiety of the analyzed inhibitors. The inhibitors' structure directly influenced reaction yields. Sterically demanding aminotriazoles and acyl moieties both affected the product formation negatively. However, the screening yielded several promising candidates for new covalent thrombin inhibitors, which might find their application as prospective anticoagulants.
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Affiliation(s)
- Catharina Erbacher
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Mathis Athmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Erik Kröger
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Laureen Dahrendorf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Lukas Imberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Dmitrii V Kalinin
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
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12
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Black BJ, Ghazal RE, Lojek N, Williams V, Rajput JS, Lawson JM. Phenotypic Screening of Prospective Analgesics Among FDA-Approved Compounds using an iPSC-Based Model of Acute and Chronic Inflammatory Nociception. Adv Sci (Weinh) 2024; 11:e2303724. [PMID: 38189546 PMCID: PMC10953557 DOI: 10.1002/advs.202303724] [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: 06/07/2023] [Revised: 11/26/2023] [Indexed: 01/09/2024]
Abstract
Classical target-based drug screening is low-throughput, largely subjective, and costly. Phenotypic screening based on in vitro models is increasingly being used to identify candidate compounds that modulate complex cell/tissue functions. Chronic inflammatory nociception, and subsequent chronic pain conditions, affect peripheral sensory neuron activity (e.g., firing of action potentials) through myriad pathways, and remain unaddressed in regard to effective, non-addictive management/treatment options. Here, a chronic inflammatory nociception model is demonstrated based on induced pluripotent stem cell (iPSC) sensory neurons and glia, co-cultured on microelectrode arrays (MEAs). iPSC sensory co-cultures exhibit coordinated spontaneous extracellular action potential (EAP) firing, reaching a stable baseline after ≈27 days in vitro (DIV). Spontaneous and evoked EAP metrics are significantly modulated by 24-h incubation with tumor necrosis factor-alpha (TNF-α), representing an inflammatory phenotype. Compared with positive controls (lidocaine), this model is identified as an "excellent" stand-alone assay based on a modified Z' assay quality metric. This model is then used to screen 15 cherry-picked, off-label, Food and Drug Administration (FDA)-approved compounds; 10 of 15 are identified as "hits". Both hits and "misses" are discussed in turn. In total, this data suggests that iPSC sensory co-cultures on MEAs may represent a moderate-to-high-throughput assay for drug discovery targeting inflammatory nociception.
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Affiliation(s)
- Bryan James Black
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
| | - Rasha El Ghazal
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
| | - Neal Lojek
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
| | - Victoria Williams
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
| | - Jai Singh Rajput
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
| | - Jennifer M. Lawson
- Department of Biomedical EngineeringFrancis College of EngineeringUniversity of Massachusetts LowellLowellMA01854USA
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13
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Zheng K, Hu J, Hu C, Liu X, Wang Y, Han H, Xing W, Yang L, Zhang J, Hong Q, Hao F, Li W. Establishing an ANO1-Based Cell Model for High-Throughput Screening Targeting TRPV4 Regulators. Molecules 2024; 29:1036. [PMID: 38474548 DOI: 10.3390/molecules29051036] [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: 02/03/2024] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Transient receptor potential vanilloid 4 (TRPV4) is a widely expressed cation channel that plays an important role in many physiological and pathological processes. However, most TRPV4 drugs carry a risk of side effects. Moreover, existing screening methods are not suitable for the high-throughput screening (HTS) of drugs. In this study, a cell model and HTS method for targeting TRPV4 channel drugs were established based on a calcium-activated chloride channel protein 1 Anoctamin 1 (ANO1) and a double mutant (YFP-H148Q/I152L) of the yellow fluorescent protein (YFP). Patch-clamp experiments and fluorescence quenching kinetic experiments were used to verify that the model could sensitively detect changes in intracellular Ca2+ concentration. The functionality of the TRPV4 cell model was examined through temperature variations and different concentrations of TRPV4 modulators, and the performance of the model in HTS was also evaluated. The model was able to sensitively detect changes in the intracellular Ca2+ concentration and also excelled at screening TRPV4 drugs, and the model was more suitable for HTS. We successfully constructed a drug cell screening model targeting the TRPV4 channel, which provides a tool to study the pathophysiological functions of TRPV4 in vitro.
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Affiliation(s)
- Kai Zheng
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Jiang Hu
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Cheng Hu
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Xueying Liu
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Yanyan Wang
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Haojian Han
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Wenzhu Xing
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Liu Yang
- School of Medical Technology, Beihua University, Jilin 132000, China
| | - Junran Zhang
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiyuan Hong
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Feng Hao
- College of Laboratory Medicine, Jilin Medical University, Jilin 132000, China
| | - Wenliang Li
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin 132000, China
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14
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Gullulu O, Ozcelik E, Tuzlakoglu Ozturk M, Karagoz MS, Tazebay UH. A multi-faceted approach to unravel coding and non-coding gene fusions and target chimeric proteins in ataxia. J Biomol Struct Dyn 2024:1-21. [PMID: 38411012 DOI: 10.1080/07391102.2024.2321510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/15/2024] [Indexed: 02/28/2024]
Abstract
Ataxia represents a heterogeneous group of neurodegenerative disorders characterized by a loss of balance and coordination, often resulting from mutations in genes vital for cerebellar function and maintenance. Recent advances in genomics have identified gene fusion events as critical contributors to various cancers and neurodegenerative diseases. However, their role in ataxia pathogenesis remains largely unexplored. Our study Hdelved into this possibility by analyzing RNA sequencing data from 1443 diverse samples, including cell and mouse models, patient samples, and healthy controls. We identified 7067 novel gene fusions, potentially pivotal in disease onset. These fusions, notably in-frame, could produce chimeric proteins, disrupt gene regulation, or introduce new functions. We observed conservation of specific amino acids at fusion breakpoints and identified potential aggregate formations in fusion proteins, known to contribute to ataxia. Through AI-based protein structure prediction, we identified topological changes in three high-confidence fusion proteins-TEN1-ACOX1, PEX14-NMNAT1, and ITPR1-GRID2-which could potentially alter their functions. Subsequent virtual drug screening identified several molecules and peptides with high-affinity binding to fusion sites. Molecular dynamics simulations confirmed the stability of these protein-ligand complexes at fusion breakpoints. Additionally, we explored the role of non-coding RNA fusions as miRNA sponges. One such fusion, RP11-547P4-FLJ33910, showed strong interaction with hsa-miR-504-5p, potentially acting as its sponge. This interaction correlated with the upregulation of hsa-miR-504-5p target genes, some previously linked to ataxia. In conclusion, our study unveils new aspects of gene fusions in ataxia, suggesting their significant role in pathogenesis and opening avenues for targeted therapeutic interventions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Omer Gullulu
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Emrah Ozcelik
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
- Central Research Laboratory (GTU-MAR), Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Merve Tuzlakoglu Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
- Central Research Laboratory (GTU-MAR), Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Mustafa Safa Karagoz
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Uygar Halis Tazebay
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
- Central Research Laboratory (GTU-MAR), Gebze Technical University, Gebze, Kocaeli, Turkey
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15
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Tan YQ, Sun B, Zhang X, Zhang S, Guo H, Basappa B, Zhu T, Sethi G, Lobie PE, Pandey V. Concurrent inhibition of pBADS99 synergistically improves MEK inhibitor efficacy in KRAS G12D-mutant pancreatic ductal adenocarcinoma. Cell Death Dis 2024; 15:173. [PMID: 38409090 PMCID: PMC10897366 DOI: 10.1038/s41419-024-06551-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/28/2024]
Abstract
Therapeutic targeting of KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) has remained a significant challenge in clinical oncology. Direct targeting of KRAS has proven difficult, and inhibition of the KRAS effectors have shown limited success due to compensatory activation of survival pathways. Being a core downstream effector of the KRAS-driven p44/42 MAPK and PI3K/AKT pathways governing intrinsic apoptosis, BAD phosphorylation emerges as a promising therapeutic target. Herein, a positive association of the pBADS99/BAD ratio with higher disease stage and worse overall survival of PDAC was observed. Homology-directed repair of BAD to BADS99A or small molecule inhibition of BADS99 phosphorylation by NCK significantly reduced PDAC cell viability by promoting cell cycle arrest and apoptosis. NCK also abrogated the growth of preformed colonies of PDAC cells in 3D culture. Furthermore, high-throughput screening with an oncology drug library to identify potential combinations revealed a strong synergistic effect between NCK and MEK inhibitors in PDAC cells harboring either wild-type or mutant-KRAS. Mechanistically, both mutant-KRAS and MEK inhibition increased the phosphorylation of BADS99 in PDAC cells, an effect abrogated by NCK. Combined pBADS99-MEK inhibition demonstrated strong synergy in reducing cell viability, enhancing apoptosis, and achieving xenograft stasis in KRAS-mutant PDAC. In conclusion, the inhibition of BADS99 phosphorylation enhances the efficacy of MEK inhibition, and their combined inhibition represents a mechanistically based and potentially effective therapeutic strategy for the treatment of KRAS-mutant PDAC.
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Affiliation(s)
- Yan Qin Tan
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Food Science and Technology Program, Department of Life Sciences, BNU-HKBU United International College, Zhuhai, 519087, Guangdong, People's Republic of China
| | - Bowen Sun
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Xi Zhang
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Shuwei Zhang
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Hui Guo
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
| | - Basappa Basappa
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, 570006, Mysore, India
| | - Tao Zhu
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China
- Department of Oncology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
- Hefei National Laboratory for Physical Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Peter E Lobie
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
- Shenzhen Bay Laboratory, Shenzhen, 518055, Guangdong, People's Republic of China.
