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When Cold Is Hot: Immune Checkpoint Inhibition Therapy for Rhabdoid Tumors
Cancer Cell
Previews When Cold Is Hot: Immune Checkpoint Inhibition Therapy for Rhabdoid Tumors Mark Yarmarkovich1 and John M. Maris1,2,3,* 1Division
of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA 3Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA *Correspondence: [email protected] https://doi.org/10.1016/j.ccell.2019.11.006 2Department
Carcinogen-induced cancers typically have high mutation burdens and an inflamed microenvironment and thus are poised to respond to immune checkpoint inhibitors (ICIs). However, cancers with loss-of-function mutations in the SWI/SNF complex have few additional mutations yet also have an inflamed immunophenotype and should respond to ICI therapy. Immune checkpoint inhibition (ICI) therapy has revolutionized the approach to the subset of human cancers thought to present a sufficient number of neoepitopes to the immune systems, such as to be recognized by the existing set of T cell receptors (TCRs) in the patient’s repertoire. Tumor mutation burden (TMB) has been proposed as a predicative biomarker for ICI anti-tumor activity, as well as the expression of immune checkpoint molecules (such as PD-1), with carcinogen-induced tumors such as melanomas and lung cancers showing high TMB and PD-1 expression and the largest percentage of patients benefiting for ICI therapy in the clinic (Hellmann et al., 2018). The presence of infiltrating lymphocytes in solid malignancies (‘‘hot’’ tumor) is also considered a biomarker for ICI efficacy (Tumeh et al., 2014) and is often correlated with TMB. Childhood cancers are generally considered ‘‘cold’’ tumors due to low TMB, PD-1 expression, and T cell infiltrates. Not surprisingly, recent clinical trials of a variety of ICI strategies have shown very limited activity in pediatric cancer patients. Rhabdoid tumors are rare but highly aggressive childhood cancers with dismal patient outcomes despite highly intensive chemoradiotherapy. These tumors can arise in the brain, where they are referred to as atypical teratoid rhabdoid tumors (ATRTs), or in extracranial soft tissues, most commonly the kidney, where they are referred to as extracranial malignant rhabdoid tumors (MRTs). Rhabdoid tumors are remarkable for the unifying and pathognomonic genomic lesion of biallelic inactivation of
SMARCB1, one of the core subunits of the SWI/SNF (BAF) complex, and an otherwise quiet genome with no known additional oncogenic driver lesions (Lee et al., 2012). Due to the exquisitely low TMB, rhabdoid tumors have generally been considered the ultimate ‘‘cold’’ cancers, presumed to have little immune infiltrate and to be very poor candidates for ICI therapies. In this issue of Cancer Cell, Leruste and colleagues report the surprising finding that rhabdoid tumors are actually quite ‘‘hot,’’ with the majority highly infiltrated with T cells, including exhausted effector and clonally expanded memory CD8 populations, but also with an abundance of immunosuppressive myeloid-derived cells (Leruste et al., 2019). This work dovetails nicely with a report in the current issue of Cell Reports from Chun and colleagues that arrives at largely the same major conclusions using independent samples and orthogonal technologies (Chun et al., 2019). These important papers build off of prior work showing that ATRTs can be further subdivided into three epigenetic subgroups (TYR, SHH, and MYC) that define distinct SMARCB1 genotype-phenotype association. (Johann et al., 2016). Both new studies report unique immune signatures for each intracranial ATRT subgroup, as well as MRTs, and find extraordinarily high immune infiltration in MRTs and ATRTMYC cases, while ATRT-SHH tumors were found by both groups to be immunogenically silent, similar to many other pediatric cancers. Thus, these studies both provide clear evidence for the deployment of immune checkpoint
