Socializing Individualized T-Cell Cancer Immunotherapy.

Abstract

Tumors typically accumulate hundreds of mutations in “driver” genes critical to transformation as well as in other “passenger” genes.1Hanahan D Weinberg RA Hallmarks of cancer: the next generation.Cell. 2011; 144: 646-674Abstract Full Text Full Text PDF PubMed Scopus (43056) Google Scholar These mutations can generate neoantigens—mutated versions of normal proteins that become recognizable by patients' own T cells.2Schumacher TN Schreiber RD Neoantigens in cancer immunotherapy.Science. 2015; 348: 69-74Crossref PubMed Scopus (3010) Google Scholar,3Feldman SA Assadipour Y Kriley I Goff SL Rosenberg SA Adoptive cell therapy—tumor-infiltrating lymphocytes, T-cell receptors, and chimeric antigen receptors.Semin Oncol. 2015; 42: 626-639Crossref PubMed Scopus (64) Google Scholar Such T cells recovered from patients have been used as a source of tumor-hunting T-cell therapies, representing the epitome of individualized medicine as a way to treat tumors.4Rosenberg SA Restifo NP Adoptive cell transfer as personalized immunotherapy for human cancer.Science. 2015; 348: 62-68Crossref PubMed Scopus (1533) Google Scholar,5Lu YC Yao X Crystal JS Li YF El-Gamil M Gross C et al.Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions.Clin Cancer Res. 2014; 20: 3401-3410Crossref PubMed Scopus (291) Google Scholar Unfortunately, at best only a very small handful of potential neoantigens are recognized by a patient's own T cells,6Tran E Ahmadzadeh M Lu YC Gros A Turcotte S Robbins PF et al.Immunogenicity of somatic mutations in human gastrointestinal cancers.Science. 2015; 350: 1387-1390Crossref PubMed Scopus (507) Google Scholar probably because of the unrelenting immunosuppressive tactics exerted chronically on the patient's own T-cell repertoire. Now, Strönen et al. have shown that T cells from normal, healthy donors can recognize many more neoantigens from a given patient than the patient's own T-cell repertoire allows.7Strönen E Toebes M Kelderman S van Buuren MM Yang W van Rooij N et al.Targeting of cancer neoantigens with donor-derived T-cell receptor repertoires.Science. 2016; 352: 1337-1341Crossref PubMed Scopus (299) Google Scholar A situation in which a greater number of neoantigens are recognized by more T cells can only be good news for the treatment of malignant tumors. These results suggest that even individualized cancer immunotherapy might benefit from reaching out into the community for extra T-cell help. Cancer cells mutate, and they do it very well.1Hanahan D Weinberg RA Hallmarks of cancer: the next generation.Cell. 2011; 144: 646-674Abstract Full Text Full Text PDF PubMed Scopus (43056) Google Scholar,8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar Not surprisingly, we generally take a very dim view of the genetic flexibility of tumor cells, because the plasticity of the cancer cell genome allows for rapid adaptation away from sensitivity to drugs, radiation, or immune killing. However, recent studies suggest that the vice of variability in the cancer genome may alternatively be viewed as a virtue of (immune) visibility. The ability to sequence cancer genomes has confirmed that tumors are typically composed of a heterogeneous population of cells, each of which carries subsets of mutations.8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar Some of these are clonal throughout the tumor population and are transformation-critical “driver” mutations (such as in proto-oncogenes or tumor suppressors), which represent the very “roots” of the cancer.8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar,10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar Other “passenger” mutations accumulate, which may have no specific role in conferring a proliferative advantage, and are only seen in subpopulations of cells (the “branches” of the cancer).8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar,10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar From an immunotherapy viewpoint, a hypermutable cancer genome (mutanome) has a silver lining. Most of us have a set of T cells, each of which expresses a different T-cell receptor (TCR). The variety (repertoire) of TCRs ensures that our T cells recognize most pathogen-derived proteins in infected cells. They do this because cells