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering and Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
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16
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Meikopoulos T, Gika H, Theodoridis G, Begou O. Detection of 26 Drugs of Abuse and Metabolites in Quantitative Dried Blood Spots by Liquid Chromatography-Mass Spectrometry. Molecules 2024; 29:975. [PMID: 38474487 DOI: 10.3390/molecules29050975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/11/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
A method was developed for the determination of 26 drugs of abuse from different classes, including illicit drugs in quantitative dried blood spots (qDBSs), with the aim to provide a convenient method for drug testing by using only 10 μL of capillary blood. A satisfactory limit of quantification (LOQ) of 2.5 ng/mL for 9 of the compounds and 5 ng/mL for 17 of the compounds and a limit of detection (LOD) of 0.75 ng/mL for 9 of the compounds and 1.5 ng/mL for 17 of the compounds were achieved for all analytes. Reversed-phase liquid chromatography was applied on a C18 column coupled to MS, providing selective detections with both +ESI and -ESI modes. Extraction from the qDBS was performed using AcN-MeOH, 1:1 (v/v), with recovery ranging from 84.6% to 106%, while no significant effect of the hematocrit was observed. The studied drugs of abuse were found to be stable over five days under three different storage conditions (at ambient temperature 21 °C, at -20 °C, and at 35 °C), thus offering a highly attractive approach for drug screening by minimally invasive sampling for individuals that could find application in forensic toxicology analysis.
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Affiliation(s)
- Thomas Meikopoulos
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- BIOMIC_Auth, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), 57001 Thessaloniki, Greece
| | - Helen Gika
- BIOMIC_Auth, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), 57001 Thessaloniki, Greece
- Laboratory of Forensic Medicine & Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Theodoridis
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- BIOMIC_Auth, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), 57001 Thessaloniki, Greece
- ThetaBiomarkers, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), Balkan Center, 10th Km Thessaloniki-Thermi Rd., P.O. Box 8318, 57001 Thessaloniki, Greece
| | - Olga Begou
- BIOMIC_Auth, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), 57001 Thessaloniki, Greece
- ThetaBiomarkers, Center for Interdisciplinary Research, and Innovation (CIRI-AUTH), Balkan Center, 10th Km Thessaloniki-Thermi Rd., P.O. Box 8318, 57001 Thessaloniki, Greece
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17
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Skardal A. Grand challenges in organoid and organ-on-a-chip technologies. Front Bioeng Biotechnol 2024; 12:1366280. [PMID: 38456004 PMCID: PMC10919399 DOI: 10.3389/fbioe.2024.1366280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 03/09/2024] Open
Affiliation(s)
- Aleksander Skardal
- Department of Biomedical Engineering, College of Engineering, The Ohio State University, Columbus, OH, United States
- Center for Cancer Engineering, The Ohio State University, Columbus, OH, United States
- Cancer Biology Program, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, OH, United States
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18
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Miranda GASC, Corrêa IA, Amorim ÉA, Caldas LA, Carneiro FÁ, da Costa LJ, Granjeiro JM, Tanuri A, de Souza W, Baptista LS. Cost-effective 3D lung tissue spheroid as a model for SARS-CoV-2 infection and drug screening. Artif Organs 2024. [PMID: 38385713 DOI: 10.1111/aor.14729] [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: 10/26/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND The SARS-CoV-2 pandemic has spurred an unparalleled scientific endeavor to elucidate the virus' structure, infection mechanisms, and pathogenesis. Two-dimensional culture systems have been instrumental in shedding light on numerous aspects of COVID-19. However, these in vitro systems lack the physiological complexity to comprehend the infection process and explore treatment options. Three-dimensional (3D) models have been proposed to fill the gap between 2D cultures and in vivo studies. Specifically, spheroids, composed of lung cell types, have been suggested for studying SARS-CoV-2 infection and serving as a drug screening platform. METHODS 3D lung spheroids were prepared by coculturing human alveolar or bronchial epithelial cells with human lung stromal cells. The morphology, size, and ultrastructure of spheroids before and after SARS-CoV-2 infection were analyzed using optical and electron microscopy. Immunohistochemistry was used to detect spike protein and, thus, the virus presence in the spheroids. Multiplex analysis elucidated the cytokine release after virus infection. RESULTS The spheroids were stable and kept their size and morphology after SARS-CoV-2 infection despite the presence of multivesicular bodies, endoplasmic reticulum rearrangement, tubular compartment-enclosed vesicles, and the accumulation of viral particles. The spheroid responded to the infection releasing IL-6 and IL-8 cytokines. CONCLUSION This study demonstrates that coculture spheroids of epithelial and stromal cells can serve as a cost-effective infection model for the SARS-CoV-2 virus. We suggest using this 3D spheroid as a drug screening platform to explore new treatments related to the cytokines released during virus infection, especially for long COVID treatment.
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Affiliation(s)
| | - Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Érica Almeida Amorim
- Gcell 3D, Rio de Janeiro, Brazil
- Laboratório de Ultraestrutura celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucio Ayres Caldas
- Laboratório de Ultraestrutura celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Núcleo Multidisciplinar de Pesquisa (Numpex-bio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiana Ávila Carneiro
- Laboratório de Ultraestrutura celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Núcleo Multidisciplinar de Pesquisa (Numpex-bio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Mauro Granjeiro
- Laboratório de Biologia de Células Eucarióticas, Duque de Caxias, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Rio de Janeiro, Brazil
- Laboratório de Pesquisa Clínica em Odontologia, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura celular Hertha Meyer, Centro de Pesquisa em Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Centro de Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leandra Santos Baptista
- Núcleo Multidisciplinar de Pesquisa (Numpex-bio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Biologia de Células Eucarióticas, Duque de Caxias, Instituto Nacional de Metrologia, Qualidade e Tecnologia, Rio de Janeiro, Brazil
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19
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Li L, Qin S, Tan H, Zhou J. LGALS3BP is a novel and potential biomarker in clear cell renal cell carcinoma. Aging (Albany NY) 2024; 16:4033-4051. [PMID: 38393692 DOI: 10.18632/aging.205578] [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: 09/18/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common solid renal tumor. Therefore, it is necessary to explore the related tumor markers. LGALS3BP (galectin 3 binding protein) is a multifunctional glycoprotein implicated in immunity and cancer. Some studies have shown that LGALS3BP promotes the occurrence and development of tumors. However, their exact role in renal tumorigenesis remains unclear. Our study used a webserver to explore the mRNA expression and clinical features of LGALS3BP in ccRCC. Survival analysis showed that patients with high LGALS3BP expression had significantly worse OS and DFS than those with low LGALS3BP expression. LGALS3BP expression is significantly related to B cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. Furthermore, we determined that LGALS3BP is significantly associated with angiogenesis, stemness and proliferation in renal cancer. Three phenotypes may be associated with a poor prognosis. Genes related to proliferation, angiogenesis and stemness were derived from a Venn diagram of FGF2. FGF2 is negatively correlated with proliferation and positively correlated with angiogenesis. Finally, we screened for drugs that may have potential therapeutic value for ccRCC. The PCR results showed that the expression of LGALS3BP in the normal cell line was lower than that in the tumor cell lines. After LGALS3BP knockdown, the proliferation of 769-P and 786-O cells decreased. The present findings show that LGALS3BP is critical for ccRCC cell proliferation and may be a potential target and biomarker for ccRCC.
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Affiliation(s)
- Lei Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, People’s Republic of China
| | - Sen Qin
- Department of Orthopedics, The First People’s Hospital of Jingzhou, Jingzhou, Hubei, People’s Republic of China
| | - Hongwei Tan
- Department of Organ Transplantation, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
| | - Jiexue Zhou
- Department of Organ Transplantation, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, People’s Republic of China
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20
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Leng L, Xu Z, Hong B, Zhao B, Tian Y, Wang C, Yang L, Zou Z, Li L, Liu K, Peng W, Liu J, An Z, Wang Y, Duan B, Hu Z, Zheng C, Zhang S, Li X, Li M, Liu Z, Bi Z, He T, Liu B, Fan H, Song C, Tong Y, Chen S. Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery. Nat Commun 2024; 15:1537. [PMID: 38378731 PMCID: PMC10879537 DOI: 10.1038/s41467-024-45690-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Cepharanthine is a secondary metabolite isolated from Stephania. It has been reported that it has anti-conronaviruses activities including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Here, we assemble three Stephania genomes (S. japonica, S. yunnanensis, and S. cepharantha), propose the cepharanthine biosynthetic pathway, and assess the antiviral potential of compounds involved in the pathway. Among the three genomes, S. japonica has a near telomere-to-telomere assembly with one remaining gap, and S. cepharantha and S. yunnanensis have chromosome-level assemblies. Following by biosynthetic gene mining and metabolomics analysis, we identify seven cepharanthine analogs that have broad-spectrum anti-coronavirus activities, including SARS-CoV-2, Guangxi pangolin-CoV (GX_P2V), swine acute diarrhoea syndrome coronavirus (SADS-CoV), and porcine epidemic diarrhea virus (PEDV). We also show that two other genera, Nelumbo and Thalictrum, can produce cepharanthine analogs, and thus have the potential for antiviral compound discovery. Results generated from this study could accelerate broad-spectrum anti-coronavirus drug discovery.
