1
|
Tavakoli N, Fong EJ, Coleman A, Huang YK, Bigger M, Doche ME, Kim S, Lenz HJ, Graham NA, Macklin P, Finley SD, Mumenthaler SA. Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595756. [PMID: 38826317 PMCID: PMC11142224 DOI: 10.1101/2024.05.24.595756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cancer-associated fibroblasts (CAFs) play a key role in metabolic reprogramming and are well-established contributors to drug resistance in colorectal cancer (CRC). To exploit this metabolic crosstalk, we integrated a systems biology approach that identified key metabolic targets in a data-driven method and validated them experimentally. This process involved a novel machine learning-based method to computationally screen, in a high-throughput manner, the effects of enzyme perturbations predicted by a computational model of CRC metabolism. This approach reveals the network-wide effects of metabolic perturbations. Our results highlighted hexokinase (HK) as the crucial target, which subsequently became our focus for experimental validation using patient-derived tumor organoids (PDTOs). Through metabolic imaging and viability assays, we found that PDTOs cultured in CAF-conditioned media exhibited increased sensitivity to HK inhibition, confirming the model predictions. Our approach emphasizes the critical role of integrating computational and experimental techniques in exploring and exploiting CRC-CAF crosstalk.
Collapse
|
2
|
Yakovlev EV, Simkin IV, Shirokova AA, Kolotieva NA, Novikova SV, Nasyrov AD, Denisenko IR, Gursky KD, Shishkov IN, Narzaeva DE, Salmina AB, Yurchenko SO, Kryuchkov NP. Machine learning approach for recognition and morphological analysis of isolated astrocytes in phase contrast microscopy. Sci Rep 2024; 14:9846. [PMID: 38684715 PMCID: PMC11059356 DOI: 10.1038/s41598-024-59773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Astrocytes are glycolytically active cells in the central nervous system playing a crucial role in various brain processes from homeostasis to neurotransmission. Astrocytes possess a complex branched morphology, frequently examined by fluorescent microscopy. However, staining and fixation may impact the properties of astrocytes, thereby affecting the accuracy of the experimental data of astrocytes dynamics and morphology. On the other hand, phase contrast microscopy can be used to study astrocytes morphology without affecting them, but the post-processing of the resulting low-contrast images is challenging. The main result of this work is a novel approach for recognition and morphological analysis of unstained astrocytes based on machine-learning recognition of microscopic images. We conducted a series of experiments involving the cultivation of isolated astrocytes from the rat brain cortex followed by microscopy. Using the proposed approach, we tracked the temporal evolution of the average total length of branches, branching, and area per astrocyte in our experiments. We believe that the proposed approach and the obtained experimental data will be of interest and benefit to the scientific communities in cell biology, biophysics, and machine learning.
Collapse
Affiliation(s)
- Egor V Yakovlev
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia.
| | - Ivan V Simkin
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Anastasiya A Shirokova
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Nataliya A Kolotieva
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
- Research Center of Neurology, 80 Volokolamskoye Shosse, Moscow, 125367, Russia
| | - Svetlana V Novikova
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
- Research Center of Neurology, 80 Volokolamskoye Shosse, Moscow, 125367, Russia
| | - Artur D Nasyrov
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Ilya R Denisenko
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Konstantin D Gursky
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Ivan N Shishkov
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Diana E Narzaeva
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
- Research Center of Neurology, 80 Volokolamskoye Shosse, Moscow, 125367, Russia
| | - Alla B Salmina
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
- Research Center of Neurology, 80 Volokolamskoye Shosse, Moscow, 125367, Russia
| | - Stanislav O Yurchenko
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia
| | - Nikita P Kryuchkov
- Scientific-Educational Centre "Soft matter and physics of fluids", Bauman Moscow State Technical University, 2nd Baumanskaya Street 5, Moscow, 105005, Russia.
| |
Collapse
|
3
|
Xu R, Chen R, Tu C, Gong X, Liu Z, Mei L, Ren X, Li Z. 3D Models of Sarcomas: The Next-generation Tool for Personalized Medicine. PHENOMICS (CHAM, SWITZERLAND) 2024; 4:171-186. [PMID: 38884054 PMCID: PMC11169319 DOI: 10.1007/s43657-023-00111-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/18/2024]
Abstract
Sarcoma is a complex and heterogeneous cancer that has been difficult to study in vitro. While two-dimensional (2D) cell cultures and mouse models have been the dominant research tools, three-dimensional (3D) culture systems such as organoids have emerged as promising alternatives. In this review, we discuss recent developments in sarcoma organoid culture, with a focus on their potential as tools for drug screening and biobanking. We also highlight the ways in which sarcoma organoids have been used to investigate the mechanisms of gene regulation, drug resistance, metastasis, and immune interactions. Sarcoma organoids have shown to retain characteristics of in vivo biology within an in vitro system, making them a more representative model for sarcoma research. Our review suggests that sarcoma organoids offer a potential path forward for translational research in this field and may provide a platform for developing personalized therapies for sarcoma patients.
