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CLINICAL CANCER RESEARCH | PRECISION MEDICINE AND IMAGING Spatial and Temporal Heterogeneity of PD-L1 Expression and Tumor Mutational Burden in Gastroesophageal Adenocarcinoma at Baseline Diagnosis and after Chemotherapy A C Katherine I. Zhou 1 , Bryan Peterson 2 , Anthony Serritella 3 , Joseph Thomas 3 , Natalie Reizine 2 , Stephanie Moya 2 , Carol Tan 2 , Yan Wang 2 , and Daniel V.T. Catenacci 2 ABSTRACT Purpose: Intrapatient heterogeneity of programmed death ligand 1 (PD-L1) expression and tumor mutational burden (TMB) in gastroesophageal adenocarcinoma (GEA) could inuence their roles as predictive biomarkers for response to immune checkpoint inhibitors (ICI). In this retrospective analysis, we evaluated the spatiotemporal heterogeneity and prognostic relevance of PD-L1 expression and TMB in GEA. Experimental Design: A cohort of 211 patients with stage IIIV GEA was retrospectively reviewed for a total of 407 tumor samples with PD-L1 expression data and 319 tumor samples with TMB data. PD-L1 status was dened as positive if combined positive score (CPS) 1 using the 22C3 pharmDx assay. TMB levels were categorized as low, intermediate, or high (5, 515, or >15 mutations/Mb), or using a single threshold (<10 or 10 mutation/Mb), determined by next- generation sequencing using a targeted gene panel. Results: Of 407 tumors, 56% were PD-L1 negative and 44% PD- L1 positive. Of 319 tumors, 50% were TMB-low, 45% TMB-inter- mediate, and 5% TMB-high; 86% had <10 and 14% 10 mutations/ Mb. TMB level was signicantly associated with MSI-status. PD-L1 expression and TMB exhibited marked spatial heterogeneity between baseline primary and metastatic tumors (61% and 69% concordance), and temporal heterogeneity between tumors before and after chemotherapy (57%63% and 73%75% concordance). PD-L1 expression and TMB were not signicantly associated with overall survival. Conclusions: PD-L1 expression and TMB exhibit marked spatial and temporal heterogeneity in GEA. This heterogeneity should be considered when obtaining tumor samples for molecular testing and when deciding whether ICI therapy is appropriate. See related commentary by Klempner et al., p. 6401 Introduction Gastroesophageal adenocarcinoma (GEA) commonly presents with advanced disease and is associated with poor prognosis (1). Despite advances in targeted therapies, the treatment of advanced GEA still relies primarily on cytotoxic chemotherapy (2). In recent years, immune checkpoint inhibitors (ICI) have emerged as promising treatments for locally advanced or metastatic GEA, and the anti- programmed cell death protein 1 (anti-PD-1) antibody pembrolizu- mab was conditionally approved by the FDA for use in a subset of patients with GEA after progression on initial systemic treat- ments (1, 3, 4). Biomarkers including programmed death ligand 1 (PD-L1) expression and tumor mutational burden (TMB) might help dene which patients are most likely to benet from ICI therapy (5). Tumor cell PD-L1 expression (TPS) is associated with response to anti-PD-1/anti-PD-L1 therapy in some cancers (6, 7). In GEA, a PD-L1 combined positive score (CPS) of 1 helps predict benet from pembrolizumab therapy with high negative predictive value but less- than-desirable positive predictive value (1, 3, 8). TMB has also emerged as a putative biomarker associated with ICI response in multiple tumor types (911). In patients with advanced GEA treated with the anti- PD-1 antibody toripalimab, TMB 12 mutations per megabase (mut/ Mb) was associated with improved response and overall survival (OS; ref. 12). Recently, the FDA approved the use of pembrolizumab for advanced solid tumors with TMB 10 mut/Mb that progressed on prior therapy, marking the second tumor-agnostic approval of ICI therapy. This approval was based on a retrospective analysis of the nonrandomized KEYNOTE-158 trial. In this analysis, tumors with TMB 10 mut/Mb and microsatellite stability (MSS), found in 102 patients (13% of all successfully evaluated), was associated with an overall response rate of 29% to pembrolizumab monotherapy in various chemorefractory cancers, notably not including any GEA tumors (13). However, further work is needed to more precisely dene the clinical utility of TMB as a predictive biomarker in various tumor types, including GEA (5). Molecular biomarkers in GEA exhibit signicant heterogene- ity (14, 15). Heterogeneity of PD-L1 expression and TMB could inuence their roles as predictive biomarkers for ICI response. Het- erogeneity of PD-L1 expression within tumors and between tumor sites has been described for multiple cancer types (1618). In surgically resected GEAs, signicant spatial discordance of PD-L1 expression was observed between primary tumors and lymph node metasta- ses (19). In nonsmall cell lung cancer (NSCLC), TMB exhibited both intratumoral heterogeneity and discordance between primary and metastatic tumors, but it is unclear whether this observation applies to other tumor types (20). PD-L1 expression and TMB may also 1 Medical Scientist Training Program, University of Chicago, Chicago, Illinois. 2 Section of Hematology/Oncology, Department of Medicine, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois. 3 Department of Medicine, University of Chicago Medical Center, Chicago, Illinois. Note: Supplementary data for this article are available at Clinical Cancer Research Online (http://clincancerres.aacrjournals.org/). Corresponding Author: Daniel V.T. Catenacci, University of Chicago Medical Center and Biological Sciences, 900 E 57th St, Ste 7128, Chicago, IL 60637. Phone: 7737021000; E-mail: [email protected] Clin Cancer Res 2020;26:111 doi: 10.1158/1078-0432.CCR-20-2085 Ó2020 American Association for Cancer Research. AACRJournals.org | OF1 Research. on June 15, 2021. © 2020 American Association for Cancer clincancerres.aacrjournals.org Downloaded from Published OnlineFirst August 20, 2020; DOI: 10.1158/1078-0432.CCR-20-2085

