Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment
Round 1
Reviewer 1 Report
The manuscript entitled “Multiscale agent-based and hybrid modeling of the tumor immune microenvironment” is an aptly written review article enriched with recent knowledge in tumor microenvironment. Their proposed model to study components of tumor microenvironment aid in better understanding of mechanistic view to predict capabilities of therapeutic interventions in Cancer. I propose to accept this manuscript after some minor corrections as indicated below.
- Some of the references sited in this article points towards “Review Articles” instead of the direct study that was published for a particular type of cancer. Kindly replace the references (mostly review articles) with the direct published article to make the correlation proper.
Author Response
We thank the reviewers for their constructive comments. We revised the manuscript in response to the comments and we address them below.
Reviewer's Comments:
The manuscript entitled “Multiscale agent-based and hybrid modeling of the tumor immune microenvironment” is an aptly written review article enriched with recent knowledge in tumor microenvironment. Their proposed model to study components of tumor microenvironment aid in better understanding of mechanistic view to predict capabilities of therapeutic interventions in Cancer. I propose to accept this manuscript after some minor corrections as indicated below.
- Some of the references sited in this article points towards “Review Articles” instead of the direct study that was published for a particular type of cancer. Kindly replace the references (mostly review articles) with the direct published article to make the correlation proper.
We thank the reviewer for their helpful comments. We have updated the references as suggested, see lines 230-241.
Reviewer 2 Report
In this review article, the authors summarize the applications of agent–based models and hybrid modeling to understand tumor immune microenvironment and immune responses against cancer. Overall, the review reads well and the different sections highlight the different aspects, how the models have been used to understand the complex tumor microenvironment. Some suggestions:
1. Section 2, the title can be changed to “Immune system biology and Cancer”
2. Some sentences are not clear: for example, line 109-110, what is “across many time scales”? Line 286, what is “ODEs at each time step”? Lines 293-293, sentence is not clear.
3. Section 3.3: The authors need to discuss in the context of tumor.
Need to change the way references are cited. For consistency, use the authors and not start with the reference number. For example, line 302 and 341.
Author Response
We thank the reviewers for their constructive comments. We revised the manuscript in response to the comments and we address them below.
In this review article, the authors summarize the applications of agent–based models and hybrid modeling to understand tumor immune microenvironment and immune responses against cancer. Overall, the review reads well and the different sections highlight the different aspects, how the models have been used to understand the complex tumor microenvironment. Some suggestions:
1. Section 2, the title can be changed to “Immune system biology and Cancer”
We have changed the title as the reviewer suggested.
2. Some sentences are not clear: for example, line 109-110, what is “across many time scales”? Line 286, what is “ODEs at each time step”? Lines 293-293, sentence is not clear.
We thank the reviewer for pointing these out. We have changed them as follows:
“In addition, different functions of the immune system occur at different time scales, ranging from minutes to years.” (Lines 158-159)
“Marino et al. developed a hybrid ABM where lymph node activities were simulated using ordinary differential equations and the lung compartment was simulated using agents.” (Lines 367-370)
“A variety of cancer immunotherapy strategies exist that range from boosting the overall immune response to specifically targeting cancer immunity. Some examples of immunotherapies are treatment vaccines, adoptive cell transfer, and immune checkpoint inhibitor treatments.” (Lines 381-386)
3. Section 3.3: The authors need to discuss in the context of tumor.
Thank you for your suggestion. As stated in lines 355-359, ABMs developed for the study of lymphatics thus far mainly focus on the lymph node. And in the lymph node they mainly focus on T cells. Hybrid models of tumor growth have also incorporated LNs, which have been discussed in this section. We have also included studies by Marino et al. who combined ABM and ODE model to study Mtb infection. The model includes blood and LN component. They focus on formation of granulomas in lung, which are organized structures of immune cells in lung. Although these structures are not cancerous, the methodology can be applied to study of tumors.
Need to change the way references are cited. For consistency, use the authors and not start with the reference number. For example, line 302 and 341.
We thank the reviewer for highlighting this inconsistency. We have changed the references so that the citations are consistent.
Reviewer 3 Report
This review paper is well written. Two items are suggested to maximize the impact of this publication.
1. The Introduction statement in Section 3 (before Section 3.1 begins) should clarify what criteria this review is using to include or exclude studies to be mentioned.
2. It would be helpful as a quick reference to provide a table at the end of Section 3 that lists the studies mentioned, their focus, and the corresponding citations(s).