process proteins (either normal self-proteins or foreign pathogen–derived proteins) by chopping them up into epitopes (8–13 amino acids in length). These epitopes are then fed onto major histocompatibility complex (MHC) molecules and presented as an epitope–MHC complex to T cells expressing TCRs (Figure 1). If the TCR binds well to the MHC–epitope complex'similar to a firm handshake—and receives additional stimulatory signals, the T cell becomes activated and kills the target cell with which it is “shaking hands.”11Rossjohn J Gras S Miles JJ Turner SJ Godfrey DI McCluskey J T cell antigen receptor recognition of antigen-presenting molecules.Annu Rev Immunol. 2015; 33: 169-200Crossref PubMed Scopus (444) Google Scholar As T cells mature in the thymus, when a T cell expresses a TCR that can shake hands very firmly with an MHC–epitope complex from a normal self-protein, it is rapidly killed, leading to negative selection of T cells that react with normal self-proteins. The functional consequences of this negative selection of self-reactive T cells are twofold. First, the only T cells that are circulating in most of us, including cancer patients, are those that can make, at best, only extremely floppy handshakes with MHC–epitopes from normal self-proteins; second, as a result of that, we are generally free of autoimmune disease11Rossjohn J Gras S Miles JJ Turner SJ Godfrey DI McCluskey J T cell antigen receptor recognition of antigen-presenting molecules.Annu Rev Immunol. 2015; 33: 169-200Crossref PubMed Scopus (444) Google Scholar (Figure 1a). However, something as small as a single point mutation in an epitope of a protein can dramatically increase its binding affinity to an MHC molecule. In turn, this can convert the TCR-MHC–epitope handshake from floppy to firm, leading to T cell–mediated killing of the cell. This is why immunologists have become quite excited by sequencing data showing the accumulation of mutations within the root/branches of human tumors compared with normal tissues.8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar,10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar The hope, now supported by human and mouse data, is that some of these acquired mutations will generate so-called neoantigens that can be recognized by the patient's own T cells. Neoantigens are created when an amino acid mutation in an MHC-binding epitope from an otherwise normal protein allows that epitope to bind with higher affinity to the MHC molecule than does the same epitope derived from the normal protein2Schumacher TN Schreiber RD Neoantigens in cancer immunotherapy.Science. 2015; 348: 69-74Crossref PubMed Scopus (3010) Google Scholar,3Feldman SA Assadipour Y Kriley I Goff SL Rosenberg SA Adoptive cell therapy—tumor-infiltrating lymphocytes, T-cell receptors, and chimeric antigen receptors.Semin Oncol. 2015; 42: 626-639Crossref PubMed Scopus (64) Google Scholar,5Lu YC Yao X Crystal JS Li YF El-Gamil M Gross C et al.Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions.Clin Cancer Res. 2014; 20: 3401-3410Crossref PubMed Scopus (291) Google Scholar,6Tran E Ahmadzadeh M Lu YC Gros A Turcotte S Robbins PF et al.Immunogenicity of somatic mutations in human gastrointestinal cancers.Science. 2015; 350: 1387-1390Crossref PubMed Scopus (507) Google Scholar (Figure 1b,c). This leads to a much stronger handshake between the MHC–epitope and any available TCR expressed on a patient's own T cells. Significantly, however, there are still no TCRs that recognize the MHC–epitope complex of the normal unmutated protein. Consistent with this hope, those tumors with the highest rates of somatic mutation also tend to be those considered the most immunogenic and amenable to immunotherapies.10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar,12Rizvi NA Hellmann MD Snyder A Kvistborg P Makarov V Havel JJ et al.Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.Science. 2015; 348: 124-128Crossref PubMed Scopus (5567) Google Scholar Similarly, there is now overwhelming evidence that a proportion of acquired mutations in tumor cells generate neoantigens containing novel immunogenic epitopes—compared with the unmutated epitopes from nontumor cells—against which T cells can react in the same patient2Schumacher TN Schreiber RD Neoantigens in cancer immunotherapy.Science. 