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  • CLINICAL CANCER RESEARCH | PRECISION MEDICINE AND IMAGING

    Spatial and Temporal Heterogeneity of PD-L1 Expressionand Tumor Mutational Burden in GastroesophagealAdenocarcinoma at Baseline Diagnosis and afterChemotherapy A CKatherine I. Zhou1, Bryan Peterson2, Anthony Serritella3, Joseph Thomas3, Natalie Reizine2,Stephanie Moya2, Carol Tan2, Yan Wang2, and Daniel V.T. Catenacci2

    ABSTRACT◥

    Purpose: Intrapatient heterogeneity of programmed deathligand 1 (PD-L1) expression and tumor mutational burden (TMB)in gastroesophageal adenocarcinoma (GEA) could influence theirroles as predictive biomarkers for response to immune checkpointinhibitors (ICI). In this retrospective analysis, we evaluated thespatiotemporal heterogeneity and prognostic relevance of PD-L1expression and TMB in GEA.

    Experimental Design: A cohort of 211 patients with stage II–IVGEA was retrospectively reviewed for a total of 407 tumor sampleswith PD-L1 expression data and 319 tumor samples with TMB data.PD-L1 statuswas defined as positive if combinedpositive score (CPS)≥1 using the 22C3 pharmDx assay. TMB levels were categorized aslow, intermediate, or high (≤5, 5–15, or >15mutations/Mb), or usinga single threshold (

  • demonstrate temporal heterogeneity from before to after chemother-apy. However, conflicting studies suggest that chemotherapy mightincrease, decrease, or have no effect on these biomarkers (21–25).Further characterization of the spatial and temporal heterogeneity ofPD-L1 expression and TMB could define optimal sites and timing fortheir measurement, and aid in their interpretation as predictivebiomarkers for ICI therapeutic benefit.

    PD-L1 expression and TMB might also have intrinsic prognosticvalue. PD-L1 expression correlatedwith poor prognosis in some tumortypes, but has no correlation or a correlation with favorable prognosisin others (26, 27). The prognostic significance of PD-L1 expression inGEA also has conflicting results (28–30). TMB-high has been linked topoor prognosis in NSCLC and esophageal cancer, and to favorableprognosis in colorectal cancer (31, 32). In addition to potentially realprognostic differences between histologies, discrepancies could also bedue to differences in methodology and scoring thresholds for PD-L1expression and TMB across studies. Moreover, underlying confound-ing factors such as Epstein–Barr virus (EBV) or microsatellite insta-bility (MSI) status may have contributed to the observed discordance.Overall, the prognostic significance of PD-L1 expression and TMB inGEA remains unclear.