blockade in large subsets of children with rhabdoid tumors. These two manuscripts propose divergent mechanisms to explain the immunophenotypic landscape of rhabdoid tumors. Leruste and colleagues provide substantial evidence supporting SMARCB1 deficiency leading to derepression of multiple endogenous retroviral element (ERV) loci, generating double-stranded RNAs that activate an interferon response and presentation of virus-like tumor-specific antigens on the major histocompatibility complex (MHC). It is of interest that other cancers with mutations in the SWI/SNF complex and low TMB such as clear-cell renal-cell carcinomas and small-cell carcinomas of the ovaries also show a robust immune infiltrate (Miao et al., 2018; Pan et al., 2018), and that aberrant expression of transposable elements like ERVs are a very common source of tumor-specific MHCrestricted antigens that can be recognized by the adaptive immune system (Laumont et al., 2018). Conversely, Chun and colleagues also tested for evidence of derepression of ERVs, finding increased H3K27ac in the highly inflamed subgroups as compared to non-inflamed rhabdoid tumors, but did not find differential methylation or expression of retroviral elements. They did find high expression levels of several lineage-restricted developmental genes, either through direct co-deletion of the immune modulator MIF gene at the SMARCB1 locus or via other mechanisms that are currently not defined. In either case, future studies will be needed to elucidate the antigen specificities of the clonally expanded T cells
Cancer Cell 36, December 9, 2019 ª 2019 Elsevier Inc. 575
Cancer Cell
Previews found in rhabdoid tumors and whether these T cell receptors are indeed reactive against peptides on MHC derived from expression of endogenous retrovirus or other tumor-associated genes. Interestingly, another study published in this journal last month identified members of the PRC2 complex, which are also overexpressed in most rhabdoid tumors, as key epigenetic regulators of MHC downregulation in neuroblastoma cells (Burr et al., 2019). They demonstrate that inhibition of the enzymatic subunit responsible for chromatin remodeling, EZH2, significantly upregulated genes involved in antigen processing and presentation, and increased the T cell response. These studies provide rationale for further increasing the immune recognition of rhabdoid tumor and other cancers with low MHC expression using the pairing of ICI with EZH2 inhibitors. Given that the SHH subtype is associated with MYCN overexpression, this provides rationale for further investigation in using EZH2 inhibitors to induce immunogenicity in these tumors. Despite some unresolved differences in the mechanistic explanation of immune infiltrates in epigenetic subset-specific rhabdoid tumors, these manuscripts have a clear and immediate translational impact. Leruste and colleagues show impressive efficacy of anti-PD-1 monotherapy in a relevant immune competent mouse model of ATRT, which, due to the quality of the data in these manuscripts and clinical experience with ICI, is likely all that is needed to launch immunotherapy trials for patients with rhabdoid tumors. These should be designed to
576 Cancer Cell 36, December 9, 2019
enrich for subjects most likely to respond based on epigenetic subgroup, and also to collect the precious samples to study whether predicted (or even measured) tumor-specific antigenic load is a biomarker of response. Importantly, developing trials that will utilize immunotherapy in a way to mitigate against the effects of highly intensive chemoradiotherapy are needed, as traditional use at first relapse is at risk for missing a very important clinical signal, as these tumors typically recur while patients are significantly immunosuppressed. For a disease with such poor outcomes, one could consider a window design in which patients receive ICI therapy with deep immune correlate studies prior to exposure to chemotherapy. Now that it is clear that presumably ‘‘cold’’ rhabdoid tumors are actually ‘‘hot’’ and poised to unleash the adaptive immune system on a highly refractory childhood cancer, innovative clinical trial design is required to realize the therapeutic potential discovered in these complementary papers.
REFERENCES Burr, M.L., Sparbier, C.E., Chan, K.L., Chan, Y.C., Kersbergen, A., Lam, E.Y.N., Azidis-Yates, E., Vassiliadis, D., Bell, C.C., Gilan, O., et al. (2019). An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer. Cancer Cell 36, 385–401. Chun, H.E., Johann, P.D., Milne, K., Zapatka, M., Buellesbach, A., Ishaque, N., Iskar, M., Erkek, S., Wei, L., Tessier-Cloutier, B., et al. (2019). Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration. Cell Rep. 29, 2338–2354.
