Wedding of Molecular Alterations and Immune Checkpoint Blockade

Genomics as a Matchmaker

Elena Fountzilas, MD, PhD; Razelle Kurzrock, MD; Henry Hiep Vo, PhD; Apostolia-Maria Tsimberidou MD, PhD


J Natl Cancer Inst. 2021;113(12):1634-1647. 

In This Article

Investigational Biomarkers Conferring Sensitivity to Immunotherapy

Beyond MSI-H (which results in high TMB) and TMB of at least 10 mut/mb, there are several biomarkers that may confer sensitivity to immune checkpoint blockade. These genomic biomarkers include, but are not limited to, alterations in chromatin remodeling genes, PD-L1 amplification, specific MHC types that permit neo-antigen presentation, and specific mutational signatures that are associated with increased TMB and/or increased immunogenicity of neo-antigens (Table 1 and Figure 1).

Figure 1.

US Food and Drug Administration–approved and investigational biomarkers associated with response to immuno-oncology therapy. APOBEC = apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like; ARID1A = AT-rich interaction domain 1A; BAP1 = BRCA1-associated protein 1; MHC-I = major histocompatibility complex class-I; PBRM1 = polybromo-1; PD-L1 = programmed cell death-ligand 1; POLD1 = DNA polymerase delta 1; POLE = DNA polymerase epsilon; SMARCA4 = SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 4; SMARCB1 = SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B, member 1; TMB = tumor mutational burden.

Chromatin Remodeling (SWI/SNF Complex)

Cells have developed several mechanisms to manipulate DNA and package it into chromatin. The building block of chromatin is the nucleosome. ATP-dependent chromatin remodeling complexes such as switch/sucrose non-fermentable (SWI/SNF) complexes are specialized protein machinery complexes able to restructure the nucleosome to make its DNA accessible during transcription, DNA repair, and replication. Several genes that make up these complexes, including those in the ARID and SMARC families and PBRM1, have been associated with responsiveness to immune checkpoint blockade.[15,16,19,24,77] Mechanistically, reexpression of endogenous retroviruses resulting from deficiency of the SWI/SNF complex chromatin remodeling complex may contribute to activation of the immune response in these malignancies.[78]

ARID1A Alterations. The AT-rich interaction domain 1 A (ARID1A) gene encodes a subunit of the ATP-dependent chromatin remodeling SWI/SNF complex.[79,80] Inactivating mutations in ARID1A are frequently identified in many tumor types: ovarian clear cell (45%), endometrial (45%), gastric (19%), and hepatocellular (14%) carcinomas.[81–85] ARID1A functional loss has been clinically and experimentally correlated with immunotherapy response.[15,16,86]

ARID1A deficiency interferes with MMR system regulation, leading to increased tumor mutational load and higher PD-L1 expression and more immune infiltrates.[15,17,86,87] During DNA replication, ARID1A binds and recruits MSH2, a key MMR protein, to chromatin.[15] ARID1A-deficient ovarian tumors in syngeneic mice were characterized by increased mutation load, tumor-infiltrating lymphocytes, and PD-L1 expression.[15] Anti–PD-L1 antibody administration led to improved survival rates of mice with ARID1A-deficient vs ARID1A–wild-type ovarian tumors. Further, in 3304 patients with diverse tumor types, ARID1A molecular alterations correlated with MSI-H and TMB-H, but immunotherapy response in ARID1A-altered tumors was independent of these factors.[16] In patients treated with immunotherapeutic agents, those with ARID1A-altered vs wild-type tumors had improved PFS (11 vs 4 months; P = .006).[16] These data indicate that ARID1A alterations should be further validated as a pan-cancer predictive biomarker for immune checkpoint blockade response.

PBRM1 Molecular Alterations. Polybromo-1 (PBRM1) is a tumor suppressor gene that encodes a subunit of the SWI/SNF complex and participates in regulation of the cell cycle, apoptosis, and centromeric cohesion. The data regarding PBRM1 alterations and response to checkpoint blockade are mixed, with some studies suggesting that aberrant PBRM1 is predictive and others indicating that it is not.