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Affiliation(s)
- Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Bixia Hong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Binbin Zhao
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Ya Tian
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Can Wang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Lulu Yang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhongmei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Lingyu Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Ke Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Wanjun Peng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Jiangning Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, 100730, China
| | - Zhoujie An
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yalin Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Chuan Zheng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Sanyin Zhang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xiaodong Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhaoyu Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zenghao Bi
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Tianxing He
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baimei Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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21
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Rao X, Qiao Z, Yang Y, Deng Y, Zhang Z, Yu X, Guo X. Unveiling Epigenetic Vulnerabilities in Triple-Negative Breast Cancer through 3D Organoid Drug Screening. Pharmaceuticals (Basel) 2024; 17:225. [PMID: 38399440 PMCID: PMC10892330 DOI: 10.3390/ph17020225] [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: 12/20/2023] [Revised: 01/16/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Triple-negative breast cancer (TNBC) poses a therapeutic challenge due to its aggressive nature and lack of targeted therapies. Epigenetic modifications contribute to TNBC tumorigenesis and drug resistance, offering potential therapeutic targets. Recent advancements in three-dimensional (3D) organoid cultures, enabling precise drug screening, hold immense promise for identifying novel compounds targeting TNBC. In this study, we established two patient-derived TNBC organoids and implemented a high-throughput drug screening system using these organoids and two TNBC cell lines. Screening a library of 169 epigenetic compounds, we found that organoid-based systems offer remarkable precision in drug response assessment compared to cell-based models. The top 30 compounds showing the highest drug sensitivity in the initial screening were further assessed in a secondary screen. Four compounds, panobinostat, pacritinib, TAK-901, and JIB-04, targeting histone deacetylase, JAK/STAT, histone demethylases, and aurora kinase pathways, respectively, exhibited potent anti-tumor activity in TNBC organoids, surpassing the effect of paclitaxel. Our study highlights the potential of these novel epigenetic drugs as effective therapeutic agents for TNBC and demonstrates the valuable role of patient-derived organoids in advancing drug discovery.
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Affiliation(s)
- Xinxin Rao
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Zhibin Qiao
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Yang Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Yun Deng
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Xiaoli Yu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
| | - Xiaomao Guo
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China; (X.R.); (Z.Q.); (Y.Y.); (Y.D.); (Z.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai 200032, China
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22
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Malyshev AV, Pavshintcev VV, Mitkin NA, Sukhanova IA, Gedzun VR, Zlobin AS, Doronin II, Babkin GA, Sawyer TK. The novel peptide LCGM-10 attenuates metabotropic glutamate receptor 5 activity and demonstrates behavioral effects in animal models. Front Behav Neurosci 2024; 18:1333258. [PMID: 38385004 PMCID: PMC10879279 DOI: 10.3389/fnbeh.2024.1333258] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
We employed a structural bioinformatics approach to develop novel peptides with predicted affinity to the binding site for negative allosteric modulators (NAMs) of metabotropic glutamate receptor 5 (mGluR5). Primary screening in zebrafish (Danio rerio) revealed a stimulatory effect of two peptides, LCGM-10 and LCGM-15. Target validation studies using calcium ion flux imaging and a luciferase reporter assay confirmed mGluR5 as the target. LCGM-10 showed greater potency than LCGM-15; it was comparable to that of the mGluR5 NAM 2-methyl-6-(phenylethynyl) pyridine (MPEP). Rodent behavioral screening in the open field and elevated plus maze revealed increased locomotor activity in both tests after acute LCGM-10 treatment, supported by further analysis of home cage spontaneous locomotor activity (SLA). The stimulating effect of a single LCGM-10 administration on SLA was evident up to 60 min after administration and was not accompanied by hypokinetic rebound observed for caffeine. According to our results, LCGM-10 has therapeutic potential to treat hypo- and dyskinesias of various etiologies. Further investigation of LCGM-10 effects in the delay discounting model of impulsive choice in rats revealed reduced trait impulsivity after single and chronic administrations, suggesting potential implication for attention deficit hyperactivity disorder, obsessive compulsive disorder, and addictions.
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23
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Lu W, Zhang J, Huang W, Zhang Z, Jia X, Wang Z, Shi L, Li C, Wolynes PG, Zheng S. DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model. Nat Commun 2024; 15:1071. [PMID: 38316797 PMCID: PMC10844226 DOI: 10.1038/s41467-024-45461-2] [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: 08/24/2023] [Accepted: 01/24/2024] [Indexed: 02/07/2024] Open
Abstract
While significant advances have been made in predicting static protein structures, the inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein function and facilitating drug discovery. Traditional docking methods, frequently used in studying protein-ligand interactions, typically treat proteins as rigid. While molecular dynamics simulations can propose appropriate protein conformations, they're computationally demanding due to rare transitions between biologically relevant equilibrium states. In this study, we present DynamicBind, a deep learning method that employs equivariant geometric diffusion networks to construct a smooth energy landscape, promoting efficient transitions between different equilibrium states. DynamicBind accurately recovers ligand-specific conformations from unbound protein structures without the need for holo-structures or extensive sampling. Remarkably, it demonstrates state-of-the-art performance in docking and virtual screening benchmarks. Our experiments reveal that DynamicBind can accommodate a wide range of large protein conformational changes and identify cryptic pockets in unseen protein targets. As a result, DynamicBind shows potential in accelerating the development of small molecules for previously undruggable targets and expanding the horizons of computational drug discovery.
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Affiliation(s)
- Wei Lu
- Galixir Technologies, 200100, Shanghai, China.
| | | | - Weifeng Huang
- School of Pharmaceutical Science, Sun Yat-sen University, 510006, Guangzhou, China
| | | | - Xiangyu Jia
- Galixir Technologies, 200100, Shanghai, China
| | - Zhenyu Wang
- Galixir Technologies, 200100, Shanghai, China
| | - Leilei Shi
- Galixir Technologies, 200100, Shanghai, China
| | - Chengtao Li
- Galixir Technologies, 200100, Shanghai, China
| | - Peter G Wolynes
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Shuangjia Zheng
- Global Institute of Future Technology, Shanghai Jiao Tong University, 200240, Shanghai, China.
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24
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Chen W, Kang Y, Sheng W, Huang Q, Cheng J, Pei S, Meng Y. A new 4-gene-based prognostic model accurately predicts breast cancer prognosis and immunotherapy response by integrating WGCNA and bioinformatics analysis. Front Immunol 2024; 15:1331841. [PMID: 38370403 PMCID: PMC10869553 DOI: 10.3389/fimmu.2024.1331841] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Background Breast cancer (BRCA) is a common malignancy in women, and its resistance to immunotherapy is a major challenge. Abnormal expression of genes is important in the occurrence and development of BRCA and may also affect the prognosis of patients. Although many BRCA prognosis model scores have been developed, they are only applicable to a limited number of disease subtypes. Our goal is to develop a new prognostic score that is more accurate and applicable to a wider range of BRCA patients. Methods BRCA patient data from The Cancer Genome Atlas database was used to identify breast cancer-related genes (BRGs). Differential expression analysis of BRGs was performed using the 'limma' package in R. Prognostic BRGs were identified using co-expression and univariate Cox analysis. A predictive model of four BRGs was established using Cox regression and the LASSO algorithm. Model performance was evaluated using K-M survival and receiver operating characteristic curve analysis. The predictive ability of the signature in immune microenvironment and immunotherapy was investigated. In vitro experiments validated POLQ function. Results Our study identified a four-BRG prognostic signature that outperformed conventional clinicopathological characteristics in predicting survival outcomes in BRCA patients. The signature effectively stratified BRCA patients into high- and low-risk groups and showed potential in predicting the response to immunotherapy. Notably, significant differences were observed in immune cell abundance between the two groups. In vitro experiments demonstrated that POLQ knockdown significantly reduced the viability, proliferation, and invasion capacity of MDA-MB-231 or HCC1806 cells. Conclusion Our 4-BRG signature has the potential as an independent biomarker for predicting prognosis and treatment response in BRCA patients, complementing existing clinicopathological characteristics.
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Affiliation(s)
- Wenlong Chen
- Department of Thyroid and Breast Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Yakun Kang
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenyi Sheng
- Department of Thyroid and Breast Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Qiyan Huang
- Department of Thyroid and Breast Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jiale Cheng
- Department of Thyroid and Breast Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - You Meng
- Department of Thyroid and Breast Surgery, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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25
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Mansouri M, Lamichhane A, Das D, Aucejo F, Tavana H, Leipzig ND. Comparison of Engineered Liver 3D Models and the Role of Oxygenation for Patient-Derived Tumor Cells and Immortalized Cell Lines Cocultured with Tumor Stroma in the Detection of Hepatotoxins. Adv Biol (Weinh) 2024; 8:e2300386. [PMID: 37845003 DOI: 10.1002/adbi.202300386] [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: 07/28/2023] [Revised: 09/25/2023] [Indexed: 10/18/2023]
Abstract
In metabolically active tumors, responses of cells to drugs are heavily influenced by oxygen availability via the surrounding vasculature alongside the extracellular matrix signaling. The objective of this study is to investigate hepatotoxicity by replicating critical features of hepatocellular carcinoma (HCC). This includes replicating 3D structures, metabolic activities, and tumor-specific markers. The internal environment of spheroids comprised of cancerous human patient-derived hepatocytes using microparticles is modulated to enhance the oxygenation state and recreate cell-extracellular matrix interactions. Furthermore, the role of hepatic stellate cells in maintaining hepatocyte survival and function is explored and hepatocytes from two cellular sources (immortalized and patient-derived) to create four formulations with and without microparticles are utilized. To investigate drug-induced changes in metabolism and apoptosis in liver cells, coculture spheroids with and without microparticles are exposed to three hepatotoxic drugs. The use of microparticles increases levels of apoptotic markers in both liver models under drug treatments. This coincides with reduced levels of anti-apoptotic proteins and increased levels of pro-apoptotic proteins. Moreover, cells from different origins undergo apoptosis through distinct apoptotic pathways in response to identical drugs. This 3D microphysiological system offers a viable tool for liver cancer research to investigate mechanisms of apoptosis under different microenvironmental conditions.
