This page includes Agent-based three-dimensional cancer-tumour-microenvironment (TME) models were developed within the scope of the TÜBİTAK 1001 Project with the number 120S987.
In this study, the brain tumour and tumour microenvironment are being mathematically modelled using PhysiCell/BioFVM and PhysiCell Studio. More than ten thousand individual cells and more than fifty substrates already implemented and under development in our in-silico tissue including their biological and physical properties according to literature information in addition to spatial and omics data collected from healthy and tumour tissues. In this way Cancer-TME is reconstructed at the individual agent level, that can reflect heterogeneity among different cell types even between individual cells, thanks to PhysiCell’s agent-based-continuum structure.
Glioblastoma and Tumor Microenvironment
Glioblastoma (GM) is one of most common and aggressive malignant brain tumours with poor prognosis. The median overall survival of GBM patients is only 15 months. [Cybulska, 2022]. GM Characterized by hypervascularized and necrotic microenvironment caused by hypoxia, the tumour and its microenvironment form a complex tangle of interactions [Balañà, 2021]. Tumour tissue communicates with the surrounding healthy tissue and often manipulate it for its own favor.
Our 3D brain tissue with glioblastoma, can serve virtual laboratory to test or discover novel drug targets such as associated gene products and metabolites which can play significant role in development of brain tumours.
Adenocarcinoma and Tumor Microenvironment
Non-small cell lung carcinoma, (NSCLC) Corresponding to 85% of all lung cancers, NSCLC is the most common type of lung cancer. 50% of the NSCLC cases are lung adenocarcinomas (LUADs), being the most common subtype of NSCLC. With a 5-year survival rate of 15%, LUAD is the most frequent cause of cancer-related death. The late diagnosis of the cases, and the high inter- and intratumoral heterogeneity challenge the treatment efforts.
Hepatocellular carcinoma and Tumor Microenvironment
Hepatocellular carcinoma (HCC), 90% of all liver cancer cases are HCC, which is the most common type of liver cancer. HCC is the third most frequent cause of cancer-related death in the world. The severity of the HCC is underpinned by the fact that the worldwide incidence and mortality of the disease are very close to each other. HCC progression is characterized by the interaction of cancer cells with the cellular and non-cellular components of the TME such as immune cells, parenchymal cells, hypoxia, and ECM.
This page is under construction, new models and information will be available by the end of January 2025, in the meantime you can check our YouTube channel.
Brain Microenviroment
Oxygen Level – Low
Oxygen Level – Mid
Oxygen Level- High
Ici Initial Time – 7
Ici Initial Time – 15
Ici Initial Time – 30
Ici Period – 7
Ici Period – 14
Ici Period – 28
Cart Dose cn – 375
Cart Dose cn -750
Cart Dose cn – 1500
Migration Speed – 2.5
Migration Speed – 5
Migration Speed – 10
Glucose Level – Low
Glucose Level – Mid
Glucose Level – High
Brain – Max Biomass 3e-4
Brain – Max Biomass 6e-4
Brain – Max Biomass 15e-4
Brain – crat_init_thres 250
Brain – crat_init_thres 500
Brain – crat_init_thres 750
Brain – cart_optxglucose Low
Brain – cart_optxglucose Mid
Brain – cart_optxglucose High
Brain – cartopxglucose_var High
Brain – cartopxglucose_var Mid
Brain – cartopxglucose_var Low
Liver Microenviroment
Liver – _cart_dose_cn – 335
https://youtube.com/shorts/WRuAt7pZakI?si=vsWMuTYScTDhm1pd
Liver – _cart_dose_cn – 675
https://youtube.com/shorts/Qw0VtlLBZOA?si=XQSsv_Wifxqit4Tb
Liver – _cart_dose_cn – 1350
https://youtube.com/shorts/mSE_5B1Pcu0?si=8Yl7HohxZ91JdA-3
Liver – _cart_init_thr – 350
https://youtube.com/shorts/C-D11SA7AQU?si=ao8OD4xw51d3MnB-
Liver – _cart_init_thr – 450
https://youtube.com/shorts/sd0fzviuRZ0?si=nDrI0FhFtr7cs-Hx
Liver – _cart_init_thr – 550
https://youtube.com/shorts/E6efGIk4thI?si=Hjg3GTQlEnT_lj3Q
Liver – _cart_optxglucose_var – High
https://youtube.com/shorts/80t9yDaG7ZA?si=Peu5m_4aJokAUWQ9