2015; 348: 69-74Crossref PubMed Scopus (3010) Google Scholar (Figure 1c). Genome sequencing, along with the use of predictive algorithms, can identify those mutations that may generate new epitopes that would fit with higher affinity into the MHC molecules that are expressed in the patient. Better binding to MHC molecules usually correlates with a higher chance of recognition by a naturally occurring TCR within the patient's T-cell repertoire. These potentially immunogenic, mutated epitopes, can be tested in in vitro antigen-presenting assays to detect any T cells from the patient's blood that can recognize the novel epitope.3Feldman SA Assadipour Y Kriley I Goff SL Rosenberg SA Adoptive cell therapy—tumor-infiltrating lymphocytes, T-cell receptors, and chimeric antigen receptors.Semin Oncol. 2015; 42: 626-639Crossref PubMed Scopus (64) Google Scholar,4Rosenberg SA Restifo NP Adoptive cell transfer as personalized immunotherapy for human cancer.Science. 2015; 348: 62-68Crossref PubMed Scopus (1533) Google Scholar,5Lu YC Yao X Crystal JS Li YF El-Gamil M Gross C et al.Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions.Clin Cancer Res. 2014; 20: 3401-3410Crossref PubMed Scopus (291) Google Scholar,6Tran E Ahmadzadeh M Lu YC Gros A Turcotte S Robbins PF et al.Immunogenicity of somatic mutations in human gastrointestinal cancers.Science. 2015; 350: 1387-1390Crossref PubMed Scopus (507) Google Scholar Tumor-reactive T cells can be (i) expanded and then adoptively transferred back into the patient to treat the tumor, or (ii) used to clone their TCR, which can then be transferred into normal T cells as a second source for tumor-hunting T-cell therapy.3Feldman SA Assadipour Y Kriley I Goff SL Rosenberg SA Adoptive cell therapy—tumor-infiltrating lymphocytes, T-cell receptors, and chimeric antigen receptors.Semin Oncol. 2015; 42: 626-639Crossref PubMed Scopus (64) Google Scholar This clinically valuable process is highly individualized to each patient; the patient's mutations are unique to that patient, and a patient's T-cell repertoire belongs exclusively to that patient.4Rosenberg SA Restifo NP Adoptive cell transfer as personalized immunotherapy for human cancer.Science. 2015; 348: 62-68Crossref PubMed Scopus (1533) Google Scholar Encouragingly, the number of mutations that generate neoantigen epitopes within patients is usually large (typically up to ~150 per tumor). Sadly, the number of neoantigens against which there is demonstrable T-cell reactivity within the same patient is usually very low (typically ~0–2 per patient).5Lu YC Yao X Crystal JS Li YF El-Gamil M Gross C et al.Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions.Clin Cancer Res. 2014; 20: 3401-3410Crossref PubMed Scopus (291) Google Scholar,6Tran E Ahmadzadeh M Lu YC Gros A Turcotte S Robbins PF et al.Immunogenicity of somatic mutations in human gastrointestinal cancers.Science. 2015; 350: 1387-1390Crossref PubMed Scopus (507) Google Scholar,10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar,13Gros A Parkhurst MR Tran E Pasetto A Robbins PF Ilyas S et al.Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients.Nat Med. 2016; 22: 433-438Crossref PubMed Scopus (562) Google Scholar This discrepancy may exist for two reasons. First, although potentially neoantigen-reactive T cells may exist within the patient's own repertoire, they can be rendered inactive, unstimulated, unable to see the antigenic epitopes––or can even be deleted, by the multiple immunosuppressive countersurveillance tactics that tumors employ to impede their immune clearance13Gros A Parkhurst MR Tran E Pasetto A Robbins PF Ilyas S et al.Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients.Nat Med. 2016; 22: 433-438Crossref PubMed Scopus (562) Google Scholar,14Tumeh PC Harview CL Yearley JH Shintaku IP Taylor EJ Robert L et al.PD-1 blockade induces responses by inhibiting adaptive immune resistance.Nature. 2014; 515: 568-571Crossref PubMed Scopus (4394) Google Scholar,15Mercadante ER Lorenz UM Breaking free of control: how conventional T cells overcome regulatory T cell suppression.Front Immunol. 2016; 7: 193Crossref PubMed Scopus (45) Google Scholar,16van der Burg SH Arens R Ossendorp F van Hall T Melief CJ Vaccines for established cancer: overcoming the challenges posed by immune evasion.Nat Rev Cancer. 