    In this retrospective analysis, the largest andmost comprehensive ofits kind, we examined the heterogeneity and prognostic significance ofPD-L1 expression and TMB in 211 patients with GEA (33, 34). Toevaluate spatial and temporal heterogeneity, we compared baselinePD-L1 expression and TMB in paired primary and metastatic tumorsfrom newly diagnosed stage IVB GEA, and in paired pre- andposttreatment tumors from stage II–IV GEA. To assess prognosticsignificance, we evaluated OS of patients with stage IVBGEA stratifiedby PD-L1 expression or TMB.

    Materials and MethodsPatients

    The studies were conducted in accordance with the Declaration ofHelsinki. We retrospectively reviewed a cohort of 211 patients diag-nosed with stage II–IV GEA between 2011 and 2020 with at least onetumor sample with PD-L1 expression or TMB data. Informed writtenconsent was obtained from each patient or each patient's guardian.Patient and tumor characteristics were obtained from the clinically

    annotatedUniversity ofChicagoGI database using institutional reviewboard (IRB)-approved tissue banking protocols. No assurance wasfiled as this was not necessary. Sample size was determined by availabledata. Baseline samples were defined as obtained prior to or up to10 days after initiation of first-line chemotherapy. Samples obtained>10 days after initiation of first-line chemotherapy were consideredposttreatment samples. OS was defined as time from diagnosis todeath. Median follow-up time was 15.5 months for analysis of PD-L1expression, and 14.5 months for analysis of TMB.

    BiomarkersAll samples were processed through routine Clinical Laboratory

    Improvement Amendments (CLIA)-certified labs for clinical care andstored per standards set by the College of American Pathologists(CAP). Assays were conducted by independent commercial compa-nies with CLIA labs, and blinded to all patient clinical/pathologiccharacteristics, as well as treatment and outcomes. PD-L1 CPS (8) andHER2 IHC (with HER2 FISH if necessary; ref. 35) were evaluated perroutine clinical standards. PD-L1-status was defined as positive (PD-L1þ) if CPS ≥1, and negative (PDL1-) if CPS 5mut/Mb, ≤15mut/Mb), or high (TMB-H, >15 mut/Mb), based on the thresholds used in Foundation Med-icine reports. A post hoc analysis was performed using a binary cutoff at10 mut/Mb given the recent FDA approval (13). Each patient had alltheir tumor samples assessed at either Foundation Medicine orTempus Labs, with no intrapatient sample crossover between vendors.

    Statistical analysisRelationships between PD-L1 status, MSI status, and TMB level

    were evaluated by Fisher exact test, using one tumor sample per patientto respect the assumption of independence. PD-L1 status or TMBlevels of paired baseline primary and metastatic tumors, and of pairedpre- and posttreatment tumors, were compared by McNemar testusing one pair of tumors per patient to respect the assumption ofindependence. OS was analyzed using Kaplan–Meier curves, log-ranktests, and Cox proportional-hazards models, using one tumor or pairof tumors per patient to respect the assumption of independence.Single tumors or pairs of tumors were selected by prioritizing theearliest primary tumor sample, then earliest metastatic tumor sample.Candidate variables considered for inclusion in Cox proportional-hazards models were: age, sex, race, ethnicity, ECOG status at diag-nosis, tumor location, Lauren histologic classification, differentiation,presence of signet cells, HER2 status, PD-L1 status, MSI status,exposure to anti-HER2 therapy, and exposure to ICI therapy. In thesemodels, missing data were treated as a separate category (“unknown”).For all analyses, we considered P < 0.05 as significant. Statisticalanalysis was performed using R-v3.6.2.

    ResultsIn a cohort of 211 patients with stage II–IV GEA, 189 patients had

    407 tumor samples with PD-L1 expression data, and 162 patients had319 tumor samples with TMB data (Table 1).