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Affiliation(s)
- Mona Mansouri
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Astha Lamichhane
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Dola Das
- Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44106, USA
| | - Federico Aucejo
- Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Hossein Tavana
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Nic D Leipzig
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, OH, 44325, USA
- Department of Biomedical Engineering, The University of Akron, Akron, OH, 44325, USA
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26
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Fung M, Armstrong JJ, Zhang R, Vinokurtseva A, Liu H, Hutnik C. Development and Verification of a Novel Three-Dimensional Aqueous Outflow Model for High-Throughput Drug Screening. Bioengineering (Basel) 2024; 11:142. [PMID: 38391628 PMCID: PMC10885921 DOI: 10.3390/bioengineering11020142] [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: 12/30/2023] [Revised: 01/20/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Distal outflow bleb-forming procedures in ophthalmic surgery expose subconjunctival tissue to inflammatory cytokines present in the aqueous humor, resulting in impaired outflow and, consequently, increased intraocular pressure. Clinically, this manifests as an increased risk of surgical failure often necessitating revision. This study (1) introduces a novel high-throughput screening platform for testing potential anti-fibrotic compounds and (2) assesses the clinical viability of modulating the transforming growth factor beta-SMAD2/3 pathway as a key contributor to post-operative outflow reduction, using the signal transduction inhibitor verteporfin. Human Tenon's capsule fibroblasts (HTCFs) were cultured within a 3D collagen matrix in a microfluidic system modelling aqueous humor drainage. The perfusate was augmented with transforming growth factor beta 1 (TGFβ1), and afferent pressure to the tissue-mimetic was continuously monitored to detect treatment-related pressure elevations. Co-treatment with verteporfin was employed to evaluate its capacity to counteract TGFβ1 induced pressure changes. Immunofluorescent studies were conducted on the tissue-mimetic to corroborate the pressure data with cellular changes. Introduction of TGFβ1 induced treatment-related afferent pressure increase in the tissue-mimetic. HTCFs treated with TGFβ1 displayed visibly enlarged cytoskeletons and stress fiber formation, consistent with myofibroblast transformation. Importantly, verteporfin effectively mitigated these changes, reducing both afferent pressure increases and cytoskeletal alterations. In summary, this study models the pathological filtration bleb response to TGFβ1, while demonstrating verteporfin's effectiveness in ameliorating both functional and cellular changes caused by TGFβ1. These demonstrate modulation of the aforementioned pathway as a potential avenue for addressing post-operative changes and reductions in filtration bleb outflow capacity. Furthermore, the establishment of a high-throughput screening platform offers a valuable pre-animal testing tool for investigating potential compounds to facilitate surgical wound healing.
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Affiliation(s)
- Matthew Fung
- Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - James J Armstrong
- Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
- Department of Ophthalmology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - Richard Zhang
- Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - Anastasiya Vinokurtseva
- Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
- Department of Ophthalmology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - Hong Liu
- Department of Ophthalmology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
| | - Cindy Hutnik
- Department of Ophthalmology, Schulich School of Medicine & Dentistry, Western University, London, ON N6A 3K7, Canada
- Department of Ophthalmology, Ivey Eye Institute, St. Joseph's Health Center, London, ON N6A 4V2, Canada
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27
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Romov IM, Nowzari RA, Page CP, Benes MR, Borzok MA, Wright NT. Prevention of Protease-Induced Degradation of Desmoplakin via Small Molecule Binding. J Pers Med 2024; 14:163. [PMID: 38392596 PMCID: PMC10890502 DOI: 10.3390/jpm14020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Desmoplakin (DSP) is a large (~260 kDa) protein found in the desmosome, the subcellular structure that links the intermediate filament network of one cell to its neighbor. A mutation "hot-spot" within the NH2-terminal of the DSP protein (residues 299-515) is associated with arrhythmogenic cardiomyopathy. In a subset of DSP variants, disease is linked to calpain hypersensitivity. Previous studies show that calpain hypersensitivity can be corrected in vitro through the addition of a bulky residue neighboring the cleavage site, suggesting that physically blocking calpain accessibility is a viable strategy to restore DSP levels. Here, we aim to find drug-like molecules that also block calpain-dependent degradation of DSP. To do this, we screened ~2500 small molecules to identify compounds that specifically rescue DSP protein levels in the presence of proteases. We find that several molecules, including sodium dodecyl sulfate, palmitoylethanolamide, GW0742, salirasib, eprosarten mesylate, and GSK1838705A prevent wildtype and disease-variant-carrying DSP protein degradation in the presence of both trypsin and calpain without altering protease function. Computational screenings did not predict which molecules would protect DSP, likely due to a lack of specific DSP-drug interactions. Molecular dynamic simulations of DSP-drug complexes suggest that some long hydrophobic molecules can bind in a shallow hydrophobic groove that runs alongside the protease cleavage site. Identification of these compounds lays the groundwork for pharmacological treatment for individuals harboring these hypersensitive DSP variants.
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Affiliation(s)
- Isabel M Romov
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Roujon A Nowzari
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Clay P Page
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Madeleine R Benes
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - Maegen A Borzok
- Department of Biochemistry, Chemistry, Engineering and Physics, Commonwealth University of Pennsylvania, Mansfield, PA 16933, USA
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
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28
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Lin K, Chang YC, Billmann M, Ward HN, Le K, Hassan AZ, Bhojoo U, Chan K, Costanzo M, Moffat J, Boone C, Bielinsky AK, Myers CL. A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. Sci Rep 2024; 14:2508. [PMID: 38291084 PMCID: PMC10828508 DOI: 10.1038/s41598-024-51735-y] [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: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds' known modes-of-action (MoA) were enriched among the compounds' CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.
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Affiliation(s)
- Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Khoi Le
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Arshia Z Hassan
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Urvi Bhojoo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Katherine Chan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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Zanardi A, Nardini I, Raia S, Conti A, Ferrini B, D'Adamo P, Gilberti E, DePalma G, Belloli S, Monterisi C, Coliva A, Rainone P, Moresco RM, Mori F, Zurlo G, Scali C, Natali L, Pancanti A, Giovacchini P, Magherini G, Tovani G, Salvini L, Cicaloni V, Tinti C, Tinti L, Lana D, Magni G, Giovannini MG, Gringeri A, Caricasole A, Alessio M. New orphan disease therapies from the proteome of industrial plasma processing waste- a treatment for aceruloplasminemia. Commun Biol 2024; 7:140. [PMID: 38291108 PMCID: PMC10828504 DOI: 10.1038/s42003-024-05820-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
Plasma-derived therapeutic proteins are produced through an industrial fractionation process where proteins are purified from individual intermediates, some of which remain unused and are discarded. Relatively few plasma-derived proteins are exploited clinically, with most of available plasma being directed towards the manufacture of immunoglobulin and albumin. Although the plasma proteome provides opportunities to develop novel protein replacement therapies, particularly for rare diseases, the high cost of plasma together with small patient populations impact negatively on the development of plasma-derived orphan drugs. Enabling therapeutics development from unused plasma fractionation intermediates would therefore constitute a substantial innovation. To this objective, we characterized the proteome of unused plasma fractionation intermediates and prioritized proteins for their potential as new candidate therapies for human disease. We selected ceruloplasmin, a plasma ferroxidase, as a potential therapy for aceruloplasminemia, an adult-onset ultra-rare neurological disease caused by iron accumulation as a result of ceruloplasmin mutations. Intraperitoneally administered ceruloplasmin, purified from an unused plasma fractionation intermediate, was able to prevent neurological, hepatic and hematological phenotypes in ceruloplasmin-deficient mice. These data demonstrate the feasibility of transforming industrial waste plasma fraction into a raw material for manufacturing of new candidate proteins for replacement therapies, optimizing plasma use and reducing waste generation.
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Affiliation(s)
- Alan Zanardi
- Proteome Biochemistry, COSR-Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ilaria Nardini
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Sara Raia
- Proteome Biochemistry, COSR-Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Antonio Conti
- Proteome Biochemistry, COSR-Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Barbara Ferrini
- Proteome Biochemistry, COSR-Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Patrizia D'Adamo
- Mouse Behavior Facility, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Enrica Gilberti
- Unit of Occupational Health and Industrial Hygiene, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Giuseppe DePalma
- Unit of Occupational Health and Industrial Hygiene, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
| | - Sara Belloli
- Nuclear Medicine and PET Cyclotron Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Institute of Molecular Bioimaging and Physiology-IBFM, CNR, Segrate, Italy
| | - Cristina Monterisi
- Nuclear Medicine and PET Cyclotron Unit, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Angela Coliva
- Nuclear Medicine and PET Cyclotron Unit, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Paolo Rainone
- Nuclear Medicine and PET Cyclotron Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Institute of Molecular Bioimaging and Physiology-IBFM, CNR, Segrate, Italy
- Medicine and Surgery Department, University of Milano - Bicocca, Monza, Italy
| | - Rosa Maria Moresco
- Nuclear Medicine and PET Cyclotron Unit, IRCCS Ospedale San Raffaele, Milano, Italy
- Institute of Molecular Bioimaging and Physiology-IBFM, CNR, Segrate, Italy
- Medicine and Surgery Department, University of Milano - Bicocca, Monza, Italy
| | - Filippo Mori
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Giada Zurlo
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Carla Scali
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Letizia Natali
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Annalisa Pancanti
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | | | - Giulio Magherini
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | - Greta Tovani
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy
| | | | | | | | - Laura Tinti
- Toscana Life Sciences Foundation, Siena, Italy
| | - Daniele Lana
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Firenze, Italy
| | - Giada Magni
- Institute of Applied Physics "Nello Carrara", National Research Council (IFAC-CNR), Sesto Fiorentino, Italy
| | - Maria Grazia Giovannini
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Firenze, Italy
| | | | - Andrea Caricasole
- Research and Innovation, Kedrion S.p.A., Loc, Bolognana, Gallicano, Italy.
| | - Massimo Alessio
- Proteome Biochemistry, COSR-Centre for Omics Sciences, IRCCS Ospedale San Raffaele, Milano, Italy.