Author Response
We thank the reviewers for their constructive comments. We revised the manuscript in response to the comments and we address them below.
This review paper is well written. Two items are suggested to maximize the impact of this publication.
1. The Introduction statement in Section 3 (before Section 3.1 begins) should clarify what criteria this review is using to include or exclude studies to be mentioned.
We have included the following review criteria to Section 3. “In order to be included in the review, the work needs to have an immune component, a tumor component, and include ABMs. We limited our focus to papers that were published within the last ten years. However, we also included some studies on diseases other than cancer where we feel that the methodology is relevant and could be applied to cancer; we also refer to a few general software tools that can be readily adapted to cancer.” (Lines 242-248)
2. It would be helpful as a quick reference to provide a table at the end of Section 3 that lists the studies mentioned, their focus, and the corresponding citations(s).
We added Table 1 summarizing the models in the studies mentioned on pg. 19
Reviewer 4 Report
The brief overview of the immune system was perhaps too simplistic and lacked several topics in oncoimmunology that should be included, even by citing a review (for example, trained immunity, T-cell exhaustion, no mention of e.g. neutrophils in cancer,etc.) My suggestion would be to at least mention these new results, or perhas not include such a review of the immune system.
A similar review as the one being presented, granted not focusing on ABMs, that should be mentioned is the work of Konsotorum et al on computational modeling and immunotherapy pmid 28659410.
There was a miscitation (I think) in line 173[47], which makes me think that the authors should carefully check their citations.
Line 27-Extra period at the end.
Line 35- “Including cells resident in the tissue and immune cells” is sort of confusing. Immune cells can be resident in the tissue. Suggested- Including immune cells and other cells resident in the tissue.
Line 42- See reviews (authors suggest two papers).
Line 67-“recognize non-self...” non-self what?
Here in the review of the immune system, several cell types remain unmentioned, which is OK, but clarify that you are giving a brief overview. Neutrophils play an important role in cancer and so do NK cells. Also, some studies suggest that the innate immune system also has the capability of memory (Trained immunity).
Line 95- Macrophages CAN aid in tumor progression.
Figure 2- Several other modeling frameworks exist for the cellular scale (Boolean networks, Petri Nets, etc.) For the tissue-scale, it’s also worth mentioning cellular-Potts. (This is mentioned in line 169, but not in the figure.
Line 159- I am unsure of what the authors mean my “predicting emergent behavior”.
Line 162- First time they mention rule-based modeling- please briefly explain what this means.
Line 171- Correct to the immune system’s function.
Line 173- Is citation [47] really the right citation for this? Doesn’t seem like it from reading the citation’s abstract
Line 185- In my opinion, PhysiCell should be added to this list. PMID 29474446.
Line 186-“Next ...” seems to be too abrupt of a switch here. Maybe we now discuss
In line 200, you refer to the authors, but in line 204, you use kather er al. Please be consistent.
Line 206- Suggested: Aims to increase
Section 3.1- Here only two articles are mentioned. I think it’s worth mentioning some more articles in such a review (see e.g. PMID 29445035). Although it is not necessary to be completely comprehensive, it is worthwhile giving more examples
Line 223- “to grow, BUT it is also”
Line 232- Again, either the authors or Alfonso et al. Don’t use both.
Line 242,243- Such as ?...
Line 259- This is the first time you use lattice-based. For someone that knows nothing about ABM, this is a meaningless statement.
Line 275- Why is it important that the grid size is the size of one T-cell?
Line 278-282- These statements are sort of confusing and can be significantly reduced in length. It took me a few reads to notice the distinction between general studies of the lymphatic system and cancer models. Please rewrite this.
Line 285-286 (Lymph node activities? Meaningless statement.
Line 288-What is “the” infection? An MTb infection?
Line 300- Why mention ODE models if focused on ABMs? This has been done as well (245,247). I would remove any mentions of ODE models in the section were we are focused on ABMs
Line 308-Suggested: After calibrating and validating the model,
Line 312- Why mention Netlogo? Has software been mentioned for the other models?
Line 319- “The model includes immune cells, macrophages, DCs” (macrophages and DCs are immune cells, are there others?)
Line 320-321 “Effectively eliminated tumor?”
Line 321- Citation for the fact on CD137 is missing.
Line 327-T-cell therapy ad another cancer therapy: -> T-cell therapy and oncolytic virus therapy
Line 354- What is the cell death paradox?
Line 373- If this is the first time angiogenesis is mentioned, please define.