Hellmann, M.D., Nathanson, T., Rizvi, H., Creelan, B.C., Sanchez-Vega, F., Ahuja, A., Ni, A., Novik, J.B., Mangarin, L.M.B., Abu-Akeel, M., et al. (2018). Genomic features of response to combination immunotherapy in patients with advanced non-small-cell lung cancer. Cancer Cell 33, 843–852. Johann, P.D., Erkek, S., Zapatka, M., Kerl, K., Buchhalter, I., Hovestadt, V., Jones, D.T.W., Sturm, D., Hermann, C., Segura Wang, M., et al. (2016). Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes. Cancer Cell 29, 379–393. Laumont, C.M., Vincent, K., Hesnard, L., Audemard, E´., Bonneil, E´., Laverdure, J.P., Gendron, P., Courcelles, M., Hardy, M.P., Coˆte´, C., et al. (2018). Noncoding regions are the main source of targetable tumor-specific antigens. Sci. Transl. Med. 10, eaau5516. Lee, R.S., Stewart, C., Carter, S.L., Ambrogio, L., Cibulskis, K., Sougnez, C., Lawrence, M.S., Auclair, D., Mora, J., Golub, T.R., et al. (2012). A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J. Clin. Invest. 122, 2983–2988. Leruste, A., Tosello, J., Ramos, R.N., Tauzie`deEspariat, A., Brohard, S., Han, Z.-Y., Beccaria, K., Andrianteranagna, M., Caudana, P., Nikolic, J., et al. (2019). Clonally expanded T cells reveal immunogenicity of rhabdoid tumors. Cancer Cell 36, this issue, 597–612. Miao, D., Margolis, C.A., Gao, W., Voss, M.H., Li, W., Martini, D.J., Norton, C., Bosse´, D., Wankowicz, S.M., Cullen, D., et al. (2018). Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 359, 801–806. Pan, D., Kobayashi, A., Jiang, P., Ferrari de Andrade, L., Tay, R.E., Luoma, A.M., Tsoucas, D., Qiu, X., Lim, K., Rao, P., et al. (2018). A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775. Tumeh, P.C., Harview, C.L., Yearley, J.H., Shintaku, I.P., Taylor, E.J., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014). PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571.
Previews When Cold Is Hot: Immune Checkpoint Inhibition Therapy for Rhabdoid Tumors Mark Yarmarkovich1 and John M. Maris1,2,3,* 1Division
of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA 3Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA *Correspondence: [email protected] https://doi.org/10.1016/j.ccell.2019.11.006 2Department
Carcinogen-induced cancers typically have high mutation burdens and an inflamed microenvironment and thus are poised to respond to immune checkpoint inhibitors (ICIs). However, cancers with loss-of-function mutations in the SWI/SNF complex have few additional mutations yet also have an inflamed immunophenotype and should respond to ICI therapy. Immune checkpoint inhibition (ICI) therapy has revolutionized the approach to the subset of human cancers thought to present a sufficient number of neoepitopes to the immune systems, such as to be recognized by the existing set of T cell receptors (TCRs) in the patient’s repertoire. Tumor mutation burden (TMB) has been proposed as a predicative biomarker for ICI anti-tumor activity, as well as the expression of immune checkpoint molecules (such as PD-1), with carcinogen-induced tumors such as melanomas and lung cancers showing high TMB and PD-1 expression and the largest percentage of patients benefiting for ICI therapy in the clinic (Hellmann et al., 2018). The presence of infiltrating lymphocytes in solid malignancies (‘‘hot’’ tumor) is also considered a biomarker for ICI efficacy (Tumeh et al., 2014) and is often correlated with TMB. Childhood cancers are generally considered ‘‘cold’’ tumors due to low TMB, PD-1 expression, and T cell infiltrates. Not surprisingly, recent clinical trials of a variety of ICI strategies have shown very limited activity in pediatric cancer patients. Rhabdoid tumors are rare but highly aggressive childhood cancers with dismal patient outcomes despite highly intensive chemoradiotherapy. These tumors can arise in the brain, where they are referred to as atypical teratoid rhabdoid tumors (ATRTs), or in extracranial soft tissues, most commonly the kidney, where they are referred to as extracranial malignant rhabdoid tumors (MRTs). Rhabdoid tumors are remarkable for the unifying and pathognomonic genomic lesion of biallelic inactivation of