Collapse
Affiliation(s)
- Ruiling Xu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Ruiqi Chen
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Xiaofeng Gong
- College of Life Science, Fudan University, Shanghai, 200433 China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Lin Mei
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Xiaolei Ren
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, No. 139 Renmin Road, Changsha, 410011 Hunan China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, No. 139 Renmin Road, Changsha, 410011 Hunan China
| |
Collapse
|
4
|
Jayathilake PG, Victori P, Pavillet CE, Lee CH, Voukantsis D, Miar A, Arora A, Harris AL, Morten KJ, Buffa FM. Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study. PLoS Comput Biol 2024; 20:e1011944. [PMID: 38489376 DOI: 10.1371/journal.pcbi.1011944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/27/2024] [Accepted: 02/24/2024] [Indexed: 03/17/2024] Open
Abstract
Deregulated metabolism is one of the hallmarks of cancer. It is well-known that tumour cells tend to metabolize glucose via glycolysis even when oxygen is available and mitochondrial respiration is functional. However, the lower energy efficiency of aerobic glycolysis with respect to mitochondrial respiration makes this behaviour, namely the Warburg effect, counter-intuitive, although it has now been recognized as source of anabolic precursors. On the other hand, there is evidence that oxygenated tumour cells could be fuelled by exogenous lactate produced from glycolysis. We employed a multi-scale approach that integrates multi-agent modelling, diffusion-reaction, stoichiometric equations, and Boolean networks to study metabolic cooperation between hypoxic and oxygenated cells exposed to varying oxygen, nutrient, and inhibitor concentrations. The results show that the cooperation reduces the depletion of environmental glucose, resulting in an overall advantage of using aerobic glycolysis. In addition, the oxygen level was found to be decreased by symbiosis, promoting a further shift towards anaerobic glycolysis. However, the oxygenated and hypoxic populations may gradually reach quasi-equilibrium. A sensitivity analysis using Latin hypercube sampling and partial rank correlation shows that the symbiotic dynamics depends on properties of the specific cell such as the minimum glucose level needed for glycolysis. Our results suggest that strategies that block glucose transporters may be more effective to reduce tumour growth than those blocking lactate intake transporters.
Collapse
Affiliation(s)
| | - Pedro Victori
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Clara E Pavillet
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- Department of Computing Sciences and Institute for Data Science and Analytics, Bocconi University, Milan, Italy
| | - Chang Heon Lee
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Dimitrios Voukantsis
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ana Miar
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Anjali Arora
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Adrian L Harris
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Karl J Morten
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Francesca M Buffa
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- Department of Computing Sciences and Institute for Data Science and Analytics, Bocconi University, Milan, Italy
| |
Collapse
|
5
|
Babl N, Decking SM, Voll F, Althammer M, Sala-Hojman A, Ferretti R, Korf C, Schmidl C, Schmidleithner L, Nerb B, Matos C, Koehl GE, Siska P, Bruss C, Kellermeier F, Dettmer K, Oefner PJ, Wichland M, Ugele I, Bohr C, Herr W, Ramaswamy S, Heinrich T, Herhaus C, Kreutz M, Renner K. MCT4 blockade increases the efficacy of immune checkpoint blockade. J Immunother Cancer 2023; 11:e007349. [PMID: 37880183 PMCID: PMC10603342 DOI: 10.1136/jitc-2023-007349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND & AIMS Intratumoral lactate accumulation and acidosis impair T-cell function and antitumor immunity. Interestingly, expression of the lactate transporter monocarboxylate transporter (MCT) 4, but not MCT1, turned out to be prognostic for the survival of patients with rectal cancer, indicating that single MCT4 blockade might be a promising strategy to overcome glycolysis-related therapy resistance. METHODS To determine whether blockade of MCT4 alone is sufficient to improve the efficacy of immune checkpoint blockade (ICB) therapy, we examined the effects of the selective MCT1 inhibitor AZD3965 and a novel MCT4 inhibitor in a colorectal carcinoma (CRC) tumor spheroid model co-cultured with blood leukocytes in vitro and the MC38 murine CRC model in vivo in combination with an antibody against programmed cell death ligand-1(PD-L1). RESULTS Inhibition of MCT4 was sufficient to reduce lactate efflux in three-dimensional (3D) CRC spheroids but not in two-dimensional cell-cultures. Co-administration of the MCT4 inhibitor and ICB augmented immune cell infiltration, T-cell function and decreased CRC spheroid viability in a 3D co-culture model of human CRC spheroids with blood leukocytes. Accordingly, combination of MCT4 and ICB increased intratumoral pH, improved leukocyte infiltration and T-cell activation, delayed tumor growth, and prolonged survival in vivo. MCT1 inhibition exerted no further beneficial impact. CONCLUSIONS These findings demonstrate that single MCT4 inhibition represents a novel therapeutic approach to reverse lactic-acid driven immunosuppression and might be suitable to improve ICB efficacy.