Line 373-374 “Macrophages in tumor invasive fingers contribute to their survival over time”- I am not sure I understand this sentence.
Line 377-378- If 121 is not an ABM model, why mention it here?
Line 392- Have NK cells been defined before?(Natural killer)
Line 413-414 How do you compare an agent-based model to a Gillespie Algorithm? This sentence makes no sense to me.
Line 455- There is a trailing \
Line 481- With drugS]
Line 486- There is a missing opening parenthesis
Line 499- Affect should be affects
Line 502- What stochastic nature? Not
In the abstract, it is mentioned that the role of digital pathology in parametrizing and validating spatial computational models is discussed. I don’t find such discussion sufficient to make it into the abstract, as it remains superficial (Line 508-513)
Author Response
We thank the reviewers for their constructive comments. We revised the manuscript in response to the comments and we address them below.
The brief overview of the immune system was perhaps too simplistic and lacked several topics in oncoimmunology that should be included, even by citing a review (for example, trained immunity, T-cell exhaustion, no mention of e.g. neutrophils in cancer,etc.) My suggestion would be to at least mention these new results, or perhaps not include such a review of the immune system.
We have included additional information on these topics in the introduction.
“Another way that tumors escape detection is through chronic inflammation [17]. During chronic inflammation, T-cells eventually lose their effectiveness over the course of the infection, called T cell exhaustion [18]. T cell exhaustion is also frequently found in the tumor microenvironment through the PD-L1/PD-1 pathway [19]. PD-1 blockage enhances T cell and NK (natural killer) cell activity in tumors [20,21]. Several immune checkpoint inhibitors are currently being used in treatment of patients with cancer [23,24]. ” (Lines 120-126)
“Neutrophils are less abundant in tumors but they are becoming more recognized for their duel role in the immune response to cancer [40]. Eosinophils are also commonly found within tumors [41] and have been found to enhance T cell infiltration [42]. These cells also have a duel role in the immune response and can promote or suppress tumor growth [43]. There is a complex interaction between cancer cells and the immune system.” (Lines 145-150)
We have also added NK cells and neutrophils in Fig.1
A similar review as the one being presented, granted not focusing on ABMs, that should be mentioned is the work of Konsotorum et al on computational modeling and immunotherapy pmid 28659410.
We have included a reference to this review in our immune system modeling section.
There was a miscitation (I think) in line 173[47], which makes me think that the authors should carefully check their citations.
We have corrected this citation.
Line 27-Extra period at the end.
We have removed the extra period.
Line 35- “Including cells resident in the tissue and immune cells” is sort of confusing. Immune cells can be resident in the tissue. Suggested- Including immune cells and other cells resident in the tissue.
We have corrected the sentence based on reviewer’s suggestion.
Line 42- See reviews (authors suggest two papers).
Corrected.
Line 67-“recognize non-self...” non-self what?
Here in the review of the immune system, several cell types remain unmentioned, which is OK, but clarify that you are giving a brief overview. Neutrophils play an important role in cancer and so do NK cells. Also, some studies suggest that the innate immune system also has the capability of memory (Trained immunity).
We have included several additional sentences addressed these important aspects that were not addressed. See above and
“The innate immune response is immediate, although some studies suggest these cells also have the capability for memory [10], and may be followed by an adaptive immune response.” (Lines 95-98)
Line 95- Macrophages CAN aid in tumor progression.
Corrected.
Figure 2- Several other modeling frameworks exist for the cellular scale (Boolean networks, Petri Nets, etc.) For the tissue-scale, it’s also worth mentioning cellular-Potts. (This is mentioned
in line 169, but not in the figure.
We have updated Figure 2 and added the other modeling frameworks based on the comments.
Line 159- I am unsure of what the authors mean my “predicting emergent behavior”.
We clarified this statement.
Line 162- First time they mention rule-based modeling- please briefly explain what this means.
We added an explanation to this statement.
Line 171- Correct to the immune system’s function.
Corrected.
Line 173- Is citation [47] really the right citation for this? Doesn’t seem like it from reading the citation’s abstract
The citation has been corrected.
Line 185- In my opinion, PhysiCell should be added to this list. PMID 29474446
We added PhysiCell to this list.
Line 186-“Next ...” seems to be too abrupt of a switch here. Maybe we now discuss
We made the change as suggested.
In line 200, you refer to the authors, but in line 204, you use kather er al. Please be consistent.
We changed the wording for consistency.
Line 206- Suggested: Aims to increase
Corrected.
