Review Reports - Targeting Neoantigens in Cancer: Possibilities and Opportunities in Breast Cancer

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Chaudhry et al has provided a comprehensive review about breast cancer treatment with a focus on targeting neoantigens. The manuscript includes basic introduction, highlights some clinical trial examples, and pinpoint the limitations and future directions of neoantigens targeted therapy. It is well written, and could be a good resource for the field. However, some minor points should be addressed before publication.

1. Line 75. The major issue of surgical intervention is the advanced stage of the disease, which makes it incurable by simple surgical removal, rather than physiological and psychosocial risks.

2. In section 2, starting from line 85, the authors are recommended to explicitly point out that the efficacy of ICB is very limited in breast cancer, unlike lung cancer and melanoma. This is not only an important fact of the current situation, but also makes a smooth transition for the introduction of neoantigen therapy.

3. In the future direction section, the authors should discuss more about the combination of neoantigen targeting with either ICB or CART. The current strategy to boost ICB efficiency in breast cancer is to combine it with therapy tarting DNA damage repair pathway to elevate immune response, however, this has suffered severe toxicity. Similarly, CAR T cells targeting common markers like CD20 also facing strong side effects like cytokine storm. Whether neoantigen has the potential to alleviate this dilemma by providing a more unique target is worth mentioning.

Author Response

Comment: Chaudhry et al has provided a comprehensive review about breast cancer treatment with a focus on targeting neoantigens. The manuscript includes basic introduction, highlights some clinical trial examples, and pinpoint the limitations and future directions of neoantigens targeted therapy. It is well written, and could be a good resource for the field. However, some minor points should be addressed before publication.

Response: Thank you for your comments and suggestions.

Concern 1: Line 75. The major issue of surgical intervention is the advanced stage of the disease, which makes it incurable by simple surgical removal, rather than physiological and psychosocial risks.

Response: We thank the reviewer for the recommendation. We have modified the text in the revised manuscript.

Concern 2: In section 2, starting from line 85, the authors are recommended to explicitly point out that the efficacy of ICB is very limited in breast cancer, unlike lung cancer and melanoma. This is not only an important fact of the current situation, but also makes a smooth transition for the introduction of neoantigen therapy.

Response: We thank the reviewer for the suggestion. We have modified the text in the revised manuscript.

Concern 3: In the future direction section, the authors should discuss more about the combination of neoantigen targeting with either ICB or CART. The current strategy to boost ICB efficiency in breast cancer is to combine it with therapy tarting DNA damage repair pathway to elevate immune response, however, this has suffered severe toxicity. Similarly, CAR T cells targeting common markers like CD20 also facing strong side effects like cytokine storm. Whether neoantigen has the potential to alleviate this dilemma by providing a more unique target is worth mentioning.

Response: We thank the reviewer for this suggestion and have now dedicated a portion of the Future Direction section towards extrapolating on the potential that CAR T cells harness in treating solid tumors associated with breast cancer. We briefly explain the mechanism of CAR T cells, their limitations, and weave in the possible benefit of co administering neoantigen based therapies.

Reviewer 2 Report

Comments and Suggestions for Authors

To the authors:

Chaudhry et al. provided a comprehensive summary of current research on identifying neoantigens and utilizing such neoantigens as direct targets for therapy, known as neoantigen-based immunotherapy. The authors discussed the limitations of standard treatments due to therapeutic resistance, emphasizing the need to explore new treatment options for resistant metastatic breast cancer. Neoantigen- or tumor-associated antigen-based immunotherapy is a promising strategy for the treatment of cancer and has been discussed in the following review. The manuscript is well-written, with an introductory section presenting general findings followed by an extensive review of neoantigen-based immunotherapies.

Minor Concern:

Line 62: “Chemotherapy, surgery, and radiation therapy”, shouldn’t it be the order “Surgery, radiation -, and chemotherapy”?

Line 92: “presented in the MHC of APCs”, needs to be more precise, such as this “presented on MHC of APCs” or “neo-antigenic peptides bond in the binding groove of MHC of APCs are presented to T cells”

Line 117: It is not clear how T cell immunity is responsible for “resistance”, “while neoantigens play a critical role in the efficacy of PD-1/PD-1L checkpoint inhibitors, resistance can also occur due to neoantigens loss resulting from selective clearance of neoantigen-presenting cells by T-cell immunity”. Are CD8+ T cells responsible for “killing” neoantigen presenting APCs?