Collapse
Affiliation(s)
- Nathalie Babl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sonja-Maria Decking
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Florian Voll
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Michael Althammer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | | | - Roberta Ferretti
- EMD Serono Research and Development Institute, Inc, Billerica, Massachusetts, USA, an affiliate of Merck KGaA
| | - Clarissa Korf
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
| | | | | | - Benedikt Nerb
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Carina Matos
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Gudrun E Koehl
- Department of Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Peter Siska
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Christina Bruss
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Gynecology and Obstetrics, University Hospital Regensburg, Regensburg, Germany
| | - Fabian Kellermeier
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Marvin Wichland
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
| | - Ines Ugele
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
| | - Christopher Bohr
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Shivapriya Ramaswamy
- EMD Serono Research and Development Institute, Inc, Billerica, Massachusetts, USA, an affiliate of Merck KGaA
| | | | | | - Marina Kreutz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Kathrin Renner
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Otorhinolaryngology, University Hospital Regensburg, Regensburg, Germany
| |
Collapse
|
6
|
Zhang Y, Wang K, Du Y, Yang H, Jia G, Huang D, Chen W, Shan Y. Computational Modeling to Determine the Effect of Phenotypic Heterogeneity in Tumors on the Collective Tumor-Immune Interactions. Bull Math Biol 2023; 85:51. [PMID: 37142885 DOI: 10.1007/s11538-023-01158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 04/12/2023] [Indexed: 05/06/2023]
Abstract
Tumor immunotherapy aims to maintain or enhance the killing capability of CD8+ T cells to clear tumor cells. The tumor-immune interactions affect the function of CD8+ T cells. However, the effect of phenotype heterogeneity of a tumor mass on the collective tumor-immune interactions is insufficiently investigated. We developed the cellular-level computational model based on the principle of cellular Potts model to solve the case mentioned above. We considered how asymmetric division and glucose distribution jointly regulated the transient changes in the proportion of proliferating/quiescent tumor cells in a solid tumor mass. The evolution of a tumor mass in contact with T cells was explored and validated by comparing it with previous studies. Our modeling exhibited that proliferating/quiescent tumor cells, exhibiting distinct anti-apoptotic and suppressive behaviors, redistributed within the domain accompanied by the evolution of a tumor mass. Collectively, a tumor mass prone to a quiescent state weakened the collective suppressive functions of a tumor mass on cytotoxic T cells and triggered a decline of apoptosis of tumor cells. Although quiescent tumor cells did not sufficiently do their inhibitory functions, the possibility of long-term survival was improved due to their interior location within a mass. Overall, the proposed model provides a useful framework to investigate collective-targeted strategies for improving the efficiency of immunotherapy.
Collapse
Affiliation(s)
- Yuyuan Zhang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Kaiqun Wang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Yaoyao Du
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Huiyuan Yang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Guanjie Jia
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Di Huang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Weiyi Chen
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Yanhu Shan
- School of Instrument and Electronics, North University of China, Taiyuan, 030051, China.
| |
Collapse
|
7
|
Hervas-Raluy S, Wirthl B, Guerrero PE, Robalo Rei G, Nitzler J, Coronado E, Font de Mora Sainz J, Schrefler BA, Gomez-Benito MJ, Garcia-Aznar JM, Wall WA. Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment. Comput Biol Med 2023; 159:106895. [PMID: 37060771 DOI: 10.1016/j.compbiomed.2023.106895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/09/2023] [Accepted: 04/09/2023] [Indexed: 04/17/2023]
Abstract
To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a three-dimensional tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the proposed workflow. This study demonstrates the huge challenges associated with determining precise parameters with usually only limited data for such complex processes and models, but also demonstrates in general how to indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.
Collapse
Affiliation(s)
- Silvia Hervas-Raluy
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain.