Liver – _cart_optxglucose_var – Mid
https://youtube.com/shorts/xOfWZybTdws?si=9w6ph45B6x2jGc8w
Liver – _cart_optxglucose_var – Low
https://youtube.com/shorts/_oOas1Bp5mM?si=m6JM8W61UaFHZsim
Liver – Glucose Levels – High
https://youtube.com/shorts/QKjKdNeFZ-Q?si=wt6y5LxIdaXRWji4
Liver – Glucose Levels – Mid
https://youtube.com/shorts/zO3s9zynoIg?feature=share
Liver – Glucose Levels – Low
https://youtube.com/shorts/GPO5CjBP93s?feature=share
Liver – ici period – 7
https://youtube.com/shorts/t0URu7521Zw?feature=share
Liver – ici period – 14
https://youtube.com/shorts/oV2T0V56x64?feature=share
Liver – ici period – 28
https://youtube.com/shorts/sNQ19i-qb3E?feature=share
Liver – Oxygen Levels – High
https://youtube.com/shorts/GdyVzTk_3rg?feature=share
Liver – Oxygen Levels – Mid
https://youtube.com/shorts/t0_ldv78kc4?feature=share
Liver – Oxygen Levels – Low
https://youtube.com/shorts/iTlH0kWb7g8?feature=share
Liver – Max Biomass – 0.02
https://youtube.com/shorts/4QI-x4l1jPw?feature=share
Liver – Max Biomass – 0.01
https://youtube.com/shorts/NVUHuRvDKYA?feature=share
Liver – Max Biomass – 0.005
https://youtube.com/shorts/MXrV9GAqst0?feature=share
Liver – Migration Speed – 5
https://youtube.com/shorts/U_Y2eKsQyfc?feature=share
Liver – Migration Speed – 10
https://youtube.com/shorts/Z3swjSHVB8U?feature=share
Liver – Migration Speed – 20
https://youtube.com/shorts/cdvdYT_3VbQ?feature=share
Liver – ici_optxglucose_var – High
https://youtube.com/shorts/QXZ8cxfUb0E?feature=share
Liver – ici_optxglucose_var – Mid
https://youtube.com/shorts/nf7HeTb4EqY?feature=share
Liver – ici_optxglucose_var – Low
https://youtube.com/shorts/e8-7ooEZYnQ?feature=share
Liver – ici_initial_time – 7
https://youtube.com/shorts/1NfbYXnyjWU?feature=share
Liver – ici_initial_time – 15
https://youtube.com/shorts/7BVNbvikuxA?feature=share
Liver – ici_initial_time – 30
https://youtube.com/shorts/C6sTHRV6Z0M?feature=share
Lung Microenviroment
Lung – _cart_dose_cn – 200
https://www.youtube.com/shorts/HqqH8Ex7T6M
Lung – _cart_dose_cn – 400
https://youtube.com/shorts/ma78bWNtFzw?si=8jZkVCy1UhYAomxt
Lung – _cart_dose_cn – 800
https://youtube.com/shorts/Q0Bme5OGrIg?si=ho3tRiNvuLnYITif
Lung – _cart_init_thr – 225
https://youtube.com/shorts/ycCVeAsdQvg?si=C1Uqm_3ZkjrYLg52
Lung – _cart_init_thr – 450
https://youtube.com/shorts/FAHskHWkvuM?si=ytflRWgm7V-UoeMY
Lung – _cart_init_thr – 900
https://youtube.com/shorts/LC-6Pju7ajw?si=z70r9oHQ_qrcHDWz
Lung – _cart_optxglucose_var – High
https://youtube.com/shorts/P601_1rjiR4?si=bfcqN6XkyY2JdzCf
Lung – _cart_optxglucose_var – Mid
https://youtube.com/shorts/KO1lcjSXPgw?si=Kc-l2Ig6OES2xRXn
Lung – _cart_optxglucose_var – Low
https://youtube.com/shorts/I8x9lVZeJ8Q?si=EqCbHnXir_1rkxyZ
Lung – glucose_levels – High
https://youtube.com/shorts/ekIX9G0qi3Q?si=R-Uin8iLesWzPjpv
Lung – glucose_levels – Mid
https://youtube.com/shorts/EEJ8oPmfhwY?si=slV5QjycfckWbw4l
Lung – glucose_levels – Low
https://youtube.com/shorts/SGM_sfGEcas?si=WC6w8JcQGUYHhSpe
Lung – _ici_initial_time – 7.5
https://youtube.com/shorts/etETttuKoGA?si=vGOTfm4-Z32W7dp6
Lung – _ici_initial_time – 15
https://youtube.com/shorts/iNDVlUMIaaw?si=Ozowo4SU3Zyt-FqG
Lung – _ici_initial_time – 30
https://youtube.com/shorts/DaoJgOkl-h0?si=pfCbHNbp0VENq6_H
https://youtube.com/shorts/4NME1pAtGgs?si=Kj4SUaxHd4txg2gA
Lung – _ici_period – 28
https://youtube.com/shorts/jZc6OtIPc78?si=jXlBQzlkhuSJ0wyG
Lung – Oxygen Levels – High
https://youtube.com/shorts/40N3YRLjYBw?si=KcBWElwmqIHNxIRw
Lung – Oxygen Levels – Mid
https://youtube.com/shorts/heLaaEWDobM?si=4_zskqnwIMXxhMCl
Lung – Oxygen Levels – Low
https://youtube.com/shorts/HCDVAP1xaak?si=AQav8ONg5vGrN4ts
Lung – Migration Speed – 2.5
https://youtube.com/shorts/FyAz7WPQJSI?si=IoLfJEzrcvAAXnmZ
Lung – Migration Speed – 5
https://youtube.com/shorts/5klmcJMhwGs?si=-CMaFION9U-3bU0o
Lung – Migration Speed – 10
https://youtube.com/shorts/BeP118G63Rs?si=XyCyQgcVpb7I8t3B
Lung – Max Biomass Level – 1e-5
https://youtube.com/shorts/V1UXakPWq5M?si=hjnWQMxCrP3hhVFs
Lung – Max Biomass Level – 2e-5
https://youtube.com/shorts/Au0mcJ4dS0U?si=1Cv-xr_QfL1y6hRu
Lung – Max Biomass Level – 4e-5