Line 143: “Neoantigen refers to antigens that result from somatic mutations of major histocompatibility (MHC) molecules of tumor cells distinguishing them from self-antigens.” The MHC molecules are not “mutated”; instead, the neoantigens. This needs to be corrected. In addition, it should be stated that antigens/neoantigens are processed intracellularly (antigen processing), and antigenic peptides are bound to MHC molecules. Because in line 148, it is referred to as “mutant peptides”.

Line 190: “…the overall reduced expression of genes or loss of the mutant allele in melanoma…”, this should be more precise.

Line 193: “…a few immune cells…”, should be more precise, and the expression “few” is not appropriate.

Line 203: The “…loss of diversity…”. The paragraph needs to be rewritten and clearer.

Line 210/215: Cancer, lower-case letter “c” or upper-case letter? Need to be consistent.

Line 228: The sentence does not represent the statement from the paper from Umano et al.; please revise

Line 339: Dendritic cells, does not fit into the row.

Line 374: “haplotype” and in the next sentence it was referred to “ MHC alleles”?

Line 405: Keep consistent, upper or lower case letter, “(iii) Analysis” compared to “(v) variant”

Line 422: Should be MHC class I

Line 432: Being consistent, MHC class I, lower case “c in class”

Additional comments:

1. How (or is it possible) can a general vaccine be generated considering the individual MHC alleles, peptide binding to MHC, antigen processing, or different antigen-presenting cells?

2. Comment: 5. Neoantigens and 6. TP53 tumor-associated antigen etc., it would be clearer to categorize 5. tumor-specific antigens (neoantigens) and 6. tumor-associated antigens, followed by subheadings/examples , such as TP53, etc.

3. Table 1: Figure legend refers to “Clinical Trials of Neoantigen-based therapies for Breast Cancer”. The table 1, should include which kind of neoantigens were used. TB53 or PALB2?

Comments on the Quality of English Language

Minor corrections.

Author Response

Comments: Chaudhry et al. provided a comprehensive summary of current research on identifying neoantigens and utilizing such neoantigens as direct targets for therapy, known as neoantigen-based immunotherapy. The authors discussed the limitations of standard treatments due to therapeutic resistance, emphasizing the need to explore new treatment options for resistant metastatic breast cancer. Neoantigen- or tumor-associated antigen-based immunotherapy is a promising strategy for the treatment of cancer and has been discussed in the following review. The manuscript is well-written, with an introductory section presenting general findings followed by an extensive review of neoantigen-based immunotherapies.

Response: Thank you for your comments.

Concern 1: Line 62: “Chemotherapy, surgery, and radiation therapy”, shouldn’t it be the order “Surgery, radiation -, and chemotherapy”?

Response: Thank you for your comment. We have modified the text in the revised manuscript.

Concern 2: Line 92: “presented in the MHC of APCs”, needs to be more precise, such as this “presented on MHC of APCs” or “neo-antigenic peptides bond in the binding groove of MHC of APCs are presented to T cells”

Response: Thank you for your comment. We have modified the text in the revised manuscript.

Concern 3: Line 117: It is not clear how T cell immunity is responsible for “resistance”, “while neoantigens play a critical role in the efficacy of PD-1/PD-1L checkpoint inhibitors, resistance can also occur due to neoantigens loss resulting from selective clearance of neoantigen-presenting cells by T-cell immunity”. Are CD8+ T cells responsible for “killing” neoantigen presenting APCs?

Response: Thank you for your question. We corrected this statement as “resistance can occur due to an active antitumor response resulting in immunoselection and outgrowth of neoantigen-loss variants and tumor immune escape” as the literature source does not list T cells as responsible for “killing: neoantigen presenting APCs.

Concern 4: Line 143: “Neoantigen refers to antigens that result from somatic mutations of major histocompatibility (MHC) molecules of tumor cells distinguishing them from self-antigens.” The MHC molecules are not “mutated”; instead, the neoantigens. This needs to be corrected. In addition, it should be stated that antigens/neoantigens are processed intracellularly (antigen processing), and antigenic peptides are bound to MHC molecules. Because in line 148, it is referred to as “mutant peptides”.