SMARCB1, one of the core subunits of the SWI/SNF (BAF) complex, and an otherwise quiet genome with no known additional oncogenic driver lesions (Lee et al., 2012). Due to the exquisitely low TMB, rhabdoid tumors have generally been considered the ultimate ‘‘cold’’ cancers, presumed to have little immune infiltrate and to be very poor candidates for ICI therapies. In this issue of Cancer Cell, Leruste and colleagues report the surprising finding that rhabdoid tumors are actually quite ‘‘hot,’’ with the majority highly infiltrated with T cells, including exhausted effector and clonally expanded memory CD8 populations, but also with an abundance of immunosuppressive myeloid-derived cells (Leruste et al., 2019). This work dovetails nicely with a report in the current issue of Cell Reports from Chun and colleagues that arrives at largely the same major conclusions using independent samples and orthogonal technologies (Chun et al., 2019). These important papers build off of prior work showing that ATRTs can be further subdivided into three epigenetic subgroups (TYR, SHH, and MYC) that define distinct SMARCB1 genotype-phenotype association. (Johann et al., 2016). Both new studies report unique immune signatures for each intracranial ATRT subgroup, as well as MRTs, and find extraordinarily high immune infiltration in MRTs and ATRTMYC cases, while ATRT-SHH tumors were found by both groups to be immunogenically silent, similar to many other pediatric cancers. Thus, these studies both provide clear evidence for the deployment of immune checkpoint
blockade in large subsets of children with rhabdoid tumors. These two manuscripts propose divergent mechanisms to explain the immunophenotypic landscape of rhabdoid tumors. Leruste and colleagues provide substantial evidence supporting SMARCB1 deficiency leading to derepression of multiple endogenous retroviral element (ERV) loci, generating double-stranded RNAs that activate an interferon response and presentation of virus-like tumor-specific antigens on the major histocompatibility complex (MHC). It is of interest that other cancers with mutations in the SWI/SNF complex and low TMB such as clear-cell renal-cell carcinomas and small-cell carcinomas of the ovaries also show a robust immune infiltrate (Miao et al., 2018; Pan et al., 2018), and that aberrant expression of transposable elements like ERVs are a very common source of tumor-specific MHCrestricted antigens that can be recognized by the adaptive immune system (Laumont et al., 2018). Conversely, Chun and colleagues also tested for evidence of derepression of ERVs, finding increased H3K27ac in the highly inflamed subgroups as compared to non-inflamed rhabdoid tumors, but did not find differential methylation or expression of retroviral elements. They did find high expression levels of several lineage-restricted developmental genes, either through direct co-deletion of the immune modulator MIF gene at the SMARCB1 locus or via other mechanisms that are currently not defined. In either case, future studies will be needed to elucidate the antigen specificities of the clonally expanded T cells
Cancer Cell 36, December 9, 2019 ª 2019 Elsevier Inc. 575
Cancer Cell
Previews found in rhabdoid tumors and whether these T cell receptors are indeed reactive against peptides on MHC derived from expression of endogenous retrovirus or other tumor-associated genes. Interestingly, another study published in this journal last month identified members of the PRC2 complex, which are also overexpressed in most rhabdoid tumors, as key epigenetic regulators of MHC downregulation in neuroblastoma cells (Burr et al., 2019). They demonstrate that inhibition of the enzymatic subunit responsible for chromatin remodeling, EZH2, significantly upregulated genes involved in antigen processing and presentation, and increased the T cell response. These studies provide rationale for further increasing the immune recognition of rhabdoid tumor and other cancers with low MHC expression using the pairing of ICI with EZH2 inhibitors. Given that the SHH subtype is associated