Understanding mechanisms of primary resistance to checkpoint inhibitors will lead to precision immunotherapy of advanced gastric cancer
Authors: V. Gambardella, T. Fleitas, A. Cervantes
Journal: Annals of Oncology (2019)

Immunotherapy is gaining relevance in the treatment of some advanced solid malignancies. The role of checkpoint inhibitors is being refined with the use of some valuable biomarkers, which are helping us with a more efficient use of these drugs. This is the case of high tumor mutational burden in non-small-cell lung cancers, defined by at least 10 mutations per megabase. This feature helps in selecting patients for whom immunotherapy will lead to a much better outcome over chemotherapy, independently of the programmed death-ligand 1 (PD-L1) status [1.Hellmann M.D. Ciuleanu T.E. Pluzanski A. et al.Nivolumab plus ipilimumab in lung cancer with high tumor mutational burden.N Engl J Med. 2018; 378: 2093-2104Crossref PubMed Scopus (1995) Google Scholar]. However, this is not the case in general of other solid tumors, and particularly of gastric cancer, in which trials are accruing eventually all comers. When initial phase II non-randomized trials assessed the efficacy of pembrolizumab in chemotherapy-refractory gastric cancer patients pretreated with at least two lines, response rate ranged from 11.6% to 22% [2.Fuchs C.S. Doi T. Jang R.W. et al.Safety and efficacy of pembrolizumab monotherapy in patients with previously treated advanced gastric and gastroesophageal junction cancer: phase 2 clinical KEYNOTE-059 trial.JAMA Oncol. 2018; 4: e180013Crossref PubMed Scopus (1036) Google Scholar, 3.Muro K. Chung H.C. Shankaran V. et al.Pembrolizumab for patients with PD-L1-positive advanced gastric cancer (KEYNOTE-012): a multicentre, open-label, phase 1b trial.Lancet Oncol. 2016; 17: 717-726Abstract Full Text Full Text PDF PubMed Scopus (773) Google Scholar]. A similar response rate (12%) was observed with nivolumab in the same setting of pretreated patients [4.Janjigian Y.Y. Bendell J. Calvo E. et al.CheckMate-032 study: efficacy and safety of nivolumab and nivolumab plus ipilimumab in patients with metastatic esophagogastric cancer.J Clin Oncol. 2018; 36: 2836-2844Crossref PubMed Scopus (361) Google Scholar]. Responses were seen in both PD-L1-positive and PD-L1-negative patients. In a phase III randomized study, comparing nivolumab as single-agent versus best supportive care in Asian patients with advanced gastric or gastroesophageal junction cancers, who had received at least two treatment lines, nivolumab was able to show a prolongation of survival [5.Kang Y.K. Boku N. Satoh T. et al.Nivolumab in patients with advanced gastric or gastro-oesophageal junction cancer refractory to, or intolerant of, at least two previous chemotherapy regimens (ONO-4538-12, ATTRACTION-2): a randomised, double-blind, placebo-controlled, phase 3 trial.Lancet. 2017; 390: 2461-2471Abstract Full Text Full Text PDF PubMed Scopus (1333) Google Scholar] with a hazard ratio of 0.62, but nevertheless with a limited improvement in median survival of only 1.1 months. When the ESMO-Magnitude of the Clinical Benefit Scale version 1 [6.Cherny N.I. Dafni U. Bogaerts J. et al.ESMO-magnitude of the Clinical Benefit Scale version 1.1.Ann Oncol. 2017; 28: 2340-2366Abstract Full Text Full Text PDF PubMed Scopus (325) Google Scholar] is applied to this study, the obtained score is 1, which is the minimum considered in the scale. The initial enthusiasm generated by the use of checkpoint inhibitors in advanced gastric cancer shrank when some randomized phase III trials reported negative outcomes when compared with chemotherapy. The KEYNOTE-061 trial prospectively compared pembrolizumab versus chemotherapy with weekly paclitaxel as second-line treatment in almost six hundred patients with gastric or gastroesophageal junction cancers with PD-L1 positivity in at least 1% of tumor cells [7.Shitara K. Özgüroğlu M. Bang Y.-J. et al.Pembrolizumab versus paclitaxel for previously treated, advanced gastric or gastro-oesophageal junction cancer (KEYNOTE-061): a randomised, open-label, controlled, phase 3 trial.Lancet. 