| | - Barbara Wirthl
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Pedro E Guerrero
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Gil Robalo Rei
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Jonas Nitzler
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany; Professorship for Data-Driven Materials Modeling, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Esther Coronado
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe,, Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Jaime Font de Mora Sainz
- Clinical and Translational Oncology Research Group, Instituto de Investigación La Fe,, Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Bernhard A Schrefler
- Department of Civil, Environmental and Architectural Engineering, University of Padua, Marzolo 9, Padua, 35131, Italy; Institute for Advanced Study, Technical University of Munich, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| | - Maria Jose Gomez-Benito
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Jose Manuel Garcia-Aznar
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, University of Zaragoza, Aragon Institute for Engineering Research (I3A), Maria de Luna 3, Zaragoza, 50018, Spain
| | - Wolfgang A Wall
- Institute for Computational Mechanics, Technical University of Munich, TUM School of Engineering and Design, Department of Engineering Physics & Computation, Boltzmannstraße 15, Garching b. Munich, 85748, Germany
| |
Collapse
|
8
|
Miller HA, Miller DM, van Berkel VH, Frieboes HB. Evaluation of Lung Cancer Patient Response to First-Line Chemotherapy by Integration of Tumor Core Biopsy Metabolomics with Multiscale Modeling. Ann Biomed Eng 2023; 51:820-832. [PMID: 36224485 PMCID: PMC10023290 DOI: 10.1007/s10439-022-03096-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/02/2022] [Indexed: 11/28/2022]
Abstract
The standard of care for intermediate (Stage II) and advanced (Stages III and IV) non-small cell lung cancer (NSCLC) involves chemotherapy with taxane/platinum derivatives, with or without radiation. Ideally, patients would be screened a priori to allow non-responders to be initially treated with second-line therapies. This evaluation is non-trivial, however, since tumors behave as complex multiscale systems. To address this need, this study employs a multiscale modeling approach to evaluate first-line chemotherapy response of individual patient tumors based on metabolomic analysis of tumor core biopsies obtained during routine clinical evaluation. Model parameters were calculated for a patient cohort as a function of these metabolomic profiles, previously obtained from high-resolution 2DLC-MS/MS analysis. Evaluation metrics were defined to classify patients as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD) following first-line chemotherapy. Response was simulated for each patient and compared to actual response. The results show that patient classifications were significantly separated from each other, and also when grouped as DC vs. PD and as CR/PR vs. SD/PD, by fraction of initial tumor radius metric at 6 days post simulated bolus drug injection. This study shows that patient first-line chemotherapy response can in principle be evaluated from multiscale modeling integrated with tumor tissue metabolomic data, offering a first step towards individualized lung cancer treatment prognosis.
Collapse
Affiliation(s)
- Hunter A Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
| | - Donald M Miller
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Victor H van Berkel
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
- Department of Cardiovascular and Thoracic Surgery, University of Louisville, Louisville, KY, USA
| | - Hermann B Frieboes
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA.
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA.
- Department of Bioengineering, University of Louisville, Lutz Hall 419, Louisville, KY, 40292, USA.
- Center for Predictive Medicine, University of Louisville, Louisville, KY, USA.
| |
Collapse
|
9
|
Gonçalves IG, García-Aznar JM. Hybrid computational models of multicellular tumour growth considering glucose metabolism. Comput Struct Biotechnol J 2023; 21:1262-1271. [PMID: 36814723 PMCID: PMC9939553 DOI: 10.1016/j.csbj.2023.01.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Cancer cells metabolize glucose through metabolic pathways that differ from those used by healthy and differentiated cells. In particular, tumours have been shown to consume more glucose than their healthy counterparts and to use anaerobic metabolic pathways, even under aerobic conditions. Nevertheless, scientists have still not been able to explain why cancer cells evolved to present an altered metabolism and what evolutionary advantage this might provide them. Experimental and computational models have been increasingly used in recent years to understand some of these biological questions. Multicellular tumour spheroids are effective experimental models as they replicate the initial stages of avascular solid tumour growth. Furthermore, these experiments generate data which can be used to calibrate and validate computational studies that aim to simulate tumour growth. Hybrid models are of particular relevance in this field of research because they model cells as individual agents while also incorporating continuum representations of the substances present in the surrounding microenvironment that may participate in intracellular metabolic networks as concentration or density distributions. Henceforth, in this review, we explore the potential of computational modelling to reveal the role of metabolic reprogramming in tumour growth.