    Relationship between PD-L1 status, MSI status, and TMB levelAmong 407 tumors, PD-L1 CPS ranged 0–100 with median 0 and

    interquartile range 0–3.8. PD-L1-status was positive for 44% oftumors, and CPS ≥10 for 15% (Fig. 1A and Supplementary

    Translational Relevance

    Programmed death ligand 1 (PD-L1) expression and tumormutational burden (TMB) are potential biomarkers for response toICIs. Many biomarkers exhibit heterogeneity in gastroesophagealadenocarcinoma (GEA). Intrapatient heterogeneity of PD-L1expression and TMB in GEA could influence their roles as pre-dictive biomarkers. In this analysis, the largest of its kind for GEA,PD-L1 expression andTMB exhibitedmarked spatial and temporalheterogeneity, and did not affect prognosis in advanced disease.Spatial heterogeneity was particularly noted in baseline primarytumors, which were PD-L1 positive and TMB-high but frequentlyPD-L1 negative and TMB-low in paired metastases. These resultsmay provide explanation for lack of benefit of ICI therapy in mostpatients despite positive PD-L1 scoring in primary tumors. Eval-uation of intrapatient heterogeneity of PD-L1 expression and/orTMBmay better predict which patients withGEA aremost likely tobenefit from ICI therapy.

    Zhou et al.

    Clin Cancer Res; 26(24) December 15, 2020 CLINICAL CANCER RESEARCHOF2

    Research. on June 15, 2021. © 2020 American Association for Cancerclincancerres.aacrjournals.org Downloaded from

    Published OnlineFirst August 20, 2020; DOI: 10.1158/1078-0432.CCR-20-2085

    http://clincancerres.aacrjournals.org/

  • Fig. S1A). Among 319 tumors, TMB ranged 0–54.7 mut/Mb withmedian 6mut/Mb and interquartile range 4–8.Half of the tumors wereTMB-L, 45% TMB-I, and 5% TMB-H (Fig. 1B), while 14% of thetumors had TMB ≥10 mut/Mb (Fig. 1C). After exclusion of MSI-Htumors, 2% of MSS tumors were TMB-H (>15 mut/Mb), and 12% hadTMB ≥10 mut/Mb (Fig. 1D–E). Of note, none of the MSI-H tumorswere germline. TMB level was significantly associated withMSI-status(P ¼ 1� 10�7; Fig. 1D; Supplementary Fig. S1B). Notably, 89% (8/9)of MSI-high (MSI-H) tumors were TMB-H, while only 53% (8/15) ofTMB-H tumors were MSI-H. TMB was also significantly associatedwith MSI-status using a threshold of 10 mut/Mb (P ¼ 9.4 � 10�6;Fig. 1E; Supplementary Fig. S1C). PD-L1 status was not significantlyassociated with MSI status or TMB level, although more PD-L1�

    tumors were TMB-L, and more PD-L1þ tumors were TMB-I andTMB-H (Fig. 1F and G; Supplementary Fig. S1D and S1E).

    Spatial heterogeneity of PD-L1 expression and TMBWe compared PD-L1 expression in paired baseline primary and

    baseline metastatic tumors from 62 patients (Fig. 2A–B). Thirty-sixprimary tumors were PD-L1þ, compared with 18 metastatic tumors(Fig. 2A). Baseline paired primary andmetastatic tumor PD-L1-statuswere 61% concordant (38/62), indicating marked spatial heterogene-ity. Of 26 PD-L1� primary tumors, 23 (88%) remained PD-L1� in themetastatic tumor. In contrast, of 36 PD-L1þ primary tumors, only 15(42%) remained PD-L1þ in the metastatic tumor (P ¼ 2.4 � 10�4).PD-L1 status and spatial concordance of PD-L1 status did not show aclear dependence on metastatic site (Supplementary Table S1). With athreshold CPS of 10 (Fig. 2B), concordance was 84% (52/62). Of 53primary tumors with CPS

  • marked spatial heterogeneity (Fig. 2C). Of 41 primary tumors withlow-to-intermediate TMB (TMB-L/I), 41 (100%) remained TMB-L/Iin the metastatic tumor. In contrast, of four TMB-H primary tumors,only two (50%) remained TMB-H in the metastatic tumor (P¼ 0.16).When TMB was dichotomized by low versus intermediate–high,McNemar test also did not show significance (P ¼ 0.41). Of note,both pairs of tumors that maintained TMB-H were MSI-H, while allother tumors were not. Using a single TMB threshold of 10 mut/Mb(Fig. 2D), concordance was 89% (40/45). Of 38 primary tumors withTMB 14 days apart. Concordance ofTMB with a threshold of 10 mut/Mb was 95% (18/19) for pairedsamples obtained ≤14 days apart, and 85% (22/26) for paired samplesobtained >14 days apart.