2018; 392: 123-133Abstract Full Text Full Text PDF PubMed Scopus (750) Google Scholar]. Pembrolizumab, despite a better safety profile, was not able to improve survival over weekly paclitaxel. On the other hand, median progression-free survival was significantly shorter for patients receiving pembrolizumab (1, 5 months versus 4, 1 months), which was a 27% higher risk of progression when patients were not allocated to chemotherapy. Another checkpoint inhibitor, avelumab, an anti-PD-L1 antibody, also failed in a randomized trial (Javelin 300), in which 379 chemorefractory patients, after receiving at least two lines of chemotherapy, were allocated to avelumab or an investigator choice of chemotherapy [8.Bang Y.J. Ruiz E.Y. Van Cutsem E. et al.Phase III, randomised trial of avelumab versus physician’s choice of chemotherapy as third-line treatment of patients with advanced gastric or gastro-oesophageal junction cancer: primary analysis of JAVELIN Gastric 300.Ann Oncol. 2018; 29: 2052-2060Abstract Full Text Full Text PDF PubMed Scopus (300) Google Scholar]. Overall survival, the primary end point of the study, was not improved by the use of avelumab. No benefit was observed in patients with PD-L1-positive tumors. Similar to the KEYNOTE-061, progression-free survival also favored the chemotherapy group. How can we interpret this imbalance of confirmed antitumor activity in several phase II trials with the limited, or even absence of, survival improvement in controlled studies? It could be certainly the case that immunotherapy is not for all comers in advanced gastric cancer [9.Smyth E.C. Cervantes A. Immunotherapy is not for all comers in chemotherapy-refractory advanced gastric cancer. Better predictive biomarkers are needed.Ann Oncol. 2018; 29: 2028-2029Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar] and that we should better understand which are the right predictive biomarkers that should help us in selecting patients who could get a real benefit from checkpoint inhibitors. Gastric cancer is a very heterogeneous disease. According to the molecular classification developed by the Cancer Genome Atlas Research Network, gastric cancer can be defined as Epstein Barr-related, microsatellite instability, chromosomal instability and genomic stable [10.Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma.Nature. 2014; 513: 202-209Crossref PubMed Scopus (3912) Google Scholar]. Among them, those related to Epstein–Barr and those with microsatellite instability are considered to be highly sensitive to immunotherapy. Several relatively small series have consistently indicated a clear relation of these molecular subgroups with a response to these checkpoint inhibitors [11.Kim S.T. Cristescu R. Bass A.J. et al.Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer.Nat Med. 2018; 24: 1449-1458Crossref PubMed Scopus (731) Google Scholar, 12.Derks S. Liao X. Chiaravalli A.M. et al.Abundant PD-L1 expression in Epstein-Barr Virus-infected gastric cancers.Oncotarget. 2016; 7: 32925-32932Crossref PubMed Scopus (209) Google Scholar, 13.Le D.T. Durham J.N. Smith K.N. et al.Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade.Science. 2017; 357: 409-413Crossref PubMed Scopus (3771) Google Scholar]. The question is if there is any role for these drugs in the treatment of microsatellite stable or in Epstein–Barr-negative tumors. In the series mentioned before, a few gastric cancer patients without microsatellite instability and not related to Epstein–Barr virus actually did respond to checkpoint inhibitors. In an original paper published in this issue of Annals of Oncology, Sundar et al. report on the use of alternate promoters (AP) as a mechanism of immune evasion in advanced gastric cancer and as a negative predictor of response to checkpoint inhibitors [14.Sundar R. Huang K.K. Qamra A. et al.Epigenomic promoter alterations predict for benefit from immune checkpoint inhibition in metastatic gastric cancer.Ann Oncol. 2019; 30: 424-430Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar]. To assess the clinical value of this hypothesis, they studied AP utilization with Nanostring and RNA-sequencing in two cohorts of advanced gastric patients treated with checkpoint inhibitors. Using a customized Nanostring panel for measuring transcripts related to the canonical or the AP in the test cohort, they could define a third of tumors with high AP use. These tumors presented much lower biomarkers of T-cell cytolytic activity and fewer responses to checkpoint inhibition than those others with low AP use. In a multivariate analysis, AP utilization was a strong independent predictor of immunotherapy survival [hazard ratio 0.29; 95% confidence interval (CI) 0.099–0.85, P = 0.024]. Moreover, in patients treated with pembrolizumab, when paired biopsies were analyzed, it was possible to confirm consistent shifts in AP utilization rate associated with clinical response. In particular, tumors with partial responses and stable