Collapse
Key Words
- ABM, agent-based model
- ATP, adenosine triphosphate
- CA, cellular automata
- CPM, cellular Potts model
- ECM, extracellular matrix
- FBA, Flux Balance Analysis
- FDG-PET, [18F]-fluorodeoxyglucose-positron emission tomography
- MCTS, multicellular tumour spheroids
- ODEs, ordinary differential equations
- PDEs, partial differential equations
- SBML, Systems Biology Markup Language
- Warburg effect
- agent-based models
- glucose metabolism
- hybrid modelling
- multicellular simulations
Collapse
Affiliation(s)
- Inês G. Gonçalves
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza 50018, Aragon, Spain
| | - José Manuel García-Aznar
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, Aragon Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza 50018, Aragon, Spain
| |
Collapse
|
10
|
Martins C, Pacheco C, Moreira-Barbosa C, Marques-Magalhães Â, Dias S, Araújo M, Oliveira MJ, Sarmento B. Glioblastoma immuno-endothelial multicellular microtissue as a 3D in vitro evaluation tool of anti-cancer nano-therapeutics. J Control Release 2023; 353:77-95. [PMID: 36410614 DOI: 10.1016/j.jconrel.2022.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/27/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022]
Abstract
Despite being the most prevalent and lethal type of adult brain cancer, glioblastoma (GBM) remains intractable. Promising anti-GBM nanoparticle (NP) systems have been developed to improve the anti-cancer performance of difficult-to-deliver therapeutics, with particular emphasis on tumor targeting strategies. However, current disease modeling toolboxes lack close-to-native in vitro models that emulate GBM microenvironment and bioarchitecture, thus partially hindering translation due to poorly predicted clinical responses. Herein, human GBM heterotypic multicellular tumor microtissues (MCTMs) are generated through high-throughput 3D modeling of U-251 MG tumor cells, tissue differentiated macrophages isolated from peripheral monocytes, and brain microvascular primary endothelial cells. GBM MCTMs mimicked tumor spatial organization, extracellular matrix production and necrosis areas. The bioactivity of a model drug, docetaxel (DTX), and of tumor-targeted DTX-loaded polymeric NPs with a surface L-Histidine moiety (H-NPs), were assessed in the MCTMs. MCTMs cell uptake and anti-proliferative effect was 8- and 3-times higher for H-NPs, respectively, compared to the non-targeted NPs and to free DTX. H-NPs provided a decrease of MCTMs anti-inflammatory M2-macrophages, while increasing their pro-inflammatory M1 counterparts. Moreover, H-NPs showed a particular biomolecular signature through reduced secretion of an array of medium cytokines (IFN-γ, IL-1β, IL-1Ra, IL-6, IL-8, TGF-β). Overall, MCTMs provide an in vitro biomimetic model to recapitulate key cellular and structural features of GBM and improve in vivo drug response predictability, fostering future clinical translation of anti-GBM nano-therapeutic strategies.
Collapse
Affiliation(s)
- Cláudia Martins
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Catarina Pacheco
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; CESPU - Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Catarina Moreira-Barbosa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ângela Marques-Magalhães
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sofia Dias
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marco Araújo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal
| | - Maria J Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-393 Porto, Portugal; CESPU - Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal.
| |
Collapse
|
11
|
Thalheim T, Aust G, Galle J. Organoid Cultures In Silico: Tools or Toys? BIOENGINEERING (BASEL, SWITZERLAND) 2022; 10:bioengineering10010050. [PMID: 36671623 PMCID: PMC9854934 DOI: 10.3390/bioengineering10010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023]
Abstract
The implementation of stem-cell-based organoid culture more than ten years ago started a development that created new avenues for diagnostic analyses and regenerative medicine. In parallel, computational modelling groups realized the potential of this culture system to support their theoretical approaches to study tissues in silico. These groups developed computational organoid models (COMs) that enabled testing consistency between cell biological data and developing theories of tissue self-organization. The models supported a mechanistic understanding of organoid growth and maturation and helped linking cell mechanics and tissue shape in general. What comes next? Can we use COMs as tools to complement the equipment of our biological and medical research? While these models already support experimental design, can they also quantitatively predict tissue behavior? Here, we review the current state of the art of COMs and discuss perspectives for their application.
Collapse
Affiliation(s)
- Torsten Thalheim
- Interdisciplinary Institute for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
- Correspondence:
| | - Gabriela Aust
- Department of Surgery, Research Laboratories, Leipzig University, Liebigstraße 20, 04103 Leipzig, Germany
| | - Joerg Galle
- Interdisciplinary Institute for Bioinformatics (IZBI), Leipzig University, Härtelstr. 16–18, 04107 Leipzig, Germany
| |
Collapse
|
12
|
Jia G, Yang H, Wang K, Huang D, Chen W, Shan Y. The modeling study of the effect of morphological behaviors of extracellular matrix fibers on the dynamic interaction between tumor cells and antitumor immune response. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2022; 38:e3633. [PMID: 35703086 DOI: 10.1002/cnm.3633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/28/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Low response rate limits the effective application of immunotherapy, in which the interactions between tumor cells and immune cells play a significant role. The strength of regulation could be mediated by extracellular matrix (ECM) fibers, which is still insufficiently investigated. In the study, the cellular potts model was utilized to explore the role of morphological properties of ECM in tumor-immune interactions. It was observed that high-density random ECM fibers delayed the interaction between tumor cells and T cells. Moreover, the tumor-immune interactions were ECM morphology-specific. Radial ECM fibers exhibited weaker inhibitory role in the process of contact between tumor cells and T cells. This study provided the useful mechanism of tumor-immune interactions from the viewpoint of morphological effect of ECM fibers, facilitating improving the efficiency of immunotherapy.