    Given the marked spatial heterogeneity between baseline primaryand metastatic tumor samples, we considered the possibility thatconcordant PD-L1þ status or TMB-H levels might predict betterresponse to ICI therapy. To test this hypothesis, we compared pro-gression-free survival in patients with concordant or discordant PD-L1expression or TMB (Supplementary Table S3). However, only a smallnumber of patients received ICI therapy, and with this small samplesize we were unable to reach any conclusions regarding the relation-ship between spatial concordance of PD-L1 expression or TMB andresponse to ICI therapy.

    Temporal heterogeneity of PD-L1 expression and TMBWe compared PD-L1 expression in paired pretreatment primary

    tumors and posttreatment primary or metastatic tumors from83 patients (Fig. 3A). Pretreatment primary and posttreatment tumorPD-L1 status were 63% concordant (52/83), indicating marked tem-poral heterogeneity. Similar proportions of PD-L1� and PD-L1þ

    pretreatment tumors maintained their initial PD-L1 status aftertreatment (P ¼ 0.86). With a threshold CPS of 10, concordance was75% (62/83; Fig. 3B). Similar results were obtained when the singlepair of pre- and posttreatment MSI-H tumors was excluded from theanalysis (Supplementary Fig. S3A and S3B). Moreover, similar con-cordance of PD-L1 status was observed between pre- and posttreat-ment primary tumors (63% concordance; Supplementary Fig. S3C andS3D), or pre- and posttreatment primary or metastatic tumors (57%concordance; Supplementary Fig. S3E and S3F). Higher concordance(79%) was noted between pre- and posttreatment metastatic tumors atmatching sites, but the sample size was small (Supplementary Fig. S3Gand S3H). Three PD-L1� pretreatmentmetastatic tumors converted toPD-L1þ posttreatment, whereas no PD-L1þ pretreatment metastatic

    tumors converted to PD-L1� posttreatment (P ¼ 0.083). Of note, allthe patients received at least first-line platinum-based therapy betweenpretreatment and posttreatment tumor samples. However, somepatients also received other treatments such as radiotherapy, targetedtherapy, or ICIs. These additional therapies did not have a clear effecton temporal concordance of PD-L1 status (Supplementary Table S4).

    We compared TMB in paired pretreatment primary tumors andposttreatment primary or metastatic tumors from 63 patients(Fig. 3C). Pretreatment primary and posttreatment tumor TMB levelswere 73% concordant (46/63). Of 61 pretreatment TMB-L/I primarytumors, 61 (100%) remained TMB-L/I after treatment, whereas of twoTMB-H pretreatment primary tumors, one (50%) remained TMB-Hafter treatment (P ¼ 0.32). The difference between conversion fromlow to intermediate–high TMB and from intermediate–high to lowTMB was also not significant (P ¼ 0.32). Notably, the pair of tumorsthat maintained TMB-H was MSI-H, while all other tumors were not.Using a single TMB threshold of 10 mut/Mb (Fig. 3D), concordancewas 90% (57/63). Of 56 pretreatment primary tumors with TMB

  • including exposure to ICI therapy, the impact of baseline primarytumor TMB level on OS remained insignificant (Padj ¼ 0.12). OS alsodid not significantly differ with stratification by baseline metastatictumor TMB level (P ¼ 0.61; Supplementary Fig. S6B) or baselineprimary or metastatic tumor TMB level (P ¼ 0.96; SupplementaryFig. S6C). Likewise, OS did not significantly differ with stratificationusing a threshold TMB of 10 mut/Mb (Fig. 4C; Supplementary

    Fig. S6D and S6E). OS also did not depend on change in TMB levelor TMB after chemotherapy (Supplementary Fig. S6F and S6G).

    DiscussionIn this study, we investigated the heterogeneity and prognostic

    significance of PD-L1 expression and TMB in GEA. Both PD-L1

    Figure 1.