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30
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Pina PSS, Jang Y, Emerick C, Scarini JF, Sousa SCOM, Squarize CH, Castilho RM. Novel Epigenetic Modifiers of Histones Presenting Potent Inhibitory Effects on Adenoid Cystic Carcinoma Stemness and Invasive Properties. Int J Mol Sci 2024; 25:1646. [PMID: 38338924 PMCID: PMC10855771 DOI: 10.3390/ijms25031646] [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: 12/06/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Adenoid cystic carcinoma (ACC) is a rare neoplasm known for its indolent clinical course, risk of perineural invasion, and late onset of distant metastasis. Due to the scarcity of samples and the tumor's rarity, progress in developing effective treatments has been historically limited. To tackle this issue, a high-throughput screening of epigenetic drugs was conducted to identify compounds capable of disrupting the invasive properties of the tumor and its cancer stem cells (CSCs). ACC cells were screened for changes in tumor viability, chromatin decondensation, Snail inhibition along tumor migration, and disruption of cancer stem cells. Seven compounds showed potential clinical interest, and further validation showed that Scriptaid emerged as a promising candidate for treating ACC invasion. Scriptaid demonstrated a favorable cellular toxicity index, effectively inhibited Snail expression, induced hyperacetylation of histone, reduced cell migration, and effectively disrupted tumorspheres. Additionally, LMK235 displayed encouraging results in four out of five validation assays, further highlighting its potential in combating tumor invasion in ACC. By targeting the invasive properties of the tumor and CSCs, Scriptaid and LMK235 hold promise as potential treatments for ACC, with the potential to improve patient outcomes and pave the way for further research in this critical area.
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Affiliation(s)
- Paulo S. S. Pina
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
- Department of Stomatology, School of Dentistry, University of São Paulo, Sao Paulo 05508-270, Brazil;
| | - Yeejin Jang
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
| | - Carolina Emerick
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Brazil
| | - João Figueira Scarini
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Brazil
| | - Suzana C. O. M. Sousa
- Department of Stomatology, School of Dentistry, University of São Paulo, Sao Paulo 05508-270, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA; (P.S.S.P.); (Y.J.); (C.E.); (J.F.S.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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31
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Papp D, Korcsmaros T, Hautefort I. Revolutionising immune research with organoid-based co-culture and chip systems. Clin Exp Immunol 2024:uxae004. [PMID: 38280212 DOI: 10.1093/cei/uxae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Indexed: 01/29/2024] Open
Abstract
The intertwined interactions various immune cells have with epithelial cells in our body require sophisticated experimental approaches to be studied. Due to the limitations of immortalised cell lines and animal models, there is an increasing demand for human in vitro model systems to investigate the microenvironment of immune cells in normal and in pathological conditions. Organoids, which are self-renewing, 3D cellular structures that are derived from stem cells, have started to provide gap-filling tissue modelling solutions. In this review, we first demonstrate with some of the available examples how organoid-based immune cell co-culture experiments can advance disease modelling of cancer, inflammatory bowel disease and tissue regeneration. Then, we argue that to achieve both complexity and scale, organ-on-chip models combined with cutting-edge microfluidics-based technologies can provide more precise manipulation and readouts. Finally, we discuss how genome editing techniques and the use of patient-derived organoids and immune cells can improve disease modelling and facilitate precision medicine. To achieve maximum impact and efficiency, these efforts should be supported by novel infrastructures such as organoid biobanks, organoid facilities, as well as drug screening and host-microbe interaction testing platforms. All these together or in combination can allow researchers to shed more detailed, and often patient-specific, light on the crosstalk between immune cells and epithelial cells in health and disease.
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Affiliation(s)
- D Papp
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- NIHR Imperial BRC Organoid Facility, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - T Korcsmaros
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- NIHR Imperial BRC Organoid Facility, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
| | - I Hautefort
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- NIHR Imperial BRC Organoid Facility, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, United Kingdom
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32
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Wang C, Sun M, Shao C, Schlicker L, Zhuo Y, Harim Y, Peng T, Tian W, Stöffler N, Schneider M, Helm D, Chu Y, Fu B, Jin X, Mallm JP, Mall M, Wu Y, Schulze A, Liu HK. A multidimensional atlas of human glioblastoma-like organoids reveals highly coordinated molecular networks and effective drugs. NPJ Precis Oncol 2024; 8:19. [PMID: 38273014 PMCID: PMC10811239 DOI: 10.1038/s41698-024-00500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
Recent advances in the genomics of glioblastoma (GBM) led to the introduction of molecular neuropathology but failed to translate into treatment improvement. This is largely attributed to the genetic and phenotypic heterogeneity of GBM, which are considered the major obstacle to GBM therapy. Here, we use advanced human GBM-like organoid (LEGO: Laboratory Engineered Glioblastoma-like Organoid) models and provide an unprecedented comprehensive characterization of LEGO models using single-cell transcriptome, DNA methylome, metabolome, lipidome, proteome, and phospho-proteome analysis. We discovered that genetic heterogeneity dictates functional heterogeneity across molecular layers and demonstrates that NF1 mutation drives mesenchymal signature. Most importantly, we found that glycerol lipid reprogramming is a hallmark of GBM, and several targets and drugs were discovered along this line. We also provide a genotype-based drug reference map using LEGO-based drug screen. This study provides new human GBM models and a research path toward effective GBM therapy.
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Affiliation(s)
- Changwen Wang
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
- Faculty of Medicine, Heidelberg University, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany.
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, China.
| | - Meng Sun
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Chunxuan Shao
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Lisa Schlicker
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Yue Zhuo
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Yassin Harim
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Tianping Peng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Weili Tian
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Nadja Stöffler
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Youjun Chu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Beibei Fu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, 200025, Shanghai, China
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Yonghe Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Almut Schulze
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
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Linn AK, Manopwisedjaroen S, Kanjanasirirat P, Borwornpinyo S, Hongeng S, Phanthong P, Thitithanyanont A. Unveiling the Antiviral Properties of Panduratin A through SARS-CoV-2 Infection Modeling in Cardiomyocytes. Int J Mol Sci 2024; 25:1427. [PMID: 38338708 PMCID: PMC10855687 DOI: 10.3390/ijms25031427] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Establishing a drug-screening platform is critical for the discovery of potential antiviral agents against SARS-CoV-2. In this study, we developed a platform based on human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to investigate SARS-CoV-2 infectivity, with the aim of evaluating potential antiviral agents for anti-SARS-CoV-2 activity and cardiotoxicity. Cultured myocytes of iPSC-CMs and immortalized human cardiomyocyte cell line (AC-16) were primarily characterized for the expression of cardiac markers and host receptors of SARS-CoV-2. An infectivity model for the wild-type SARS-CoV-2 strain was then established. Infection modeling involved inoculating cells with SARS-CoV-2 at varying multiplicities of infection (MOIs) and then quantifying infection using immunofluorescence and plaque assays. Only iPSC-CMs, not AC16 cells, expressed angiotensin-converting enzyme 2 (ACE-2), and quantitative assays confirmed the dose-dependent infection of iPSC-CMs by SARS-CoV-2, unlike the uninfectable AC16 cells lacking the expression of ACE2. Cytotoxicity was evaluated using MTT assays across a concentration range. An assessment of the plant-derived compound panduratin A (panA) showed cytotoxicity at higher doses (50% cytotoxic concentration (CC50) 10.09 μM) but promising antiviral activity against SARS-CoV-2 (50% inhibition concentration (IC50) 0.8-1.6 μM), suppressing infection at concentrations 10 times lower than its CC50. Plaque assays also showed decreased viral production following panA treatment. Overall, by modeling cardiac-specific infectivity, this iPSC-cardiomyocyte platform enables the reliable quantitative screening of compound cytotoxicity alongside antiviral efficacy. By combining disease pathogenesis and pharmacology, this system can facilitate the evaluation of potential novel therapeutics, such as panA, for drug discovery applications.
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Affiliation(s)
- Aung Khine Linn
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (A.K.L.); (S.B.)
| | | | | | - Suparerk Borwornpinyo
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (A.K.L.); (S.B.)
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Phetcharat Phanthong
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
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34
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Mady OY, Dewedar O, Abdine N, Zaytoon H, Haggag Y. Bioadhesive behaviors of HPMC E5: comparative analysis of various techniques, histological and human radiological evidence. Sci Rep 2024; 14:1840. [PMID: 38246953 PMCID: PMC10800332 DOI: 10.1038/s41598-024-52144-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: 08/31/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024] Open
Abstract
Enhancing drug residence duration within the stomach offers distinct advantages for both localized and systemic effects. Numerous strategies have been proposed to extend drug residence time, with mucoadhesive polymers being a notable avenue. In this context, hydroxypropyl methylcellulose E5 has been employed as both a binding agent for granulating contrast metal powder and a mucoadhesive polymer, spanning various concentrations. The in vitro bioadhesion strength of the formulated tablets was gauged against the stomach lining of rabbits, for the quantification of bioadhesive forces. The temporal aspect of bioadhesion was evaluated through two approaches: one centered on gastric fluid dynamics and another proffered by the researchers, focusing on gastric wall kinetics. The results divulged a decline in bioadhesion force concomitant with high polymer concentrations. Histological examination of stained stomach sections revealed mucosal perturbations within the rabbit stomach. These disruptions exhibited an escalating trend in conjunction with elevated polymer concentrations, culminating in extensive disturbance at a 7.5% polymer concentration. The outcomes unveiled a direct relationship between polymer concentration increments and extended contact time. Subsequent radiological tracking of contrast metal behavior within a mature human stomach indicated a residence time of 6 h due to the entrapment of displaced components at disparate locations.