Molecular alterations in PBRM1 are commonly identified in clear cell renal cell carcinoma (RCC) (approximately 40%)[77,88] and are considered a biomarker predicting response to immunotherapy.[18,19] Additionally, PBRM1 mutations have been identified in cholangiocarcinoma (17%),[89] mesothelioma (15%),[90] pancreatic cancer (8%),[91] and lung cancer (3%).[77] In patients with clear cell RCC treated with nivolumab, those harboring PBRM1 mutations had higher rates of clinical benefit (odds ratio [OR] = 2.14, 95% CI = 1.00 to ∞, P = .0497) and longer PFS (HR = 0.67, 95% CI = 0.47 to 0.96, P = .03) and OS (HR = 0.65, 95% CI = 0.44 to 0.96, P = .03) compared with patients without such mutations.[19] Other investigators, using whole-exome sequencing in 35 patients with clear cell RCC, also demonstrated that loss-of-function mutations in PBRM1 were associated with improved clinical benefit from immune checkpoint inhibitors (OR = 12.93, 95% CI = 1.54 to 190.8, P = .012).[18] Their findings were independently validated in 63 patients with clear cell RCC who had been treated with PD-1 or PD-L1 inhibitors (OR for clinical benefit = 6.10, 95% CI = 1.42 to 32.64, P = .0071).

Contrary to these data, investigators recently showed that PBRM1 knockout (assessed by mRNA and protein levels) resulted in reduced interferon-gamma (IFN-γ)–STAT1 signaling in murine and human RCC cell lines.[20] A retrospective analysis of approximately 700 patients with renal cancer from 3 independent clinical cohorts (IMmotion150 dataset, MSK-IMPACT cohort, and The Cancer Genome Atlas cohort) demonstrated that PBRM1 mutations were associated with fewer immune infiltrates and lower response rates to immunotherapy.[20] Finally, in a retrospective analysis of 441 patients with NSCLC from 2 independent cohorts (385 patients from Memorial Sloan Kettering Cancer Center and 56 from Dana Farber Cancer Institute) who received immunotherapy, the presence of PBRM1 mutations correlated with shorter OS (6 months in PBRM1-mutated vs 13 months in PBRM1–wild-type patients; P = .03), including in multivariate analysis.[77] These data collectively indicate that the predictive role of altered PBRM1 for immunotherapy is inconclusive.

SMARCA4. SMARCA4 encodes another subunit of the chromatin remodeling SWI/SNF complex. SMARCA4 molecular alterations have been identified in 4% of cancers, including lung (10%), bladder (7%), colorectal (5%), and breast (2%) cancers.[92,93]SMARCA4 alterations seem to be the "driver" molecular change in almost all small cell carcinomas of the ovary, hypercalcemic type;[94,95] loss of SMARCA4 per IHC has been reported in up to 10% of patient with NSCLC.[96]

Recently, SMARCA4 loss was used to define groups of undifferentiated carcinomas, including SMARCA4-deficient undifferentiated uterine sarcomas that share morphologic, IHC, and genetic similarities to small cell carcinoma of the ovary, hypercalcemic type,[97] and undifferentiated thoracic carcinomas.[98] Durable responses have been noted in anecdotal reports of patients with small cell carcinoma of the ovary, hypercalcemic type,[21] NSCLC,[22] and thoracic sarcoma.[23,99] Preliminary data suggest that, although SMARC4-deficient tumors have low TMB, they have high PD-L1 expression and T-cell infiltration, suggestive of an immunogenic microenvironment.[21]

SMARCB1. SMARCB1, another component of the chromatin remodeling SWI/SNF complex, functions as a tumor suppressor gene. Complete SMARCB1 and/or SMARCA4 inactivation has been associated with aggressive tumor behavior in malignant rhabdoid and atypical teratoid rhabdoid tumors,[100] and it has been suggested that SMARCB1-altered rhabdoid tumors respond to immunotherapy.[101] In a recent study, the analysis of genomic, transcriptomic, and immune microenvironment data from sarcomatoid and rhabdoid RCC demonstrated the upregulation of immune pathways and greater CD8+ T-cell infiltration and PD-L1 expression on tumor cells in these subtypes compared with other RCC subtypes.[24] Patients with sarcomatoid and rhabdoid tumors who received immunotherapy had improved outcomes compared with patients who did not.[24]

Other Alterations Possibly Associated With Immunotherapy Response

BAP1. BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene involved in the regulation of chromatin remodeling and DNA damage repair.[102,103]BAP1 copy number loss or inactivating mutations are frequently noted in mesothelioma (40%-64%) and result in the accumulation of DNA-damaged cells.[104–106]BAP1 loss promotes an immune inflammatory environment in mesothelioma.[27] Integrative genomic, proteomic, and transcriptomic analyses of 19 peritoneal mesotheliomas showed that, in tumors with BAP1 loss (vs wild type), there were higher rates of infiltrated immune cells.[27] Clinical trials demonstrated that PD-1 inhibitors are active in patients with malignant pleural mesothelioma, and these mesotheliomas frequently harbor BAP1 alterations.[25,26,106]