2016; 16: 219-233Crossref PubMed Scopus (487) Google Scholar (Figure 1c). Second, there may be no T cells in the T-cell repertoire of the patient with the appropriate TCR to bind sufficiently strongly to the majority of potential neoantigen MHC–epitope complexes. Whatever the reason, even if a patient's tumor expresses multiple neoantigens, it may be a needle-in-a-haystack situation to find T-cell clones that could be expanded as a source of highly individualized T cell–mediated immunotherapy. But what if this individualized T-cell therapy could become more community based? This is where the work by Strönen et al. takes this field to a new level.7Strönen E Toebes M Kelderman S van Buuren MM Yang W van Rooij N et al.Targeting of cancer neoantigens with donor-derived T-cell receptor repertoires.Science. 2016; 352: 1337-1341Crossref PubMed Scopus (299) Google Scholar Given the chronic insults that tumors can deliver to the immune system in a patient,15Mercadante ER Lorenz UM Breaking free of control: how conventional T cells overcome regulatory T cell suppression.Front Immunol. 2016; 7: 193Crossref PubMed Scopus (45) Google Scholar,16van der Burg SH Arens R Ossendorp F van Hall T Melief CJ Vaccines for established cancer: overcoming the challenges posed by immune evasion.Nat Rev Cancer. 2016; 16: 219-233Crossref PubMed Scopus (487) Google Scholar the authors hypothesized that T cells from healthy donors may have both a broader (more TCRs) and healthier (less immunosuppressed) anti-neoantigen T-cell repertoire than a patient's. If true, identification, expansion, and characterization of these T cells could provide additional reagents for T cell–mediated therapy of the patient's own tumor (Figure 1d,e). Sequencing of a melanoma from a stage IV patient who expressed the HLA-A*02–01 MHC molecule identified 249 mutations in expressed genes, 126 of which were predicted to bind well to the HLA-A*02–01 molecule and should therefore be good targets for TCR recognition. However, T cells grown from the patient's tumor recognized only 2 of the potential 126 neoantigens. In contrast, normal peripheral blood lymphocytes from a healthy normal donor recognized 5 of 20 of the neoantigens tested for in vitro T-cell activation. This proportion was replicated using three additional normal donors. Using a melanoma from another patient, donor-derived T cells reactive against 6 neoantigens were detected out of a predicted 27. The patient had no endogenous neoantigen-reactive T cells. Overall, up to 25% of neoantigens could be recognized by T cells from healthy donors, compared with less than 2% recognized by T cells from the patient's own tumor. The healthy donor-derived T cells with reactivity against the patient's neoantigens were able to kill target cells—including the patient's own melanoma cells—presenting the relevant epitopes in vitro (Figure 1d). Importantly, they did not kill target cells expressing matched epitopes from the corresponding normal cellular proteins. This result was particularly encouraging, because it suggests that these neoantigen-specific T cells would kill tumor cells, but not normal cells, in the patient. The authors then cloned the TCR directly from donor-derived T-cell clones that showed reactivity against specific mutated neoantigen epitopes. These TCRs were then expressed in healthy donor–derived peripheral blood mononuclear cells (PBMCs). In three of four examples of neoantigens tested, high degrees of specific T-cell activation were observed against both melanoma explants and cell lines expressing the respective neoantigen epitopes. By contrast, cells expressing the wild-type, unmutated parental proteins did not activate these TCR-transduced PBMCs. To determine the rules of how actual immunogenicity of neoantigen epitopes compared with predicted immunogenicity based on binding to the MHC, the investigators used flow cytometry to measure the off-rates of 57 different epitopes, selected on the basis of predicted binding affinity, from the HLA-A*02–01 MHC molecule. Overwhelmingly, the epitopes that generated immune responses from donor-derived T cells had significantly longer half-lives associated with the MHC compared with the epitopes that did not activate T-cell responses. In other words, for neoantigen epitopes to serve as effective immunogens