Collapse
Affiliation(s)
- Guanjie Jia
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Hao Yang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Kaiqun Wang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Di Huang
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Weiyi Chen
- Department of Biomedical Engineering, Research Center for Nano-Biomaterials and Regenerative Medicine, College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Yanhu Shan
- School of Instrument and Electronics, North University of China, Taiyuan, China
| |
Collapse
|
13
|
Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data. Ann Biomed Eng 2022; 50:314-329. [PMID: 35083584 PMCID: PMC9743982 DOI: 10.1007/s10439-022-02904-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/01/2022] [Indexed: 12/15/2022]
Abstract
Advances in omic technologies have provided insight into cancer progression and treatment response. However, the nonlinear characteristics of cancer growth present a challenge to bridge from the molecular- to the tissue-scale, as tumor behavior cannot be encapsulated by the sum of the individual molecular details gleaned experimentally. Mathematical modeling and computational simulation have been traditionally employed to facilitate analysis of nonlinear systems. In this study, for the first time tumor metabolomic data are linked via mathematical modeling to the tumor tissue-scale behavior, showing the capability to mechanistically simulate cancer progression personalized to omic information obtainable from patient tumor core biopsy analysis. Generally, a higher degree of metabolic dysregulation has been correlated with more aggressive tumor behavior. Accordingly, key parameters influenced by metabolomic data in this model include tumor proliferation, vascularization, aggressiveness, lactic acid production, monocyte infiltration and macrophage polarization, and drug effect. The model enables evaluating interactions of interest between these parameters which drive tumor growth based on the metabolomic data. The results show that the model can group patients consistently with the clinically observed outcomes of response/non-response to chemotherapy. This modeling approach provides a first step towards evaluation of tumor growth based on tumor-specific metabolomic data.
Collapse
|
14
|
Song M, Finley SD. Mechanistic characterization of endothelial sprouting mediated by pro-angiogenic signaling. Microcirculation 2021; 29:e12744. [PMID: 34890488 PMCID: PMC9285777 DOI: 10.1111/micc.12744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/04/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
Objective We aim to quantitatively characterize the crosstalk between VEGF‐ and FGF‐mediated angiogenic signaling and endothelial sprouting, to gain mechanistic insights and identify novel therapeutic strategies. Methods We constructed an experimentally validated hybrid agent‐based mathematical model that characterizes endothelial sprouting driven by FGF‐ and VEGF‐mediated signaling. We predicted the total sprout length, number of sprouts, and average length by the mono‐ and co‐stimulation of FGF and VEGF. Results The experimentally fitted and validated model predicts that FGF induces stronger angiogenic responses in the long‐term compared with VEGF stimulation. Also, FGF plays a dominant role in the combination effects in endothelial sprouting. Moreover, the model suggests that ERK and Akt pathways and cellular responses contribute differently to the sprouting process. Last, the model predicts that the strategies to modulate endothelial sprouting are context‐dependent, and our model can identify potential effective pro‐ and anti‐angiogenic targets under different conditions and study their efficacy. Conclusions The model provides detailed mechanistic insight into VEGF and FGF interactions in sprouting angiogenesis. More broadly, this model can be utilized to identify targets that influence angiogenic signaling leading to endothelial sprouting and to study the effects of pro‐ and anti‐angiogenic therapies.
Collapse
Affiliation(s)
- Min Song
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA
| | - Stacey D Finley
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, USA.,Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California, USA.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
15
|
Abstract
Multiscale computational modeling aims to connect the complex networks of effects at different length and/or time scales. For example, these networks often include intracellular molecular signaling, crosstalk, and other interactions between neighboring cell populations, and higher levels of emergent phenomena across different regions of tissues and among collections of tissues or organs interacting with each other in the whole body. Recent applications of multiscale modeling across intracellular, cellular, and/or tissue levels are highlighted here. These models incorporated the roles of biochemical and biomechanical modulation in processes that are implicated in the mechanisms of several diseases including fibrosis, joint and bone diseases, respiratory infectious diseases, and cancers.
