Decoupled neoantigen cross-presentation by dendritic cells limits anti-tumor immunity against tumors with heterogeneous neoantigen expression
Curation statements for this article:-
Curated by eLife
eLife assessment
This important work advances our understanding of the import of clonal heterogeneity in cancers in immune response to individual antigens. The evidence supporting the conclusions is convincing, and uses interesting tools, although the mechanistic basis of the observations is unclear. The work will be of broad interest to immunologists including cancer immunologists.
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (eLife)
Abstract
Cancer immunotherapies, in particular checkpoint blockade immunotherapy (CBT), can induce control of cancer growth, with a fraction of patients experiencing durable responses. However, the majority of patients currently do not respond to CBT and the molecular determinants of resistance have not been fully elucidated. Mounting clinical evidence suggests that the clonal status of neoantigens (NeoAg) impacts the anti-tumor T cell response. High intratumor heterogeneity (ITH), where the majority of NeoAgs are expressed subclonally, is correlated with poor clinical response to CBT and poor infiltration with tumor-reactive T cells. However, the mechanism by which ITH blunts tumor-reactive T cells is unclear. We developed a transplantable murine lung cancer model to characterize the immune response against a defined set of NeoAgs expressed either clonally or subclonally to model low or high ITH, respectively. Here we show that clonal expression of a weakly immunogenic NeoAg with a relatively strong NeoAg increased the immunogenicity of tumors with low but not high ITH. Mechanistically we determined that clonal NeoAg expression allowed cross-presenting dendritic cells to acquire and present both NeoAgs. Dual NeoAg presentation by dendritic cells was associated with a more mature DC phenotype and a higher stimulatory capacity. These data suggest that clonal NeoAg expression can induce more potent anti-tumor responses due to more stimulatory dendritic cell:T cell interactions. Therapeutic vaccination targeting subclonally expressed NeoAgs could be used to boost anti-tumor T cell responses.
Article activity feed
-
-
Author Response
Reviewer #1 (Public Review):
The authors aim to understand the role of clonal heterogeneity of tumors in immunogenicity of clonally expressed antigens. This is a significant problem with many basic as well as translational implications.
The strength of the manuscript lies in the novel demonstration that a poorly immunogenic tumor antigen, when paired with a stronger tumor antigen, begins to elicit significant immune response. The weakness lies in the fact that the actual mechanism of the key demonstration is never shown. There is a lot of speculation and tangential experimentation, but little actual evidence of a mechanism.
By making the key observation (mentioned in the strength section in the previous paragraph), the authors did achieve their objective albeit very partially. Their observation is based on …
Author Response
Reviewer #1 (Public Review):
The authors aim to understand the role of clonal heterogeneity of tumors in immunogenicity of clonally expressed antigens. This is a significant problem with many basic as well as translational implications.
The strength of the manuscript lies in the novel demonstration that a poorly immunogenic tumor antigen, when paired with a stronger tumor antigen, begins to elicit significant immune response. The weakness lies in the fact that the actual mechanism of the key demonstration is never shown. There is a lot of speculation and tangential experimentation, but little actual evidence of a mechanism.
By making the key observation (mentioned in the strength section in the previous paragraph), the authors did achieve their objective albeit very partially. Their observation is based on excellent experimental tools and design. This study will stimulate further experiments in this important field.
Their key observation is somewhat reminiscent of the practice of conjugating small "non-immunogenic" antigens (such as some carbohydrates) to large protein carriers (such as serum albumin) in order to elicit strong antibody response to the weaker antigen. It is interesting to contemplate if the underlying mechanisms have any commonality.
We thank the reviewer for their consideration of our work and their constructive feedback. We concur that our study has limitations and further work will be necessary to fully deconstruct the mechanism leading to the observed phenotype. We have revised the text to better reflect the aim and scope of our study. However, the goal of our work was to establish a trackable model that would allow us to model different, albeit limited, degrees of antigen expression patterns reflecting what is observed in patients with different levels of ITH. Our key observation reproduces what is observed clinically, adding strength to the model. Next, we wanted to study what was different about the induced immune responses to develop strategies to better treat tumors with heterogeneous NeoAg expression patterns that currently do not respond to checkpoint blockade therapy. Studying KP-HetHigh and KP-HetLow tumors revealed that tumor debris-carrying cDC1 draining from KP-HetLow tumors phagocytosed both NeoAgs. This population of cDC1, carrying both NeoAgs, had a more stimulatory phenotype compared to cDC1 without tumor debris or cDC1 that had engulfed only one NeoAg. We were able to develop a targeted therapy including CD40 agonism based on our key observations: KP-HetLow had a more robust response towards the weaker NeoAg which was associated with more stimulatory cDC1 presenting both NeoAgs compared to KP-HetHigh tumors. The stronger immune response increased responsiveness to CBT.
The reviewer makes an interesting point about conjugate vaccines, which canonically elicit greater responses because they engage multiple immune cells, namely T cells with B cells, resulting in stronger antibody responses. The prevalence of tumor debris-carrying cDC1 with both neoantigens in KP-HetLow does make us consider that this population of cDC1 may be engaging multiple immune populations, i.e., different neoantigen-specific T cells. We suggest this as a possible mechanism for greater Aatf responses, but further work is necessary to determine if the same cDC1 can directly interact with both neoantigen-specific T cells.