for normal T-cell repertoires, the handshake with MHC must be not only firm (rather than flimsy) but also prolonged (as opposed to brief). It remains to be seen if these neoantigen targets of T-cell responses can be therapeutically useful in both mouse models and in patients (Figure 1e). For instance, they may be expressed on only a proportion of the tumor cells (i.e., nonclonal),10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar leaving large numbers of tumor cells not bearing neoantigens to proliferate unchecked (Figure 1e). Neoantigen expression may also be rapidly lost from tumor cells if TCR-transduced PBMC therapeutic pressure is applied in vivo, as means of immune evasion. This would be especially likely when the neoantigens are derived from passenger mutations in the branches of the tumor, with no ongoing importance to maintenance of malignant phenotype.8Alexandrov LB Nik-Zainal S Wedge DC Aparicio SA Behjati S Biankin AV et al.Signatures of mutational processes in human cancer.Nature. 2013; 500: 415-421Crossref PubMed Scopus (6263) Google Scholar,9Nik-Zainal S Davies H Staaf J Ramakrishna M Glodzik D Zou X et al.Landscape of somatic mutations in 560 breast cancer whole-genome sequences.Nature. 2016; 534: 47-54Crossref PubMed Scopus (1267) Google Scholar,10McGranahan N Furness AJ Rosenthal R Ramskov S Lyngaa R Saini SK et al.Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.Science. 2016; 351: 1463-1469Crossref PubMed Scopus (1962) Google Scholar,12Rizvi NA Hellmann MD Snyder A Kvistborg P Makarov V Havel JJ et al.Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.Science. 2015; 348: 124-128Crossref PubMed Scopus (5567) Google Scholar The use of PBMCs transduced with multiple neoantigen-targeting TCRs would alleviate both of these problems by forcing the tumor to lose multiple proteins at the same time in order to survive. The TCR targeting approach also faces some pretty stiff competition from chimeric antigen receptor technology.17van der Stegen SJ Hamieh M Sadelain M The pharmacology of second-generation chimeric antigen receptors.Nat Rev Drug Discov. 2015; 14: 499-509Crossref PubMed Scopus (333) Google Scholar However, the TCR camp can argue that they can target proteins (or epitopes thereof) that are not exclusively expressed on the surface of tumor cells. Moreover, clinical results so far suggest that TCR targeting may have the upper hand in attacking solid tumors5Lu YC Yao X Crystal JS Li YF El-Gamil M Gross C et al.Efficient identification of mutated cancer antigens recognized by T cells associated with durable tumor regressions.Clin Cancer Res. 2014; 20: 3401-3410Crossref PubMed Scopus (291) Google Scholar,6Tran E Ahmadzadeh M Lu YC Gros A Turcotte S Robbins PF et al.Immunogenicity of somatic mutations in human gastrointestinal cancers.Science. 2015; 350: 1387-1390Crossref PubMed Scopus (507) Google Scholar as opposed to hematologic tumors.17van der Stegen SJ Hamieh M Sadelain M The pharmacology of second-generation chimeric antigen receptors.Nat Rev Drug Discov. 2015; 14: 499-509Crossref PubMed Scopus (333) Google Scholar There is also the risk that TCR-transduced PBMCs hunting tumor cells will also cross-react with normal cells expressing the unmutated protein leading to autoimmune toxicities––which can be severe with adoptive T cell-transfer therapies.18Morgan RA Yang JC Kitano M Dudley ME Laurencot CM Rosenberg SA Case report of a serious adverse event following the administration of T cells transduced with a chimeric antigen receptor recognizing ERBB2.Mol Ther. 2010; 18: 843-851Abstract Full Text Full Text PDF PubMed Scopus (1762) Google Scholar The prospect of generating greater numbers of tumor-reactive TCRs against greater numbers of tumor-specific neoantigens has to be good news for the burgeoning field of individualized T-cell cancer immunotherapy. The really encouraging finding here is that the patient's own T-cell repertoire, often functionally decimated by the effects of chronic exposure to tumor cells, no longer has to be the sole provider of tumor-fighting T cells. Instead, a fresh, expanded and invigorated source of TCRs capable of “shaking hands” with tumor cellscan be made available from normal healthy donors, thereby expanding the individualized nature of T-cell immunotherapy to a truly community-based effort.