MHC Genotype. In addition to the quality of the neo-antigens, the host immune system's ability to efficiently present driver neo-antigens to T cells plays a critical role in immune response. The MHC class-I (MHC-I) genotype is predictive of response to immunotherapy in combination with TMB.[28] The ability to present neo-antigens, defined by the Patient Harmonic-mean Best Rank (PHBR) score, was calculated in 83 patients with diverse malignancies who received immune checkpoint inhibitors. The PHBR score represents the ability of a specific human leukocyte antigen (HLA) class I genotype to bind and present a missense mutation; a lower PHBR score is suggestive of more efficient antigen presentation.[107] Among patients with higher TMB (>20 mut/mb), those whose tumors had low PHBR scores had higher ORRs (78% vs 43%; P = .049) and longer PFS (26.8 vs 5.8 months; P = .03) compared with patients with PHBR-high tumors.[28] The PHBR score did not predict response in patients with TMB-low tumors. Other investigators have also demonstrated that HLA-corrected TMB can reconcile the observed disparity in relationships between TMB and checkpoint blockade responses.[108] Furthermore, MHC class II–restricted neo-antigens also play a crucial role in the antitumor response that is nonoverlapping with that of MHC class I–restricted neo-antigens and, therefore, needs to be considered when identifying patients who will most benefit from immunotherapy.[109,110]

Mutational Signatures. Neo-antigens are mutated peptides that enable the immune cells to recognize the tumor cell as foreign. The specific types of neo-antigens that stimulate a strong immune reaction remain unclear, but certain mutational signatures appear to be predictive of high immunogenicity and immunotherapy response. For instance, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like, a family of evolutionarily conserved cytidine deaminases involved in viral infections) hyperactivity has been implicated in localized hypermutagenesis (also designated as kataegis) in patients with breast cancer.[111] In a study of 99 patients with diverse tumor types who received immunotherapy, APOBEC-related mutagenesis was associated with higher response rates (OR = 9.69, P = .0106) and longer PFS (3.1 vs 2.1 months; P = .0239), independent of TMB.[29] APOBEC-related neo-antigens tend to be more hydrophobic, and therefore more immunogenic, because they are better presented by the MHC and more easily recognized by T cells. Similarly, neo-antigens produced from an ultraviolet (UV)–mutated genome had increased hydrophobicity and immunogenicity.[30] A high UV signature correlated with longer PFS and OS in patients with low or intermediateTMB tumors after checkpoint inhibitor treatment, but there was no association in patients with TMB-H (>20 mut/mb) tumors.

PD-L1 Amplification. PD-L1 expression, assessed by IHC, is currently approved as a biomarker for treatment with anti–PD-1 or anti–PD-L1 agents, albeit one with technical limitations.[5]PD-L1 gene amplification, as assessed by next-generation sequencing, is the hallmark of Hodgkin disease, which is highly responsive to checkpoint blockade,[112] and also correlates with solid tumor immunotherapy responsiveness, although studied in only a small number of patients.[31] In a retrospective analysis of comprehensive tumor molecular profiling data from 118 187 patients with diverse cancers, the prevalence of PD-L1 amplification was 0.7% (843 of 118 187 patients).[31] Solid tumors with the highest proportions of PD-L1 amplification (PD-L1 amplified/cases analyzed) were undifferentiated soft-tissue sarcoma (3.9%), head and neck squamous cell carcinoma (3.1%), breast carcinoma (1.9%), and lung squamous cell carcinoma (1.7%). Of 13 patients with solid tumors with PD-L1 amplification, 9 had received treatment with checkpoint blockade; the ORR was 66.7%, and the median PFS was 15.2 months.[31] Interestingly, PD-L1 amplification did not always correlate with PD-L1 overexpression by IHC, even in responders, perhaps because of the technical limitations of IHC.

POLE/POLD1 Mutations. DNA polymerase epsilon (POLE) and DNA polymerase delta 1 (POLD1) alterations correlate with immunotherapy response. These proteins play a critical role in DNA replication and repair regulation. In 47 721 patients (pan-cancer), POLE and POLD1 mutations were identified in 2.79% and 1.37%, respectively.[32] Patients with POLE- or POLD1-mutated tumors had longer OS compared with patients with wild-type tumors after immunotherapy.[32] Alterations in POLE or POLD1 have been associated with statistically significantly higher tumor mutational burden,[33] higher CD8+ lymphocyte infiltration levels, and increased expression of cytotoxic T-cell markers compared with POLE or POLD1 wild-type tumors.[113] In ongoing clinical trials (NCT02693535, NCT02912572, NCT03810339), patients with POLE or POLD1 mutations are selected for treatment with immunotherapy. For instance, in the Targeted Agent and Profiling Utilization Registry study (NCT02693535), a non-randomized clinical trial, patients with POLE or POLD1 mutations (or high mutational load) are selected for treatment with pembrolizumab or nivolumab and ipilimumab.