Section 3.1- Here only two articles are mentioned. I think it’s worth mentioning some more articles in such a review (see e.g. PMID 29445035). Although it is not necessary to be completely comprehensive, it is worthwhile giving more examples
We have given more examples, such as the one listed above, but did not go into depth for non ABMs. (Lines 260-261)
Line 223- “to grow, BUT it is also”
Corrected.
Line 232- Again, either the authors or Alfonso et al. Don’t use both.
Corrected.
Line 242,243- Such as ?...
We added an example to this statement.
Line 259- This is the first time you use lattice-based. For someone that knows nothing about ABM, this is a meaningless statement.
We have now introduced the concept of lattice in lines 223-226. Lattice-based is removed from this sentence.
Line 275- Why is it important that the grid size is the size of one T-cell?
This statement is removed.
Line 278-282- These statements are sort of confusing and can be significantly reduced in length. It took me a few reads to notice the distinction between general studies of the lymphatic system and cancer models. Please rewrite this.
This section has been re-written for clarity
Line 285-286 (Lymph node activities? Meaningless statement.
Text has been revised for clarity. We have removed “lymph node activities”.
Line 288-What is “the” infection? An MTb infection?
Text has been revised for clarity. “the infection” is removed.
Line 300- Why mention ODE models if focused on ABMs? This has been done as well (245,247). I would remove any mentions of ODE models in the section were we are focused on ABMs
We have removed references to ODEs in ABM sections unless we are specifically addressing them as part of a hybrid model.
Line 308-Suggested: After calibrating and validating the model.
We made the changes as suggested.
Line 312- Why mention Netlogo? Has software been mentioned for the other models?
This has been removed.
Line 319- “The model includes immune cells, macrophages, DCs” (macrophages and DCs are immune cells, are there others?)
We revised this sentence.
Line 320-321 “Effectively eliminated tumor?”
Corrected.
Line 321- Citation for the fact on CD137 is missing.
We added a reference to CD137.
Line 327-T-cell therapy ad another cancer therapy: -> T-cell therapy and oncolytic virus therapy
We reworded this sentence.
Line 354- What is the cell death paradox?
We have revised this statement.
Line 373- If this is the first time angiogenesis is mentioned, please define.
We changed this sentence.
Line 373-374 “Macrophages in tumor invasive fingers contribute to their survival over time”- I
am not sure I understand this sentence.
We have revised this sentence for clarity.
Line 377-378- If 121 is not an ABM model, why mention it here?
We removed this reference from the manuscript.
Line 392- Have NK cells been defined before?(Natural killer)
Definition added on pg.4, line 124
Line 413-414 How do you compare an agent-based model to a Gillespie Algorithm? This sentence makes no sense to me.
We removed this statement.
Line 455- There is a trailing \
Removed.
Line 481- With drugS]
Corrected.
Line 486- There is a missing opening parenthesis
Corrected.
Line 499- Affect should be affects
Corrected.
Line 502- What stochastic nature? Not
We removed this statement.
In the abstract, it is mentioned that the role of digital pathology in parametrizing and validating spatial computational models is discussed. I don’t find such discussion sufficient to make it into the abstract, as it remains superficial (Line 508-513)
We have removed this reference from the abstract.
Round 2
Reviewer 4 Report
Line 138-142
"A multiscale setting can include both approaches...-" This seems misplaced. It almsot seems to refer to the fact that you can have a mix of deterministic and and stochastic models, but it actually refers to discrete vs continuous.
Line 172- Not sure what "is capable of emergenet behavior" means here. Capturing emergenet behavior?
Line 182- Lattice free or lattice based is not really dependent on how agents are distributed. This is misleading.
Line 247- Not sure which citation is Uppal et al refering to. Can you add the number after so reader does not have to go to bibliography?
Line 287-The new mode? Should this be the new model?
Line 290-Which paper is Moreau et al? Please add citation number as this occurs a few times afterwards in the article
Is it T-cell or T cell in the paper? Please be consistent
Line 299-Not sure that it can be used to optimize treatment strategies. Is there any proof that it actually works?
Line 303-"In the draining lymph node"-Is there only one draining lymph node?
Line 306-307 What are lymph node and blood compartment activities?This could really mean anything. Please clarify.
Line 315-Not sure what "processes .. are shared" means.
Some times the authors use DCs and other times they use Dedritic cells. Please be consistent.
Line 399-What does it mean to survive as a finger?