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Affiliation(s)
- Omar Y Mady
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Omar Dewedar
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Tanta University, Tanta, Egypt.
| | - Noorelhoda Abdine
- Department of Histology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Hossam Zaytoon
- Department of Radiology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Yusuf Haggag
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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35
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Quradha MM, Duru ME, Kucukaydin S, Tamfu AN, Iqbal M, Bibi H, Khan R, Ceylan O. Comparative assessment of phenolic composition profile and biological activities of green extract and conventional extracts of Salvia sclarea. Sci Rep 2024; 14:1885. [PMID: 38253648 PMCID: PMC10803343 DOI: 10.1038/s41598-024-51661-z] [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: 06/19/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In recent years, there have been an attempt to develop safe and environmental friendly solvents to replace conventional solvents, and use for extraction bioactive compounds from natural sources. A current investigation involved the preparation of green, methanolic, and ultrasonic extracts of S. sclarea, and compared their phenolic profiling using HPLC-DAD, antibacterial, antioxidant, and enzyme inhibition activities. The HPLC-DAD analysis revealed that Rosmarinic acid was the main content in all extracts, with Ellagic acid only present in the green extract. The green extract exhibited superior anti-biofilm activity against S. Aureus and E. Faecalis compared to the other extracts at MIC concentration. Furthermore, the green extract also displayed the highest inhibition of swarming motility in P. Aeruginosa with inhibition range 68.0 ± 2.1 (MIC) to 19.5 ± 0.6 (MIC/4). and better enzyme inhibitory activity against BChE (with IC50 = 131.6 ± 0.98 µg/mL) and AChE (with inhibition 47.00 ± 1.50%) compared to the other extracts; while, the ultrasonic extract showed strong inhibition of violacein production by C. Violaceum with a inhibition range 05.5 ± 0.1 (MIC/32) to 100 ± 0.00 (MIC), followed by the green extract with a inhibition range 15.0 ± 0.5 (MIC/8) to 100 ± 0.00 (MIC), additionally, the ultrasonic and methanoic extracts showed significant activity against urease enzyme with (IC50 = 171.6 ± 0.95 µg/mL and IC5 0 = 187.5 ± 1.32 µg/mL) respectively. Both the green and methanolic extracts showed considerable antioxidant activities, as β-carotene-linoleic acid (IC50 = 5.61 ± 0.47 µg/mL and 5.37 ± 0.27 µg/mL), DPPH· (IC50 = 19.20 ± 0.70 µg/mL and 16.31 ± 0.23 µg/mL), ABTS·+(IC50 = 8.64 ± 0.63 µg/mL and 6.50 ± 0.45 µg/mL) and CUPRAC (A0.5 = 17.22 ± 0.36 µg/mL and 12.28 ± 0.12 µg/mL) respectively, likewise the green extract performing better in metal chelating compared to the other extracts. The green extraction is reported as a cost effective and solvent free method for extracting natural products that produces compounds free of toxic chemicals. This could be the method to be used in the industries as a renewable method.
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Affiliation(s)
- Mohammed Mansour Quradha
- College of Education, Seiyun University, Seiyun, Yemen.
- Pharmacy Department, Medical Sciences, Aljanad University for Science and Technology, Taiz, Yemen.
| | - Mehmet Emin Duru
- Department of Chemistry, Faculty of Science, Mugla Sitki Kocman University, Mugla, 48000, Turkey
| | - Selcuk Kucukaydin
- Department of Medical Services and Techniques, Koycegiz Vocational School of Health Services, Mugla Sıtkı Kocman University, Koycegiz/Mugla, Turkey
| | - Alfred Ngenge Tamfu
- Department of Chemical Engineering, School of Chemical Engineering and Mineral Industries, University of Ngaoundere, 454, Ngaoundere, Cameroon
| | - Mudassar Iqbal
- Department of Agricultural Chemistry and Biochemistry, The University of Agriculture, Peshawar, 25000, Pakistan
| | - Hamida Bibi
- Department of Environmental Sciences, Abdul Wali Khan University, Mardan, Pakistan
| | - Rasool Khan
- Institute of Chemical Sciences, University of Peshawar, Peshawar, 25120, Pakistan
| | - Ozgur Ceylan
- Food Quality Control and Analysis Program, Ula Ali Kocman Vocational School, Mugla Sitki Kocman University, Ula Mugla, 48147, Turkey
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Yoon S, Kilicarslan You D, Jeong U, Lee M, Kim E, Jeon TJ, Kim SM. Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations. Biosensors (Basel) 2024; 14:55. [PMID: 38275308 PMCID: PMC10813408 DOI: 10.3390/bios14010055] [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: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.
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Affiliation(s)
- Sunhee Yoon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Dilara Kilicarslan You
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Uiechan Jeong
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Mina Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Eunhye Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
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Muzzioli R, Gallo A. The Interaction and Effect of a Small MitoBlock Library as Inhibitor of ALR Protein-Protein Interaction Pathway. Int J Mol Sci 2024; 25:1174. [PMID: 38256258 PMCID: PMC10816046 DOI: 10.3390/ijms25021174] [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: 12/13/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
MIA40 and ALR of the MIA pathway mediate the import of protein precursors that form disulfides into the mitochondrial intermembrane space. This import pathway is suggested to be a linear pathway in which MIA40 first binds to the precursor via a disulfide linkage and oxidizes it. Subsequently, ALR re-oxidizes MIA40 and then ALR transfers electrons to terminal electron acceptors. However, the precise mechanism by which ALR and MIA40 coordinate translocation is unknown. With a collection of small molecule modulators (MB-5 to MB-9 and MB-13) that inhibit ALR activity, we characterized the import mechanism in mitochondria. NMR studies show that most of the compounds bind to a similar region in ALR. Mechanistic studies with small molecules demonstrate that treatment with compound MB-6 locks the precursor in a state bound to MIA40, blocking re-oxidation of MIA40 by ALR. Thus, small molecules that target a similar region in ALR alter the dynamics of the MIA import pathway differently, resulting in a set of probes that are useful for studying the catalysis of the redox-regulated import pathway in model systems.
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Finlay D, Murad R, Hong K, Lee J, Pang AWC, Lai CY, Clifford B, Burian C, Mason J, Hastie AR, Yin J, Vuori K. Detection of Genomic Structural Variations Associated with Drug Sensitivity and Resistance in Acute Leukemia. Cancers (Basel) 2024; 16:418. [PMID: 38254907 PMCID: PMC10814465 DOI: 10.3390/cancers16020418] [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: 11/20/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Acute leukemia is a particularly problematic collection of hematological cancers, and, while somewhat rare, the survival rate of patients is typically abysmal without bone marrow transplantation. Furthermore, traditional chemotherapies used as standard-of-care for patients cause significant side effects. Understanding the evolution of leukemia to identify novel targets and, therefore, drug treatment regimens is a significant medical need. Genomic rearrangements and other structural variations (SVs) have long been known to be causative and pathogenic in multiple types of cancer, including leukemia. These SVs may be involved in cancer initiation, progression, clonal evolution, and drug resistance, and a better understanding of SVs from individual patients may help guide therapeutic options. Here, we show the utilization of optical genome mapping (OGM) to detect known and novel SVs in the samples of patients with leukemia. Importantly, this technology provides an unprecedented level of granularity and quantitation unavailable to other current techniques and allows for the unbiased detection of novel SVs, which may be relevant to disease pathogenesis and/or drug resistance. Coupled with the chemosensitivities of these samples to FDA-approved oncology drugs, we show how an impartial integrative analysis of these diverse datasets can be used to associate the detected genomic rearrangements with multiple drug sensitivity profiles. Indeed, an insertion in the gene MUSK is shown to be associated with increased sensitivity to the clinically relevant agent Idarubicin, while partial tandem duplication events in the KMT2A gene are related to the efficacy of another frontline treatment, Cytarabine.
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Affiliation(s)
- Darren Finlay
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Rabi Murad
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Karl Hong
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | - Joyce Lee
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | - Chi-Yu Lai
- Bionano Genomics Inc., San Diego, CA 92121, USA
| | | | | | - James Mason
- Scripps MD Anderson, La Jolla, CA 92037, USA
| | | | - Jun Yin
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
| | - Kristiina Vuori
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; (R.M.)
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Nishiguchi G, Mascibroda LG, Young SM, Caine EA, Abdelhamed S, Kooijman JJ, Miller DJ, Das S, McGowan K, Mayasundari A, Shi Z, Barajas JM, Hiltenbrand R, Aggarwal A, Chang Y, Mishra V, Narina S, Thomas M, Loughran AJ, Kalathur R, Yu K, Zhou S, Wang X, High AA, Peng J, Pruett-Miller SM, Daniels DL, Urh M, Shelat AA, Mullighan CG, Riching KM, Zaman GJR, Fischer M, Klco JM, Rankovic Z. Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines. Nat Commun 2024; 15:482. [PMID: 38228616 PMCID: PMC10791743 DOI: 10.1038/s41467-024-44698-1] [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: 05/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.
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Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lauren G Mascibroda
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sarah M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | | | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhe Shi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Juan M Barajas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anup Aggarwal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Melvin Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Memphis, TN, 38105, USA
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Guido J R Zaman
- Oncolines B.V., Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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Brooks A, Zhang Y, Chen J, Zhao CX. Cancer Metastasis-on-a-Chip for Modeling Metastatic Cascade and Drug Screening. Adv Healthc Mater 2024:e2302436. [PMID: 38224141 DOI: 10.1002/adhm.202302436] [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: 07/28/2023] [Revised: 01/06/2024] [Indexed: 01/16/2024]
Abstract
Microfluidic chips are valuable tools for studying intricate cellular and cell-microenvironment interactions. Traditional in vitro cancer models lack accuracy in mimicking the complexities of in vivo tumor microenvironment. However, cancer-metastasis-on-a-chip (CMoC) models combine the advantages of 3D cultures and microfluidic technology, serving as powerful platforms for exploring cancer mechanisms and facilitating drug screening. These chips are able to compartmentalize the metastatic cascade, deepening the understanding of its underlying mechanisms. This article provides an overview of current CMoC models, focusing on distinctive models that simulate invasion, intravasation, circulation, extravasation, and colonization, and their applications in drug screening. Furthermore, challenges faced by CMoC and microfluidic technologies are discussed, while exploring promising future directions in cancer research. The ongoing development and integration of these models into cancer studies are expected to drive transformative advancements in the field.