    Relationship between PD-L1 status, MSI status, and TMB level. Pie charts of tumor PD-L1 status (n¼ 407; A), tumor TMB levels (n¼ 319; B), and tumor TMB using athreshold of 10 mut/Mb (n¼ 319; C). D, Relationship between TMB level and MSI status in all tumors with available data (≥1 tumor per patient). This association wassignificant by Fisher exact test using one tumor per patient (P¼ 1� 10�7; Supplementary Fig. S1B).E,Relationship between TMBandMSI status using a TMB thresholdof 10mut/Mb in all tumorswith available data (≥1 tumor per patient). This associationwas significant by Fisher exact test using one tumor per patient (P¼ 9.4� 10�6;Supplementary Fig. S1C). F, Relationship between PD-L1 status and MSI-status in all tumors with available data (≥1 tumor per patient). This association was notsignificant by Fisher exact test using one tumor per patient (P¼0.72; Supplementary Fig. S1D).G,Relationship between TMB-level and PD-L1 status in all tumorswithavailable data (≥1 tumor per patient). This association was not significant by Fisher exact test using one tumor per patient (P ¼ 0.50; Supplementary Fig. S1E). Inall tables (D–G), the number of tumors is shown, with the percentage of tumors by row indicated in parentheses. Int, intermediate; MSI-H, MSI-high; MSS,microsatellite stable.

    Spatiotemporal Heterogeneity of PD-L1 and TMB in GEA

    AACRJournals.org Clin Cancer Res; 26(24) December 15, 2020 OF5

    Research. on June 15, 2021. © 2020 American Association for Cancerclincancerres.aacrjournals.org Downloaded from

    Published OnlineFirst August 20, 2020; DOI: 10.1158/1078-0432.CCR-20-2085

    http://clincancerres.aacrjournals.org/

  • expression and TMB exhibited marked spatial heterogeneity, partic-ularly between PD-L1þ primary tumors and PD-L1� metastatictumors. PD-L1 expression and TMB also demonstrated notabletemporal heterogeneity. This spatial and temporal heterogeneity ofPD-L1 expression and TMB may impact their roles as predictivebiomarkers for ICIs. Neither PD-L1 expression nor TMB significantlyimpacted OS among patients with stage IVB GEA.

    Consistent with previous studies across tumor types (36, 38), wefound that TMB-H was significantly associated with MSI-H in GEA.Of note, a substantial proportion of TMB-H tumors were MSS. TheseMSS, TMB-H tumors might be associated with genetic alterations inother DNA damage repair pathways, which may have additionalprognostic and therapeutic implications (39). Conversely, nearly allMSI-H tumors were TMB-H, and all had ≥10 mut/Mb. A differentTMB threshold may be more predictive of ICI response among thesubset of tumors that are MSI-H, as has been previously explored inmetastatic colorectal cancer (40). Previous studies found that PD-L1

    expression correlated with high TMB in gastric but not in esophagealcancers (41, 42), while PD-L1þ correlated with MSI-H in surgicalresections of GEA (41, 43). We found no significant associationbetween PD-L1 status and either TMB level or MSI status in GEA,possibly due to inclusion of both gastric and esophageal adenocarci-nomas at advanced stages, differences in measurement of TMB orMSIamong studies, or lack of power to detect a correlation of PD-L1 statuswith either TMB or MSI given small numbers. Notably, in theKEYNOTE-059, -061, and -062 pooled analysis, 92.5% (62/67) ofMSI-H tumors had PD-L1 CPS ≥1 (44).

    We found that PD-L1 expression and TMB in GEA demonstratedsubstantial spatial heterogeneity, with under 70% concordance of PD-L1 status and TMB levels between baseline primary and metastatictumors. In previous studies of surgically resected GEA, regional lymphnode metastases had higher PD-L1þ rates than matched primarytumors (19, 43). In contrast, we found that baseline distant metastatictumors had lower PD-L1þ rates than matched baseline primary

    Figure 2.

    Comparison of PD-L1 expression and TMB in primary versusmetastatic tumors.A,PD-L1 status of paired baseline primary andbaselinemetastatic tumors (61%, 38/62concordance; P¼ 2.4� 10�4 by McNemar test). B, PD-L1 expression of paired baseline primary and baselinemetastatic tumors with threshold PD-L1 CPS of 10 (84%,52/62 concordance; P ¼ 1 by McNemar test). C, TMB levels of paired baseline primary and baseline metastatic tumors (69%, 31/45 concordance; P ¼ 0.16 for low–intermediate vs. high,P¼0.41 for low vs. intermediate–high byMcNemar test).D, TMBof paired baseline primary and baselinemetastatic tumorswith threshold TMBof 10 mut/Mb (89%; 40/45 concordance; P¼ 0.18 by McNemar test). In all tables, the number of tumors is shown, with the percentage of tumors by row indicated inparentheses. 1� , primary tumor; met, metastatic tumor; int, intermediate.