with MYCN overexpression, this provides rationale for further investigation in using EZH2 inhibitors to induce immunogenicity in these tumors. Despite some unresolved differences in the mechanistic explanation of immune infiltrates in epigenetic subset-specific rhabdoid tumors, these manuscripts have a clear and immediate translational impact. Leruste and colleagues show impressive efficacy of anti-PD-1 monotherapy in a relevant immune competent mouse model of ATRT, which, due to the quality of the data in these manuscripts and clinical experience with ICI, is likely all that is needed to launch immunotherapy trials for patients with rhabdoid tumors. These should be designed to
576 Cancer Cell 36, December 9, 2019
enrich for subjects most likely to respond based on epigenetic subgroup, and also to collect the precious samples to study whether predicted (or even measured) tumor-specific antigenic load is a biomarker of response. Importantly, developing trials that will utilize immunotherapy in a way to mitigate against the effects of highly intensive chemoradiotherapy are needed, as traditional use at first relapse is at risk for missing a very important clinical signal, as these tumors typically recur while patients are significantly immunosuppressed. For a disease with such poor outcomes, one could consider a window design in which patients receive ICI therapy with deep immune correlate studies prior to exposure to chemotherapy. Now that it is clear that presumably ‘‘cold’’ rhabdoid tumors are actually ‘‘hot’’ and poised to unleash the adaptive immune system on a highly refractory childhood cancer, innovative clinical trial design is required to realize the therapeutic potential discovered in these complementary papers.
REFERENCES Burr, M.L., Sparbier, C.E., Chan, K.L., Chan, Y.C., Kersbergen, A., Lam, E.Y.N., Azidis-Yates, E., Vassiliadis, D., Bell, C.C., Gilan, O., et al. (2019). An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer. Cancer Cell 36, 385–401. Chun, H.E., Johann, P.D., Milne, K., Zapatka, M., Buellesbach, A., Ishaque, N., Iskar, M., Erkek, S., Wei, L., Tessier-Cloutier, B., et al. (2019). Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration. Cell Rep. 29, 2338–2354.
Hellmann, M.D., Nathanson, T., Rizvi, H., Creelan, B.C., Sanchez-Vega, F., Ahuja, A., Ni, A., Novik, J.B., Mangarin, L.M.B., Abu-Akeel, M., et al. (2018). Genomic features of response to combination immunotherapy in patients with advanced non-small-cell lung cancer. Cancer Cell 33, 843–852. Johann, P.D., Erkek, S., Zapatka, M., Kerl, K., Buchhalter, I., Hovestadt, V., Jones, D.T.W., Sturm, D., Hermann, C., Segura Wang, M., et al. (2016). Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes. Cancer Cell 29, 379–393. Laumont, C.M., Vincent, K., Hesnard, L., Audemard, E´., Bonneil, E´., Laverdure, J.P., Gendron, P., Courcelles, M., Hardy, M.P., Coˆte´, C., et al. (2018). Noncoding regions are the main source of targetable tumor-specific antigens. Sci. Transl. Med. 10, eaau5516. Lee, R.S., Stewart, C., Carter, S.L., Ambrogio, L., Cibulskis, K., Sougnez, C., Lawrence, M.S., Auclair, D., Mora, J., Golub, T.R., et al. (2012). A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J. Clin. Invest. 122, 2983–2988. Leruste, A., Tosello, J., Ramos, R.N., Tauzie`deEspariat, A., Brohard, S., Han, Z.-Y., Beccaria, K., Andrianteranagna, M., Caudana, P., Nikolic, J., et al. (2019). Clonally expanded T cells reveal immunogenicity of rhabdoid tumors. Cancer Cell 36, this issue, 597–612. Miao, D., Margolis, C.A., Gao, W., Voss, M.H., Li, W., Martini, D.J., Norton, C., Bosse´, D., Wankowicz, S.M., Cullen, D., et al. (2018). Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 359, 801–806. Pan, D., Kobayashi, A., Jiang, P., Ferrari de Andrade, L., Tay, R.E., Luoma, A.M., Tsoucas, D., Qiu, X., Lim, K., Rao, P., et al. (2018). A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 359, 770–775. Tumeh, P.C., Harview, C.L., Yearley, J.H., Shintaku, I.P., Taylor, E.J., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014). PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571.