Line 402-What is spatial inhibition?
Line 413-426- I believe this paragraph is referring to two different studies, [137,138] although this is not clear how the paragraph is written. The summary of 137 is unsatisfactory. What aspect of interactions is it studying? Also, it's not clear to a first time reader what the Warburg effect is. Why is using glycolysis for energy unique?
Line 435-436 Not sure what the last sentence is saying. Is this in vivo generations of additional architectures? Please clarify
Line 25- I still do not see sufficient discussion about personalized medicine in the text to be in the abstract.
Author Response
Response to Reviewer
"A multiscale setting can include both approaches...-" This seems misplaced. It almsot seems to refer to the fact that you can have a mix of deterministic and and stochastic models, but it actually refers to discrete vs continuous.
We thank the reviewer for this correction. We have reordered the sentences for clarity, see lines 177-181.
“One is deterministic vs. stochastic; another is continuum vs. discrete models. Deterministic models have an end state that does not change if the initial conditions are the same, whereas stochastic models have randomness included in the model resulting in differences in end states even with the same initial conditions.”
Line 172- Not sure what "is capable of emergenet behavior" means here. Capturing emergenet behavior?
Emergent behavior is defined as “large-scale spatio-temperal patterns resulting from local spatial interactions.” We have noted that in the text, see line 216.
Line 182- Lattice free or lattice based is not really dependent on how agents are distributed. This is misleading.
We have revised this line for clarity, lines 228-231. “Agent-based models can be lattice-based or lattice-free depending on whether agents reside and move on a (regular or irregular) spatially discretized lattice, or have their locations and velocities represented by continuous variables, usually governed by forces. in the environment.”
Line 247- Not sure which citation is Uppal et al refering to. Can you add the number after so reader does not have to go to bibliography?
We have included the reference to Uppal on line 308.
Line 287-The new mode? Should this be the new model?
Corrected.
Line 290-Which paper is Moreau et al? Please add citation number as this occurs a few times afterwards in the article
The citation number has been added.
Is it T-cell or T cell in the paper? Please be consistent
We have changed all references to T-cell.
Line 299-Not sure that it can be used to optimize treatment strategies. Is there any proof that it actually works?
We have removed this line.
Line 303-"In the draining lymph node"-Is there only one draining lymph node?
Corrected on line 371.
Line 306-307 What are lymph node and blood compartment activities?This could really mean anything. Please clarify.
We have removed “activities” from line 375 for clarity.
Line 315-Not sure what "processes .. are shared" means.
The authors mean that the body reacts similarly in response to an infection as it does in response to cancer (e.g., activation of similar signaling pathways). Examples are given for clarity.
Some times the authors use DCs and other times they use Dedritic cells. Please be consistent.
We have removed all references to dendritic cells. The abbreviation is defined on line 344.
Line 399-What does it mean to survive as a finger?
We have removed this confusing statement.
Line 402-What is spatial inhibition?
We have defined spatial inhibition as below in line 491. “They observed that while macrophages increase tumor growth, excessive macrophage recruitment conversely leads to a decrease in tumor growth due to inhibition of proliferation due to overcrowding.”
Line 413-426- I believe this paragraph is referring to two different studies, [137,138] although this is not clear how the paragraph is written. The summary of 137 is unsatisfactory. What aspect of interactions is it studying? Also, it's not clear to a first time reader what the Warburg effect is. Why is using glycolysis for energy unique?
This paragraph was reworded for clarity and a better summary of 137 was included, lines 506-521. “A 2D agent-based model was used to study the interactions between an avascular tumor and immune cells (NK cells and cytotoxic T cells) [137]. They examined the effects of cancer cells that do not consider the microenvironment when deciding when to proliferate and those that proliferate based on the number of healthy cells surrounding it, on overall tumor growth. When an immune cell interacts with a tumor cell, either the tumor cell dies, nothing happens or the immune cell dies based on the state of the tumor. The predicted growth of the tumor was then compared to a xenograft tumor growth. Spatial heterogeneity was also examined in a different model, where cancer cells use glycolysis instead of oxidative phosphorylation to increase their energy production.”
Line 435-436 Not sure what the last sentence is saying. Is this in vivo generations of additional architectures? Please clarify
This was in comparison to other modeling methodologies. This has been clarified in line 540.
Line 25- I still do not see sufficient discussion about personalized medicine in the text to be in the abstract.
We have revised the abstract to include therapeutics instead of personalized medicine.
Author Response File: 
Author Response.pdf