    Zhou et al.

    Clin Cancer Res; 26(24) December 15, 2020 CLINICAL CANCER RESEARCHOF6

    Research. on June 15, 2021. © 2020 American Association for Cancerclincancerres.aacrjournals.org Downloaded from

    Published OnlineFirst August 20, 2020; DOI: 10.1158/1078-0432.CCR-20-2085

    http://clincancerres.aacrjournals.org/

  • tumors. This discrepancy could be due to differences in biology ofregional lymph node metastases and distant metastases, or in mea-surement of PD-L1 between studies. Together, the results from ourstudy and previous reports suggest that PD-L1 expression differs atbaseline between primary tumors, lymph nodemetastases, and distantmetastases in a large fraction of patients with GEA. Spatial heteroge-neity of TMB was previously reported in NSCLC (20). We observedthat TMB also exhibits spatial heterogeneity between primary andmetastatic tumors in GEA. Higher spatial concordance was observedusing the now clinically relevant threshold TMB of 10 mut/Mb, asexpected when using one rather than two thresholds. Of note, spatialheterogeneity using this threshold was highly directional, favoringpairing of baseline primary tumors with TMB ≥10mut/Mb to baselinemetastatic tumors with TMB

  • Figure 4.

    Overall survival stratified by PD-L1 expression or TMB. A, Kaplan–Meier overall survival curves for patients with stage IVB GEA stratified by baseline primary tumorPD-L1 status using threshold CPS of 1. HRs and log-rank test P values are shown with and without adjustment for age, sex, race, ECOG status at diagnosis, tumorlocation, Lauren histologic classification, differentiation, presence of signet cells, HER2 status, TMB level, and exposure to ICI therapy, andwith andwithout additionaladjustment for MSI status. B, Kaplan–Meier overall survival curves for patients with stage IVB GEA stratified by baseline primary tumor TMB level. HRs and log-ranktest P values are shown with and without adjustment for age, sex, race, ECOG status at diagnosis, tumor location, Lauren histologic classification, differentiation,presence of signet cells, HER2 status, PD-L1 status, and exposure to ICI therapy, and with and without additional adjustment for MSI status. C, Kaplan–Meier overallsurvival curves for patientswith stage IVBGEA stratifiedby baseline primary tumor TMBusing threshold of 10mut/Mb. HRs and log-rank testP values are shownwithand without adjustment for age, sex, race, ECOG status at diagnosis, tumor location, Lauren histologic classification, differentiation, presence of signet cells, HER2status, PD-L1 status, MSI status, and exposure to ICI therapy. For each set of survival curves, the corresponding table shows the number of patients (n), number ofevents (deaths), and overall survival in each group and in total. HR, unadjusted HR; P, unadjusted P value; HRadj, adjusted HR; Padj, adjusted P value; HRadjMSI, adjustedHR with additional adjustment for MSI status; PadjMSI, adjusted P value with additional adjustment for MSI status; 1�, primary tumor; int, intermediate; mOS, medianoverall survival; mos, months; 95% CI, 95% confidence interval; NR, not reached.

    Zhou et al.

    Clin Cancer Res; 26(24) December 15, 2020 CLINICAL CANCER RESEARCHOF8

    Research. on June 15, 2021. © 2020 American Association for Cancerclincancerres.aacrjournals.org Downloaded from

    Published OnlineFirst August 20, 2020; DOI: 10.1158/1078-0432.CCR-20-2085

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  • heterogeneity of TMB in GEA, with no statistically significant direc-tional change in TMB. As with spatial concordance, higher temporalconcordance was observed using a TMB threshold of 10mut/Mb, withnonstatistically significant directionality favoring conversion frompretreatment tumors with TMB ≥10mut/Mb to posttreatment tumorswith TMB 80%) of tumor samples were biopsies, so some of theobserved discordance of PD-L1 status could be due to intratumoralheterogeneity. It could also be valuable to further characterize intra-tumoral heterogeneity of TMB in GEA in future studies. Third, in ouranalysis of temporal heterogeneity, we did not account for varying timeon therapy, chemotherapy regimens (although all were pre/post first-line platinum-based therapy), or other treatments such as radiother-apy, targeted therapy, or ICIs. Moreover, we could not distinguishbetween the effects of chemotherapy-induced changes versus intrinsicnatural tumor evolution. A subgroup analysis of our small sample didnot show any obvious effects of radiotherapy, targeted therapies, orICIs on temporal concordance of PD-L1 status. Notably, tyrosinekinase inhibitors have been previously reported to substantiallyincrease PD-L1 expression in a subset of patients with metastatic