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Affiliation(s)
- Anastasia Brooks
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Yali Zhang
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Jiezhong Chen
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
| | - Chun-Xia Zhao
- School of Chemical Engineering, University of Adelaide, Adelaide, 5005, Australia
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41
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Geng Y, Liu Y, Wang M, Dong X, Sun X, Luo Y, Sun X. Identification and validation of platelet-related diagnostic markers and potential drug screening in ischemic stroke by integrating comprehensive bioinformatics analysis and machine learning. Front Immunol 2024; 14:1320475. [PMID: 38268925 PMCID: PMC10806171 DOI: 10.3389/fimmu.2023.1320475] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/18/2023] [Indexed: 01/26/2024] Open
Abstract
Background Ischemic stroke (IS), caused by blood and oxygen deprivation due to cerebral thrombosis, has links to activated and aggregated platelets. Discovering platelet-related biomarkers, developing diagnostic models, and screening antiplatelet drugs are crucial for IS diagnosis and treatment. Methods and results Combining and normalizing GSE16561 and GSE22255 datasets identified 1,753 upregulated and 1,187 downregulated genes. Fifty-one genes in the platelet-related module were isolated using weighted gene co-expression network analysis (WGCNA) and other analyses, including 50 upregulated and one downregulated gene. Subsequent enrichment and network analyses resulted in 25 platelet-associated genes and six diagnostic markers for a risk assessment model. This model's area under the ROC curve outperformed single genes, and in the peripheral blood of the high-risk group, immune infiltration indicated a higher proportion of CD4, resting CD4 memory, and activated CD4 memory T cells, along with a lower proportion of CD8 T cells in comparison to the low-risk group. Utilizing the gene expression matrix and the CMap database, we identified two potential drugs for IS. Finally, a rat MACO/R model was used to validate the diagnostic markers' expression and the drugs' predicted anticoagulant effects. Conclusion We identified six IS platelet-related biomarkers (APP, THBS1, F13A1, SRC, PPBP, and VCL) for a robust diagnostic model. The drugs alpha-linolenic acid and ciprofibrate have potential antiplatelet effects in IS. This study advances early IS diagnosis and treatment.
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Affiliation(s)
- Yifei Geng
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
| | - Yuchen Liu
- Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
- School of Clinical Science, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China
| | - Min Wang
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
| | - Xi Dong
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
| | - Xiao Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
| | - Yun Luo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing Key Laboratory of Innovative Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Beijing, China
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Suleman M, Ahmad T, shah K, Albekairi NA, Alshammari A, Khan A, Wei DQ, Yassine HM, Crovella S. Exploring the natural products chemical space to abrogate the F3L-dsRNA interface of monkeypox virus to enhance the immune responses using molecular screening and free energy calculations. Front Pharmacol 2024; 14:1328308. [PMID: 38269277 PMCID: PMC10805857 DOI: 10.3389/fphar.2023.1328308] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/19/2023] [Indexed: 01/26/2024] Open
Abstract
Amid the ongoing monkeypox outbreak, there is an urgent need for the rapid development of effective therapeutic interventions capable of countering the immune evasion mechanisms employed by the monkeypox virus (MPXV). The evasion strategy involves the binding of the F3L protein to dsRNA, resulting in diminished interferon (IFN) production. Consequently, our current research focuses on utilizing virtual drug screening techniques to target the RNA binding domain of the F3L protein. Out of the 954 compounds within the South African natural compound database, only four demonstrated notable docking scores: -6.55, -6.47, -6.37, and -6.35 kcal/mol. The dissociation constant (KD) analysis revealed a stronger binding affinity of the top hits 1-4 (-5.34, -5.32, -5.29, and -5.36 kcal/mol) with the F3L in the MPXV. All-atom simulations of the top-ranked hits 1 to 4 consistently exhibited stable dynamics, suggesting their potential to interact effectively with interface residues. This was further substantiated through analyses of parameters such as radius of gyration (Rg), Root Mean Square Fluctuation, and hydrogen bonding. Cumulative assessments of binding free energy confirmed the top-performing candidates among all the compounds, with values of -35.90, -52.74, -28.17, and -32.11 kcal/mol for top hits 1-4, respectively. These results indicate that compounds top hit 1-4 could hold significant promise for advancing innovative drug therapies, suggesting their suitability for both in vivo and in vitro experiments.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Tanveer Ahmad
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Khadim shah
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
- College of Health Sciences-QU Health, Qatar University, Doha, Qatar
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar
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Zhang J, Li L. Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Radix Astragali against hypopharyngeal carcinoma. Sci Rep 2024; 14:516. [PMID: 38177197 PMCID: PMC10767094 DOI: 10.1038/s41598-023-50605-3] [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: 05/03/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
To explore the anti-tumor effects of Radix Astragali on hypopharyngeal carcinoma and its mechanism. We have bioinformatically analyzed the potential targets of Radix Astragali and predicted the molecular mechanism of Radix Astragali treating of hypopharyngeal carcinoma. The binding process of the hub targets that could prolong the survival time of hypopharyngeal cancer patients with Radix Astragali was simulated by molecular docking. The results showed that 17 out of 36 hub targets could effectively improve the 5-year survival rate of hypopharyngeal cancer patients. Radix Astragali acts on hypopharyngeal carcinoma by regulating a signaling network formed by hub targets connecting multiple signaling pathways and is expected to become a drug for treating and prolonging hypopharyngeal carcinoma patients' survival time.
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Affiliation(s)
- Jianing Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Lianhe Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China.
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Senthil R, Archunan G, Vithya D, Saravanan KM. Hexadecanoic acid analogs as potential CviR-mediated quorum sensing inhibitors in Chromobacterium violaceum: an in silico study. J Biomol Struct Dyn 2024:1-10. [PMID: 38165661 DOI: 10.1080/07391102.2023.2299945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
Chromobacterium violaceum is a Gram-negative, rod-shaped and opportunistic human pathogen. C. violaceum is resistant to various antibiotics due to the production of quorum sensing (QS)-controlled virulence factor and biofilm formation. Hence, we need to find alternative strategies to overcome the antimicrobial resistance and biofilm formation in Gram-negative bacteria. QS is a mechanism in which bacteria's ability to regulate the virulence factors and biofilm formations leads to disease progression. Previously, hexadecanoic acid was identified as a CviR-mediated quorum-sensing inhibitor. In this study, we aimed to discover potential analogs of hexadecanoic acid as a CviR-mediated quorum-sensing inhibitor against C. violaceum by using ADME/T prediction, density functional theory, molecular docking, molecular dynamics and free energy binding calculations. ADME/T properties predicted for analogs were acceptable for human oral absorption and feasibility. The highest occupied molecular orbitals and lowest unoccupied molecular orbitals gap energies predicted and found oleic acid with -0.3748 energies. Docosatrienoic acid exhibited the highest binding affinity -8.15 Kcal/mol and strong and stable interactions with the amino acid residues on the active site of the CviR protein. These compounds on MD simulations for 100 ns show strong hydrogen-bonding interactions with the protein and remain stable inside the active site. Our results suggest hexadecanoic acid analogs could serve as anti-QS and anti-biofilm molecules for treating C. violaceum infections. However, further validation and investigation of these inhibitors against CviR are needed to claim their candidacy for clinical trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Renganathan Senthil
- Department of Bioinformatics, School of Lifesciences, Vel's Institute of Science, Technology and Advanced Studies, Pallavaram, Chennai, Tamil Nadu, India
- Lysine Biotech Private Limited, Taramani, Chennai, Tamil Nadu, India
| | - Govindaraju Archunan
- Dean-Research, Maruthupandiyar College (Affiliated to Bharathidasan University), Thanjavur, Tamil Nadu, India
| | - Dharmaraj Vithya
- Department of Biotechnology, Dhanalakshmi Srinivasan College of Arts and Science for Women (Affiliated to Bharathidasan University), Perambalur, Tamil Nadu, India
| | - Konda Mani Saravanan
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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45
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Laiolo J, Graikioti DG, Barbieri CL, Joray MB, Antoniou AI, Vera DMA, Athanassopoulos CM, Carpinella MC. Novel betulin derivatives as multidrug reversal agents targeting P-glycoprotein. Sci Rep 2024; 14:70. [PMID: 38167542 PMCID: PMC10762177 DOI: 10.1038/s41598-023-49939-9] [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: 05/01/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Chemotherapy is a powerful means of cancer treatment but its efficacy is compromised by the emergence of multidrug resistance (MDR), mainly linked to the efflux transporter ABCB1/P-glycoprotein (P-gp). Based on the chemical structure of betulin, identified in our previous work as an effective modulator of the P-gp function, a series of analogs were designed, synthesized and evaluated as a source of novel inhibitors. Compounds 6g and 6i inhibited rhodamine 123 efflux in the P-gp overexpressed leukemia cells, K562/Dox, at concentrations of 0.19 µM and 0.39 µM, respectively, and increased the intracellular accumulation of doxorubicin at the submicromolar concentration of 0.098 µM. Compounds 6g and 6i were able to restore the sensitivity of K562/Dox to Dox at 0.024 µM and 0.19 µM, respectively. Structure-activity relationship analysis and molecular modeling revealed important information about the structural features conferring activity. All the active compounds fitted in a specific region involving mainly transmembrane helices (TMH) 4-6 from one homologous half and TMH 7 and 12 from the other, also showing close contacts with TMH 6 and 12. Compounds that bound preferentially to another region were inactive, regardless of their free energy of binding. It should be noted that compounds 6g and 6i were devoid of toxic effects against peripheral blood mononuclear normal cells and erythrocytes. The data obtained indicates that both compounds might be proposed as scaffolds for obtaining promising P-gp inhibitors for overcoming MDR.
