Perez-Garcia19 - Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas

  public model
Model Identifier
BIOMD0000000814
Short description
This is a model built by COPASI4.24(Build 197) This a model from the article: Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas Víctor M. Pérez-García, Luis E. Ayala-Hernández, Juan Belmonte-Beitia, Philippe Schucht, Michael Murek, Andreas Raabe, Juan Sepúlveda. PLoS Comput Biol. 2019 Jul; 15(7): e1006778. Abstract: Here we put forward a mathematical model describing the response of low-grade (WHO grade II) oligodendrogliomas (LGO) to temozolomide (TMZ). The model describes the longitudinal volumetric dynamics of tumor response to TMZ of a cohort of 11 LGO patients treated with TMZ. After finding patient-specific parameters, different therapeutic strategies were tried computationally on the ‘in-silico twins’ of those patients. Chemotherapy schedules with larger-than-standard rest periods between consecutive cycles had either the same or better long-term efficacy than the standard 28-day cycles. The results were confirmed in a large trial of 2000 virtual patients. These long-cycle schemes would also have reduced toxicity and defer the appearance of resistances. On the basis of those results, a combination scheme consisting of five induction TMZ cycles given monthly plus 12 maintenance cycles given every three months was found to provide substantial survival benefits for the in-silico twins of the 11 LGO patients (median 5.69 years, range: 0.67 to 68.45 years) and in a large virtual trial including 2000 patients. We used 220 sets of experiments in-silico to show that a clinical trial incorporating 100 patients per arm (standard intensive treatment versus 5 + 12 scheme) could demonstrate the superiority of the novel scheme after a follow-up period of 10 years. Thus, the proposed treatment plan could be the basis for a standardized TMZ treatment for LGO patients with survival benefits. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92
Format
SBML (L2V4)
Related Publication
  • Computational design of improved standardized chemotherapy protocols for grade II oligodendrogliomas.
  • Pérez-García VM, Ayala-Hernández LE, Belmonte-Beitia J, Schucht P, Murek M, Raabe A, Sepúlveda J
  • PLoS computational biology , 7/ 2019 , Volume 15 , Issue 7 , pages: e1006778 , PubMed ID: 31306418
  • Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Avda. Camilo José Cela, 3, 13071 Ciudad Real, Spain.
  • Here we put forward a mathematical model describing the response of low-grade (WHO grade II) oligodendrogliomas (LGO) to temozolomide (TMZ). The model describes the longitudinal volumetric dynamics of tumor response to TMZ of a cohort of 11 LGO patients treated with TMZ. After finding patient-specific parameters, different therapeutic strategies were tried computationally on the 'in-silico twins' of those patients. Chemotherapy schedules with larger-than-standard rest periods between consecutive cycles had either the same or better long-term efficacy than the standard 28-day cycles. The results were confirmed in a large trial of 2000 virtual patients. These long-cycle schemes would also have reduced toxicity and defer the appearance of resistances. On the basis of those results, a combination scheme consisting of five induction TMZ cycles given monthly plus 12 maintenance cycles given every three months was found to provide substantial survival benefits for the in-silico twins of the 11 LGO patients (median 5.69 years, range: 0.67 to 68.45 years) and in a large virtual trial including 2000 patients. We used 220 sets of experiments in-silico to show that a clinical trial incorporating 100 patients per arm (standard intensive treatment versus 5 + 12 scheme) could demonstrate the superiority of the novel scheme after a follow-up period of 10 years. Thus, the proposed treatment plan could be the basis for a standardized TMZ treatment for LGO patients with survival benefits.
Contributors
Submitter of the first revision: Szeyi Ng
Submitter of this revision: Szeyi Ng
Modellers: Szeyi Ng

Metadata information

is (2 statements)
BioModels Database BIOMD0000000814
BioModels Database MODEL1909170002

isDescribedBy (1 statement)
PubMed 31306418

hasProperty (5 statements)
Experimental Factor Ontology cancer
Mathematical Modelling Ontology Ordinary differential equation model
Experimental Factor Ontology oligodendroglioma
NCIt Temozolomide
NCIt Chemotherapy


Curation status
Curated


Tags

Connected external resources

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Model files

Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.xml SBML L2V4 file for the model 77.93 KB Preview | Download

Additional files

Fig 3e.png PNG plot of the model simulation 32.67 KB Preview | Download
Nuevo_Modelo_P105.m Correction MATLAB file sent by the author 2.07 KB Preview | Download
Nuevo_Modelo_TMZ_P105.m Correction MATLAB file sent by the author 574.00 Bytes Preview | Download
Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.cps COPASI 4.24 (Build 197) file for the model 71.35 KB Preview | Download
Perez-Garcia19 Computational design of improved standardized chemotherapy protocols for grade 2 oligodendrogliomas.sedml Sedml L1V2 file producing figure 2 6.02 KB Preview | Download

  • Model originally submitted by : Szeyi Ng
  • Submitted: Sep 17, 2019 11:17:13 AM
  • Last Modified: Sep 26, 2019 9:41:39 AM
Revisions
  • Version: 5 public model Download this version
    • Submitted on: Sep 26, 2019 9:41:39 AM
    • Submitted by: Szeyi Ng
    • With comment: Edited model metadata online.
  • Version: 3 public model Download this version
    • Submitted on: Sep 17, 2019 11:17:13 AM
    • Submitted by: Szeyi Ng
    • With comment: Automatically added model identifier BIOMD0000000814

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
Drug Concentration C

Chemotherapy ; Concentration
0.0 mol
Tumor Cell Population P

cancer
144.952075141053 mol
Damaged Tumor Cells D

cancer ; Abnormal
0.0 mol
Reactions
Reactions Rate Parameters
Drug_Concentration_C => compartment*lambda*Drug_Concentration_C lambda = 8.3184 1/d
Tumor_Cell_Population_P => ; Drug_Concentration_C compartment*alpha_2*Tumor_Cell_Population_P*Drug_Concentration_C alpha_2 = 0.1396877593
Tumor_Cell_Population_P => Damaged_Tumor_Cells_D; Drug_Concentration_C compartment*alpha_1*Tumor_Cell_Population_P*Drug_Concentration_C alpha_1 = 0.1027971308
=> Tumor_Cell_Population_P; Damaged_Tumor_Cells_D compartment*rho*Tumor_Cell_Population_P*(1-(Tumor_Cell_Population_P+Damaged_Tumor_Cells_D)/K) K = 261.799 m^3; rho = 0.002931927433 1/d
Damaged_Tumor_Cells_D => ; Tumor_Cell_Population_P compartment*rho*Damaged_Tumor_Cells_D*(1-(Tumor_Cell_Population_P+Damaged_Tumor_Cells_D)/K)/kappa K = 261.799 m^3; kappa = 1.0; rho = 0.002931927433 1/d
Curator's comment:
(added: 17 Sep 2019, 11:16:19, updated: 26 Sep 2019, 09:42:22)
I reproduced Fig.3(e) by using cps file and COPASI. The figure plotted is tumor size, which is Tumor Cell Population P + Damaged Tumor Cells D. Extra data provided from the author: b=1.9 m^(2), β=2.1*10^(-6)/ml and C is equal to b*β*d with d=150mg/m(^2), that is 0.5985 µg/ml. One dose given on days 1 to 5 and 23 rest days. there are 20 cycles. Initial values: P=144.9520751, C=0, D=0 COPASI is not very stable when performing the events, please use dose1-5 to check if 20 doses are given at correct times.