Collapse
|
16
|
Gregg RW, Shabnam F, Shoemaker JE. Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production. Bioinformatics 2021; 37:1428-1434. [PMID: 33196784 DOI: 10.1093/bioinformatics/btaa969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/13/2020] [Accepted: 11/04/2020] [Indexed: 01/25/2023] Open
Abstract
MOTIVATION The cGAS pathway is a component of the innate immune system responsible for the detection of pathogenic DNA and upregulation of interferon beta (IFNβ). Experimental evidence shows that IFNβ signaling occurs in highly heterogeneous cells and is stochastic in nature; however, the benefits of these attributes remain unclear. To investigate how stochasticity and heterogeneity affect IFNβ production, an agent-based model is developed to simulate both DNA transfection and viral infection. RESULTS We show that heterogeneity can enhance IFNβ responses during infection. Furthermore, by varying the degree of IFNβ stochasticity, we find that only a percentage of cells (20-30%) need to respond during infection. Going beyond this range provides no additional protection against cell death or reduction of viral load. Overall, these simulations suggest that heterogeneity and stochasticity are important for moderating immune potency while minimizing cell death during infection. AVAILABILITY AND IMPLEMENTATION Model repository is available at: https://github.com/ImmuSystems-Lab/AgentBasedModel-cGASPathway. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Robert W Gregg
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA
| | - Fathima Shabnam
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA
| | - Jason E Shoemaker
- Department of Chemical and Petroleum Engineering, 15260, Pittsburgh, PA 15260, USA.,McGowan Institute for Regenerative Medicine, 15219, Pittsburgh, PA 15260, USA.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| |
Collapse
|
17
|
Al-Hity G, Yang F, Campillo-Funollet E, Greenstein AE, Hunt H, Mampay M, Intabli H, Falcinelli M, Madzvamuse A, Venkataraman C, Flint MS. An integrated framework for quantifying immune-tumour interactions in a 3D co-culture model. Commun Biol 2021; 4:781. [PMID: 34168276 PMCID: PMC8225809 DOI: 10.1038/s42003-021-02296-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/03/2021] [Indexed: 02/05/2023] Open
Abstract
Investigational in vitro models that reflect the complexity of the interaction between the immune system and tumours are limited and difficult to establish. Herein, we present a platform to study the tumour-immune interaction using a co-culture between cancer spheroids and activated immune cells. An algorithm was developed for analysis of confocal images of the co-culture to evaluate the following quantitatively; immune cell infiltration, spheroid roundness and spheroid growth. As a proof of concept, the effect of the glucocorticoid stress hormone, cortisol was tested on 66CL4 co-culture model. Results were comparable to 66CL4 syngeneic in vivo mouse model undergoing psychological stress. Furthermore, administration of glucocorticoid receptor antagonists demonstrated the use of this model to determine the effect of treatments on the immune-tumour interplay. In conclusion, we provide a method of quantifying the interaction between the immune system and cancer, which can become a screening tool in immunotherapy design.
Collapse
Affiliation(s)
- Gheed Al-Hity
- School of Pharmacy and Biomolecular sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton, BN2, 4GJ, UK
| | - FengWei Yang
- Department of Chemical and Process Engineering, University of Surrey, Surrey, UK
| | | | - Andrew E Greenstein
- Corcept Therapeutics, 149 Commonwealth Drive, Menlo Park, California, 94025, United States
| | - Hazel Hunt
- Corcept Therapeutics, 149 Commonwealth Drive, Menlo Park, California, 94025, United States
| | - Myrthe Mampay
- School of Pharmacy and Biomolecular sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton, BN2, 4GJ, UK
| | - Haya Intabli
- School of Pharmacy and Biomolecular sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton, BN2, 4GJ, UK
| | - Marta Falcinelli
- School of Pharmacy and Biomolecular sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton, BN2, 4GJ, UK
| | - Anotida Madzvamuse
- School of Mathematical and Physical Sciences, University of Sussex, Department of Mathematics, Falmer, Brighton, BN1 9QH, UK.
| | - Chandrasekhar Venkataraman
- School of Mathematical and Physical Sciences, University of Sussex, Department of Mathematics, Falmer, Brighton, BN1 9QH, UK.
| | - Melanie S Flint
- School of Pharmacy and Biomolecular sciences, University of Brighton, Centre for Stress and Age-related Diseases, Moulsecoomb, Brighton, BN2, 4GJ, UK.
| |
Collapse
|
18
|
Mosier JA, Wu Y, Reinhart-King CA. Recent advances in understanding the role of metabolic heterogeneities in cell migration. Fac Rev 2021; 10:8. [PMID: 33659926 PMCID: PMC7894266 DOI: 10.12703/r/10-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Migration is an energy-intensive, multi-step process involving cell adhesion, protrusion, and detachment. Each of these steps require cells to generate and consume energy, regulating their morphological changes and force generation. Given the need for energy to move, cellular metabolism has emerged as a critical regulator of both single cell and collective migration. Recently, metabolic heterogeneity has been highlighted as a potential determinant of collective cell behavior, as individual cells may play distinct roles in collective migration. Several tools and techniques have been developed and adapted to study cellular energetics during migration including live-cell probes to characterize energy utilization and metabolic state and methodologies to sort cells based on their metabolic profile. Here, we review the recent advances in techniques, parsing the metabolic heterogeneities inherent in cell populations and their contributions to cell migration.