    gastric cancer (48). However, none of the patients in our analysisreceived tyrosine kinase inhibitors between the pre- and posttreatmentsamples. Large prospective studies are needed to determine the effect ofchemotherapy and other therapies on PD-L1 expression and TMB inGEA, andmutational signatures could help distinguish variants causedby chemotherapy or tumor evolution (25, 49). Fourth, while we did notfind associations of PD-L1 or TMB with OS in stage IVB GEA, ouranalysis may have been affected by residual confounding, and wecannot exclude associations with progression-free survival or in early-stage GEA. Finally, given the retrospective nature and small samplesizes in this study, larger independent studies are needed to confirmour conclusions regarding spatial and temporal heterogeneity of PD-L1 expression and TMB in GEA.

    In conclusion, this study evaluating heterogeneity of PD-L1 expres-sion and TMB in GEA demonstrated marked spatial and temporaldiscordance, which may impact their use as predictive biomarkers forICIs. Further studies are needed to confirm our results, and todetermine the optimal location and timing for measurement of thesebiomarkers. Multisite sampling, repeat testing after treatment, andblood-based testing each warrant further investigation as possibleapproaches to account for heterogeneity of PD-L1 expression andTMB. It may be that homogeneous disease, with concordant PD-L1þ

    and/or TMB-H profiles throughout, or particularly the metastaticdisease profile if discordant, could be significant positive predictorsof outcome. While our dataset was relatively small and heterogeneousto address this important question, it is being addressed within somestudies (50). Understanding the heterogeneity and prognostic value ofthese biomarkers could ultimately help select GEA patients who aremost likely to benefit from ICIs.

    Disclosure of Potential Conflicts of InterestD.V.T. Catenacci reports personal fees from Merck, BMS, Five Prime, Gritstone,

    Astellas, Pieris, Daiichi Sankyo, Lilly, Genentech Roche, Tempus, Foundation Med-icine, Guardant 360, Seattle Genetics, Taiho, Zymeworks, QED, Archer, and Nateraduring the conduct of the study. No potential conflicts of interest were disclosed by theother authors.

    Authors’ ContributionsK.I. Zhou: Conceptualization, formal analysis, investigation, writing-original

    draft, writing-review and editing. B. Peterson: Data curation, writing-review andediting. A. Serritella: Writing-review and editing. J. Thomas: Writing-review andediting.N.Reizine:Writing-review and editing. S.Moya:Writing-review and editing.Y.-H. Tan: Writing-review and editing. Y. Wang: Conceptualization, resources,supervision, funding acquisition, project administration, writing-review and editing.D.V.T. Catenacci: Conceptualization, resources, supervision, funding acquisition,project administration, writing-review and editing.

    AcknowledgmentsThis work was supported by the NIH Medical Scientist Training Program

    (T32GM007281) and the University of Chicago Biological Sciences Division andFrank Family Endowment (to K.I. Zhou); and NIH K23 award (CA178203–01A1),UCCCC (University of Chicago Comprehensive Cancer Center) Award in PrecisionOncology—CCSG (Cancer Center Support Grant; P30CA014599), Castle Founda-tion, LLK (Live Like Katie) Foundation Award, Ullman Scholar Award and the SalFerrara II Fund for PANGEA (to D.V.T. Catenacci).

    The costs of publication of this article were defrayed in part by the payment of pagecharges. This article must therefore be hereby marked advertisement in accordancewith 18 U.S.C. Section 1734 solely to indicate this fact.

    Received May 28, 2020; revised July 15, 2020; accepted August 17, 2020;published first August 20, 2020.

    Spatiotemporal Heterogeneity of PD-L1 and TMB in GEA

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  • Published OnlineFirst August 20, 2020.Clin Cancer Res Katherine I. Zhou, Bryan Peterson, Anthony Serritella, et al. ChemotherapyAdenocarcinoma at Baseline Diagnosis and afterand Tumor Mutational Burden in Gastroesophageal Spatial and Temporal Heterogeneity of PD-L1 Expression

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