disease exhibited 1.5-fold or higher increase in AP usage score in the post-treatment biopsy samples compared with pre-treatment biopsy samples, while all five tumors with progressive disease exhibited reductions in AP usage scores in the post-treatment biopsy samples. The AP-high group had only one microsatellite unstable tumor and no EBV tumors, suggesting that this mechanism of resistance appears to be largely restricted to the chromosomal unstable or genomic stable subgroups. Promoters are cis-regulatory elements that function linking gene transcription initiation to upstream regulatory stimuli, integrating diverse inputs [15.Lenhard B. Sandelin A. Carninci P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation.Nat Rev Genet. 2012; 13: 233-245Crossref PubMed Scopus (331) Google Scholar]. Differential usage of alternative promoters causes the generation of distinct 5′-untranslated regions (and first exons in transcripts, which in turn can influence mRNA expression levels [16.Bieberstein N.I. Carrillo Oesterreich F. Straube K. Neugebauer KM. First exon length controls active chromatin signatures and transcription.Cell Rep. 2012; 2: 62-68Abstract Full Text Full Text PDF PubMed Scopus (120) Google Scholar], translational efficiencies [17.Zammarchi F. Boutsalis G. Cartegni L. 5′ UTR control of native ERG and of Tmprss2: eRG variants activity in prostate cancer.PLoS One. 2013; 8: e49721.Crossref PubMed Scopus (24) Google Scholar, 18.Ong C.K. Leong C. Tan P.H. et al.The role of 5′ untranslated region in translational suppression of OKL38 mRNA in hepatocellular carcinoma.Oncogene. 2007; 26: 1155-1165Crossref PubMed Scopus (15) Google Scholar], and the generation of different protein isoforms through gain and loss of 5′-coding domains [19.Valen E. Pascarella G. Chalk A. et al.Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.Genome Res. 2009; 19: 255-265Crossref PubMed Scopus (118) Google Scholar]. The use of alternative transcription start sites through alterations in epigenetic promoter regions causes reduced expression of immunogenic N-terminal peptides, which may facilitate immune evasion in early gastric cancer. Tumor immunoediting is recognized as one of the processes developed by cancer cells to evade host immune surveillance [20.Schumacher T.N. Schreiber RD. Neoantigens in cancer immunotherapy.Science. 2015; 348: 69-74Crossref PubMed Scopus (2981) Google Scholar, 21.Mittal D. Gubin M.M. Schreiber R.D. Smyth MJ. New insights into cancer immunoediting and its three component phases—elimination, equilibrium and escape.Curr Opin Immunol. 2014; 27: 16-25Crossref PubMed Scopus (958) Google Scholar]. To explore potential contributions of somatic promoters in localized gastric cancer immunoediting, in a previously published article [22.Qamra A. Xing M. Padmanabhan N. et al.Immunogenic diversity in gastric adenocarcinoma epigenomic promoter alterations amplify gene isoform and immunogenic diversity in gastric adenocarcinoma.Cancer Discov. 2017; 7: 630-651Crossref PubMed Scopus (37) Google Scholar], the authors found somatic promoter-associated N-terminal peptides with high predicted affinity binding to various major histocompatibility complex class I human leukocyte antigen alleles, which are required for antigen presentation to CD8+ cytotoxic T cells and tumor immunity. The importance of these findings is also confirmed in the present article in advanced gastric tumors. This elegant investigation suggests the hypothesis that gastric cancers adopt AP as a mechanism of immune evasion, and these tumors may be resistant to anti-PD1 immune checkpoint inhibition. AP utilization could be considered as a potential mechanism of primary resistance to immune checkpoint inhibition, and a novel negative predictive biomarker for immunotherapy, independent from other established biomarkers such as mutational burden and PD-L1 scores. We concur that further validation of these findings are needed in prospective trials. The confirmation of AP high as a negative predictive biomarker could be an important step to reach precision immunotherapy through a more cost effective approach on the use of checkpoint inhibitors for advanced gastric cancer. This work has been supported by the Ministerio de Economía y Competitividad. Instituto de Salud Carlos III with grants to Andrés Cervantes (FIS PI18/001909) and Tania Fleitas (FIS PI 18/01508). Tania Fleitas has a Joan Rodes contract 17/0026 and Valentina Gambardella has a Rio-Hortega contract CM18 and was a recipient of an ESMO translational research fellowship.