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Affiliation(s)
- Jerónimo Laiolo
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Dafni G Graikioti
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504, Patras, Greece
| | - Cecilia L Barbieri
- Department of Chemistry and Biochemistry, College of Exact and Natural Sciences, Universidad Nacional de Mar del Plata - QUIAMM - INBIOTEC CONICET, Mar del Plata, Argentina
| | - Mariana B Joray
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC and CIDIE CONICET-UCC, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Antonia I Antoniou
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, University of Patras, 26504, Patras, Greece
| | - D Mariano A Vera
- Department of Chemistry and Biochemistry, College of Exact and Natural Sciences, Universidad Nacional de Mar del Plata - QUIAMM - INBIOTEC CONICET, Mar del Plata, Argentina.
| | | | - María C Carpinella
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC and CIDIE CONICET-UCC, Universidad Católica de Córdoba, Córdoba, Argentina.
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46
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Mu HY, Lin CM, Chu LA, Lin YH, Li J, Liu CY, Huang HC, Cheng SL, Lee TY, Lee HM, Chen HM, Tsai YJ, Chen Y, Huang JH. Ex Vivo Evaluation of Combination Immunotherapy Using Tumor-Microenvironment-on-Chip. Adv Healthc Mater 2024; 13:e2302268. [PMID: 37748773 DOI: 10.1002/adhm.202302268] [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: 07/17/2023] [Revised: 09/03/2023] [Indexed: 09/27/2023]
Abstract
Combination immunotherapy has emerged as a promising strategy to address the challenges associated with immune checkpoint inhibitor (ICI) therapy in breast cancer. The efficacy of combination immunotherapy hinges upon the intricate and dynamic nature of the tumor microenvironment (TME), characterized by cellular heterogeneity and molecular gradients. However, current methodologies for drug screening often fail to accurately replicate these complex conditions, resulting in limited predictive capacity for treatment outcomes. Here, a tumor-microenvironment-on-chip (TMoC), integrating a circulation system and ex vivo tissue culture with physiological oxygen and nutrient gradients, is described. This platform enables spatial infiltration of cytotoxic CD8+ T cells and their targeted attack on the tumor, while preserving the high complexity and heterogeneity of the TME. The TMoC is employed to assess the synergistic effect of five targeted therapy drugs and five chemotherapy drugs in combination with immunotherapy, demonstrating strong concordance between chip and animal model responses. The TMoC holds significant potential for advancing drug development and guiding clinical decision-making, as it offers valuable insights into the complex dynamics of the TME.
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Affiliation(s)
- Hsuan-Yu Mu
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Chiao-Min Lin
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Li-An Chu
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
- Brain Research Center, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Ya-Hui Lin
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Ji Li
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Chao-Yu Liu
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Hsi-Chien Huang
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Sheng-Liang Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Tsung-Ying Lee
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Hsin Mei Lee
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Hsin-Min Chen
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Yun-Jen Tsai
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Yunching Chen
- Institute of Biomedical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Jen-Huang Huang
- Department of Chemical Engineering, National Tsing Hua University, 101, Sec. 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
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47
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Wu Z, Huang D, Wang J, Zhao Y, Sun W, Shen X. Engineering Heterogeneous Tumor Models for Biomedical Applications. Adv Sci (Weinh) 2024; 11:e2304160. [PMID: 37946674 PMCID: PMC10767453 DOI: 10.1002/advs.202304160] [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: 06/22/2023] [Revised: 09/16/2023] [Indexed: 11/12/2023]
Abstract
Tumor tissue engineering holds great promise for replicating the physiological and behavioral characteristics of tumors in vitro. Advances in this field have led to new opportunities for studying the tumor microenvironment and exploring potential anti-cancer therapeutics. However, the main obstacle to the widespread adoption of tumor models is the poor understanding and insufficient reconstruction of tumor heterogeneity. In this review, the current progress of engineering heterogeneous tumor models is discussed. First, the major components of tumor heterogeneity are summarized, which encompasses various signaling pathways, cell proliferations, and spatial configurations. Then, contemporary approaches are elucidated in tumor engineering that are guided by fundamental principles of tumor biology, and the potential of a bottom-up approach in tumor engineering is highlighted. Additionally, the characterization approaches and biomedical applications of tumor models are discussed, emphasizing the significant role of engineered tumor models in scientific research and clinical trials. Lastly, the challenges of heterogeneous tumor models in promoting oncology research and tumor therapy are described and key directions for future research are provided.
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Affiliation(s)
- Zhuhao Wu
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Danqing Huang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Jinglin Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
| | - Yuanjin Zhao
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
| | - Weijian Sun
- Department of Gastrointestinal SurgeryThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Xian Shen
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China
- Department of Gastrointestinal SurgeryThe First Affiliated HospitalWenzhou Medical UniversityWenzhou325035China
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48
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Ke X, Ye C, Liu R, Liu F, Chen Q. Establishment of a novel minigenome system for the identification of drugs targeting Nipah virus replication. J Gen Virol 2024; 105. [PMID: 38180473 DOI: 10.1099/jgv.0.001944] [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] [Indexed: 01/06/2024] Open
Abstract
Nipah virus (NiV) is a deadly zoonotic pathogen with high potential to cause another pandemic. Owing to biosafety concerns, studies on living NiV must be performed in biosafety level 4 (BSL-4) laboratories, which greatly hinders the development of anti-NiV drugs. To overcome this issue, minigenome systems have been developed to study viral replication and screen for antiviral drugs. This study aimed to develop two minigenome systems (transient and stable expression) based on a helper cell line expressing the NiV P, N and L proteins required to initiate NiV RNA replication. Stable minigenome cells were resistant to ribavirin, remdesivir and favipiravir but sensitive to interferons. Cells of the transient replication system were sensitive to ribavirin and favipiravir and suitable for drug screening. Our study demonstrates a feasible and effective platform for studying NiV replication and shows great potential for high-throughput drug screening in a BSL-2 laboratory environment.
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Affiliation(s)
- Xianliang Ke
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
| | - Chang Ye
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Renyi Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Feng Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
| | - Quanjiao Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430207, PR China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, PR China
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49
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Wang M, Zhang L, Hao H, Yan M, Zhu Z. Applications of Engineered Skin Tissue for Cosmetic Component and Toxicology Detection. Cell Transplant 2024; 33:9636897241235464. [PMID: 38491929 PMCID: PMC10944590 DOI: 10.1177/09636897241235464] [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: 12/14/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 03/18/2024] Open
Abstract
The scale of the cosmetic market is increasing every day. There are many safety risks to cosmetics, but they benefit people at the same time. The skin can become red, swollen, itchy, chronically toxic, and senescent due to the misuse of cosmetics, triggering skin injuries, with contact dermatitis being the most common. Therefore, there is an urgent need for a system that can scientifically and rationally detect the composition and perform a toxicological assessment of cosmetic products. Traditional detection methods rely on instrumentation and method selection, which are less sensitive and more complex to perform. Engineered skin tissue has emerged with the advent of tissue engineering technology as an emerging bioengineering technology. The ideal engineered skin tissue is the basis for building good in vitro structures and physiological functions in this field. This review introduces the existing cosmetic testing and toxicological evaluation methods, the current development status, and the types and characteristics of engineered skin tissue. The application of engineered skin tissue in the field of cosmetic composition detection and toxicological evaluation, as well as the different types of tissue engineering scaffold materials and three-dimensional (3D) organoid preparation approaches, is highlighted in this review to provide methods and ideas for constructing the next engineered skin tissue for cosmetic raw material component analysis and toxicological evaluation.
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Affiliation(s)
- Min Wang
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China
| | - Linfeng Zhang
- College of Chemistry and Materials Engineering, Beijing Technology and Business University, Beijing, China
| | - Haojie Hao
- The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Muyang Yan
- The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Ziying Zhu
- The First Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
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50
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Aveic S, Seidelmann M, Davtalab R, Corallo D, Vogt M, Rütten S, Fischer H. Three-dimensional in vitro model of bone metastases of neuroblastoma as a tool for pharmacological evaluations. Nanotheranostics 2024; 8:1-11. [PMID: 38164505 PMCID: PMC10750120 DOI: 10.7150/ntno.85439] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
In vitro metastatic models are foreseen to introduce a breakthrough in the field of preclinical screening of more functional small-molecule pharmaceuticals and biologics. To achieve this goal, the complexity of current in vitro systems requests an appropriate upgrade to approach the three-dimensional (3D) in vivo metastatic disease. Here, we explored the potential of our 3D β-tricalcium phosphate (β-TCP) model of neuroblastoma bone metastasis for drug toxicity assessment. Tailor-made scaffolds with interconnected channels were produced by combining 3D printing and slip casting method. The organization of neuroblastoma cells into a mesenchymal stromal cell (MSC) network, cultured under bioactive conditions provided by β-TCP, was monitored by two-photon microscopy. Deposition of extracellular matrix protein Collagen I by MSCs and persistent growth of tumor cells confirmed the cell-supportive performance of our 3D model. When different neuroblastoma cells were treated with conventional chemotherapeutics, the β-TCP model provided the necessary reproducibility and accuracy of experimental readouts. Drug efficacy evaluation was done for 3D and 2D cell cultures, highlighting the need for a higher dose of chemotherapeutics under 3D conditions to achieve the expected cytotoxicity in tumor cells. Our results confirm the importance of 3D geometry in driving native connectivity between nonmalignant and tumor cells and sustain β-TCP scaffolds as a reliable and affordable drug screening platform for use in the early stages of drug discovery.
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Affiliation(s)
- Sanja Aveic
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
- Laboratory of Target Discovery and Biology of Neuroblastoma, Istituto di Ricerca Pediatrica Fondazione Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy
| | - Max Seidelmann
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Roswitha Davtalab
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Diana Corallo
- Laboratory of Target Discovery and Biology of Neuroblastoma, Istituto di Ricerca Pediatrica Fondazione Città della Speranza, Corso Stati Uniti 4, 35127 Padova, Italy
| | - Michael Vogt
- Interdisciplinary Center for Clinical Research, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Stephan Rütten
- Electron Microscopy Facility, Institute of Pathology, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Horst Fischer
- Department of Dental Materials and Biomaterials Research, RWTH Aachen University Hospital, Pauwelsstrasse 30, 52074 Aachen, Germany
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