Reviewer #2 (Public Review):
There are data to suggest that intratumour mutational heterogeneity (ITH; the proportion of all mutations that are found only within cancer subclones) is associated with worse therapeutic outcomes. Specifically, patients with more mutations (and thus neoantigens) mostly expressed by subclones (high ITH) have poorer responses to checkpoint immunotherapy. The authors set out to explore the mechanisms underlying this by studying 2 dimensions of neoantigen biology: firstly, distribution (clonal vs subclonal) and secondly, immunogenicity (weak vs strong binding to MHC class I). Using a panel of lung cancer cell lines modified to express individual or dual neoantigens in order to model clonal and subclonal expression, elegant studies show that clonal co-expression with a "strong" neoantigen can boost the immunogenicity of a "weak" neoantigen and result in tumour control. Mechanistically, this is related to engulfment of both neoantigens by cross presenting type 1 conventional dendritic cells and the associated enhanced activation state of this cell type. This is an interesting and potentially important finding that may be related to mechanisms of epitope spreading as immune responses diverge from targeting more to less immunogenic epitopes. Overall, the study is thought-provoking, informative in relation to how neoantigen immunogenicity is shaped and may have practical relevance.
We greatly appreciate the constructive comments from the reviewer and their insightful comments and questions on our work. We have edited the text in response to their feedback. We believe these changes have made the writing clearer and more effectively communicates the scope of our study and our results to the reader.
-
eLife assessment
This important work advances our understanding of the import of clonal heterogeneity in cancers in immune response to individual antigens. The evidence supporting the conclusions is convincing, and uses interesting tools, although the mechanistic basis of the observations is unclear. The work will be of broad interest to immunologists including cancer immunologists.
-
Reviewer #1 (Public Review):
The authors aim to understand the role of clonal heterogeneity of tumors in immunogenicity of clonally expressed antigens. This is a significant problem with many basic as well as translational implications.
The strength of the manuscript lies in the novel demonstration that a poorly immunogenic tumor antigen, when paired with a stronger tumor antigen, begins to elicit significant immune response. The weakness lies in the fact that the actual mechanism of the key demonstration is never shown. There is a lot of speculation and tangential experimentation, but little actual evidence of a mechanism.
By making the key observation (mentioned in the strength section in the previous paragraph), the authors did achieve their objective albeit very partially. Their observation is based on excellent experimental tools …
Reviewer #1 (Public Review):
The authors aim to understand the role of clonal heterogeneity of tumors in immunogenicity of clonally expressed antigens. This is a significant problem with many basic as well as translational implications.
The strength of the manuscript lies in the novel demonstration that a poorly immunogenic tumor antigen, when paired with a stronger tumor antigen, begins to elicit significant immune response. The weakness lies in the fact that the actual mechanism of the key demonstration is never shown. There is a lot of speculation and tangential experimentation, but little actual evidence of a mechanism.
By making the key observation (mentioned in the strength section in the previous paragraph), the authors did achieve their objective albeit very partially. Their observation is based on excellent experimental tools and design. This study will stimulate further experiments in this important field.
Their key observation is somewhat reminiscent of the practice of conjugating small "non-immunogenic" antigens (such as some carbohydrates) to large protein carriers (such as serum albumin) in order to elicit strong antibody response to the weaker antigen. It is interesting to contemplate if the underlying mechanisms have any commonality.
-
Reviewer #2 (Public Review):
There are data to suggest that intratumour mutational heterogeneity (ITH; the proportion of all mutations that are found only within cancer subclones) is associated with worse therapeutic outcomes. Specifically, patients with more mutations (and thus neoantigens) mostly expressed by subclones (high ITH) have poorer responses to checkpoint immunotherapy. The authors set out to explore the mechanisms underlying this by studying 2 dimensions of neoantigen biology: firstly, distribution (clonal vs subclonal) and secondly, immunogenicity (weak vs strong binding to MHC class I). Using a panel of lung cancer cell lines modified to express individual or dual neoantigens in order to model clonal and subclonal expression, elegant studies show that clonal co-expression with a "strong" neoantigen can boost the …
Reviewer #2 (Public Review):
There are data to suggest that intratumour mutational heterogeneity (ITH; the proportion of all mutations that are found only within cancer subclones) is associated with worse therapeutic outcomes. Specifically, patients with more mutations (and thus neoantigens) mostly expressed by subclones (high ITH) have poorer responses to checkpoint immunotherapy. The authors set out to explore the mechanisms underlying this by studying 2 dimensions of neoantigen biology: firstly, distribution (clonal vs subclonal) and secondly, immunogenicity (weak vs strong binding to MHC class I). Using a panel of lung cancer cell lines modified to express individual or dual neoantigens in order to model clonal and subclonal expression, elegant studies show that clonal co-expression with a "strong" neoantigen can boost the immunogenicity of a "weak" neoantigen and result in tumour control. Mechanistically, this is related to engulfment of both neoantigens by cross presenting type 1 conventional dendritic cells and the associated enhanced activation state of this cell type. This is an interesting and potentially important finding that may be related to mechanisms of epitope spreading as immune responses diverge from targeting more to less immunogenic epitopes. Overall, the study is thought-provoking, informative in relation to how neoantigen immunogenicity is shaped and may have practical relevance.
-