Collapse
Affiliation(s)
- Jenna A Mosier
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yusheng Wu
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | | |
Collapse
|
19
|
SARS-COV-2 infection and lung tumor microenvironment. Mol Biol Rep 2021; 48:1925-1934. [PMID: 33486674 PMCID: PMC7826145 DOI: 10.1007/s11033-021-06149-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Coronavirus Disease 2019 (COVID-19) is an acute respiratory syndrome, reported at the end of 2019 in China originally and immediately spread affecting over ten million world population to date. This pandemic is more lethal for the older population and those who previously suffered from other ailments such as cardiovascular diseases, respiratory disorders, and other immune system affecting abnormalities including cancers. Lung cancer is an important comorbidity of COVID-19. In this review, we emphasized the impact of lung tumor microenvironment (TME) on the possibility of enhanced severity of infection caused by the SARS-Co-V2. The compromised lung TME is further susceptible to the attack of viruses. The lung cells are also abundant in the virus entry receptors. Several SARS-Co-V2 proteins can modulate the lung TME by disrupting the fragile immune mechanisms contributing to cytokine storming and cellular metabolic variations. We also discussed the impact of medication used for lung cancer in the scenario of this infection. Since other respiratory infections can be a risk factor for lung cancer, COVID-19 recovered patients should be monitored for tumor development, especially if there is genetic susceptibility or it involves exposure to other risk factors.
Collapse
|
20
|
Role of Glutathione in Cancer: From Mechanisms to Therapies. Biomolecules 2020; 10:biom10101429. [PMID: 33050144 PMCID: PMC7600400 DOI: 10.3390/biom10101429] [Citation(s) in RCA: 356] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022] Open
Abstract
Glutathione (GSH) is the most abundant non-protein thiol present at millimolar concentrations in mammalian tissues. As an important intracellular antioxidant, it acts as a regulator of cellular redox state protecting cells from damage caused by lipid peroxides, reactive oxygen and nitrogen species, and xenobiotics. Recent studies have highlighted the importance of GSH in key signal transduction reactions as a controller of cell differentiation, proliferation, apoptosis, ferroptosis and immune function. Molecular changes in the GSH antioxidant system and disturbances in GSH homeostasis have been implicated in tumor initiation, progression, and treatment response. Hence, GSH has both protective and pathogenic roles. Although in healthy cells it is crucial for the removal and detoxification of carcinogens, elevated GSH levels in tumor cells are associated with tumor progression and increased resistance to chemotherapeutic drugs. Recently, several novel therapies have been developed to target the GSH antioxidant system in tumors as a means for increased response and decreased drug resistance. In this comprehensive review we explore mechanisms of GSH functionalities and different therapeutic approaches that either target GSH directly, indirectly or use GSH-based prodrugs. Consideration is also given to the computational methods used to describe GSH related processes for in silico testing of treatment effects.
Collapse
|
21
|
Heredia-Soto V, Redondo A, Kreilinger JJP, Martínez-Marín V, Berjón A, Mendiola M. 3D Culture Modelling: An Emerging Approach for Translational Cancer Research in Sarcomas. Curr Med Chem 2020; 27:4778-4788. [PMID: 31830880 DOI: 10.2174/0929867326666191212162102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/30/2019] [Accepted: 11/25/2019] [Indexed: 01/15/2023]
Abstract
Sarcomas are tumours of mesenchymal origin, which can arise in bone or soft tissues. They are rare but frequently quite aggressive and with a poor outcome. New approaches are needed to characterise these tumours and their resistance mechanisms to current therapies, responsible for tumour recurrence and treatment failure. This review is focused on the potential of three-dimensional (3D) in vitro models, including multicellular tumour spheroids (MCTS) and organoids, and the latest data about their utility for the study on important properties for tumour development. The use of spheroids as a particularly valuable alternative for compound high throughput screening (HTS) in different areas of cancer biology is also discussed, which enables the identification of new therapeutic opportunities in commonly resistant tumours.
Collapse
Affiliation(s)
| | - Andrés Redondo
- Translational Oncology Group, IdiPAZ, La Paz University Hospital, Madrid, Spain
| | - José Juan Pozo Kreilinger
- Molecular Pathology and Therapeutic Targets Group, Idi- PAZ,La Paz University Hospital, Madrid, Spain
| | | | - Alberto Berjón
- Molecular Pathology and Therapeutic Targets Group, Idi- PAZ,La Paz University Hospital, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Idi- PAZ,La Paz University Hospital, Madrid, Spain
| |
Collapse
|
22
|
Spatio-temporal aspects of the interplay of cancer and the immune system. J Biol Phys 2019; 45:395-400. [PMID: 31773382 PMCID: PMC6917631 DOI: 10.1007/s10867-019-09535-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/07/2019] [Indexed: 10/26/2022] Open
Abstract
The conventional mean-field kinetic models describing the interplay of cancer and the immune system are temporal and predict exponential growth or elimination of the population of tumour cells provided their number is small and their effect on the immune system is negligible. More complex kinetics are associated with non-linear features of the response of the immune system. The generic model presented in this communication takes into account that the rates of the birth and death of tumour cells inside a tumour spheroid can significantly depend on the radial coordinate due to diffusion limitations in the supply of nutrients and/or transport of the species (cells and proteins) belonging to the immune system. In this case, non-trivial kinetic regimes are shown to be possible even without appreciable perturbation of the immune system.
Collapse
|