Blood tumor mutational burden and response to pembrolizumab plus chemotherapy in non-small cell lung cancer: KEYNOTE-782

BACKGROUND

First-line pembrolizumab plus chemotherapy has shown clinical benefit in patients with metastatic non-small cell lung cancer (NSCLC) regardless of tissue tumor mutational burden (tTMB) status. Blood tumor mutational burden (bTMB), assessed using plasma-derived circulating tumor DNA (ctDNA), may be a surrogate for tTMB. The KEYNOTE-782 study evaluated the correlation of bTMB with the efficacy of first-line pembrolizumab plus chemotherapy in NSCLC.

METHODS

Previously untreated patients with stage IV nonsquamous NSCLC received pembrolizumab 200 mg plus pemetrexed 500 mg/m2 and investigator's choice of carboplatin area under the curve 5 mg/mL/min or cisplatin 75 mg/m2 for 4 cycles, then pembrolizumab plus pemetrexed for ≤31 additional cycles every 3 weeks. Study objectives were to evaluate the association of baseline bTMB with objective response rate (ORR) (RECIST v1.1 by investigator assessment; primary), progression-free survival (PFS; RECIST v1.1 by investigator assessment), overall survival (OS), and adverse events (AEs; all secondary). A next-generation sequencing assay (GRAIL LLC) with a ctDNA panel that included lung cancer-associated and immune gene targets was used to measure bTMB.

RESULTS

117 patients were enrolled; median time from first dose to data cutoff was 19.3 months (range, 1.0-35.5). ORR was 40.2 % (95 % CI 31.2-49.6 %), median PFS was 7.2 months (95 % CI 5.6-9.8) and median OS was 18.1 months (95 % CI 13.5-25.6). Treatment-related AEs occurred in 113 patients (96.6 %; grade 3-5, n = 56 [47.9 %]). Of patients with evaluable bTMB (n = 101), the area under the receiver operating characteristics curve for continuous bTMB to discriminate response was 0.47 (95 % CI 0.36-0.59). Baseline bTMB was not associated with PFS or OS (posterior probabilities of positive association: 16.8 % and 7.8 %, respectively).

CONCLUSIONS

AEs were consistent with the established safety profile of first-line pembrolizumab plus chemotherapy in NSCLC. Baseline bTMB did not show evidence of an association with efficacy.

Molecular epidemiology study of programmed death ligand 1 and ligand 2 protein expression assessed by immunohistochemistry in extensive-stage small-cell lung cancer

Objectives

Prevalence of tumor PD-L1 expression in extensive-stage small-cell lung cancer (ES-SCLC) is variable, and data on PD-L2 expression are limited. The prognostic values of these biomarkers are not well understood. The current study was conducted to address these data gaps.

Methods

A retrospective cohort study of Danish patients with histologically confirmed ES-SCLC and evaluable tumor samples who were receiving usual care before the introduction of immunotherapy was conducted. Protein expression of PD-L1 and PD-L2 was determined by immunohistochemistry (IHC) using the PD-L1 IHC 22C3 pharmDx assay and a PD-L2 IHC assay using a propriety mouse monoclonal antibody. A combined positive score (CPS) of ≥1 was used to define biomarker positivity. Kaplan-Meier plots and Cox proportional hazard models were employed to assess the relationship between PD-L1 and PD-L2 protein expression and OS.

Results

Among 80 patients, 31% (n=25) and 36% (n=29) had disease positive for PD-L1 and PD-L2, respectively. Overall, 85% (n=68) of patients had concordant PD-L1/PD-L2 status; 26% (n=21) had double positive disease (both PD-L1 and PD-L2 CPS ≥1) and 59% (n=47) had double negative disease (both PD-L1 and PD-L2 CPS <1). PD-L1 and PD-L2 positivity were each associated with longer OS (unadjusted hazard ratios [HRs], 0.35 [95% CI, 0.21-0.61] and 0.50 [95% CI, 0.31-0.82]); the associations persisted after adjustment for several known prognostic factors (HRs, 0.41 [95% CI, 0.22-0.75] and 0.44 [95% CI, 0.25-0.79] for PD-L1 and PD-L2 positivity, respectively). When evaluating OS in patients with double positive disease, unadjusted and adjusted HRs for double positive compared with double negative were similar to those with only PD-L1 or PD-L2 positivity (unadjusted HR, 0.36 [95% CI, 0.20-0.64]; adjusted HR, 0.36 [0.18-0.73]).

Conclusion

PD-L1 and PD-L2 positivity were observed in approximately one-third of assessed ES-SCLC tumor samples and were highly congruent. Patients with PD-L1 and PD-L2 positivity, alone or combined, were associated with longer OS, independent of other prognostic factors.

Multicenter retrospective evaluation of magnetic resonance imaging in pediatric and congenital heart disease patients with cardiac implantable electronic devices

BACKGROUND

Guidelines addressing magnetic resonance imaging (MRI) in patients with cardiac implantable electronic devices (CIEDs) provide algorithms for imaging pediatric and congenital heart disease (CHD) patients. Guideline acceptance varies by institution. Guidelines also do not support routine MRI scans in patients with epicardial or abandoned leads, common in pediatric and CHD patients.

OBJECTIVE

The purpose of this study was to determine the incidence of MRI-related complications in pediatric and CHD patients with CIEDs, including epicardial and/or abandoned leads.

METHODS

A multicenter retrospective review included patients with CIEDs who underwent any MRI between 2007 and 2022 at congenital cardiac centers. The primary outcome was any patient adverse event or clinically significant CIED change after MRI, defined as pacing lead capture threshold increase >0.5 V with output change, P- or R- wave amplitude decrease >50% with sensitivity change, or impedance change >50%.

RESULTS

Across 14 institutions, 314 patients (median age 18.8 [1.3; 31.4] years) underwent 389 MRIs. There were 288 pacemakers (74%) and 87 implantable cardioverter-defibrillators (22%); 52% contained epicardial leads, and 14 (4%) were abandoned leads only. Symptoms or CIED changes occurred in 4.9% of MRI scans (6.1% of patients). On 9 occasions (2%), warmth or pain occurred. Pacing capture threshold or lead impedance changes occurred in 1.4% and 2.0% of CIEDs post-MRI and at follow-up.

CONCLUSION

Our data provide evidence that MRIs can be performed in pediatric and CHD patients with CIEDs, including non-MRI-conditional CIEDs and epicardial and/or abandoned leads, with rare minor symptoms or CIED changes but no other complications.

Associations of tissue tumor mutational burden and mutational status with clinical outcomes in KEYNOTE-042: pembrolizumab versus chemotherapy for advanced PD-L1-positive NSCLC

BACKGROUND

We evaluated whether tissue tumor mutational burden (tTMB) and STK11, KEAP1, and KRAS mutations have clinical utility as biomarkers for pembrolizumab monotherapy versus platinum-based chemotherapy in patients with programmed death ligand- 1 (PD-L1)-positive (tumor proportion score ≥1%) advanced/metastatic non-small-cell lung cancer (NSCLC) without EGFR/ALK alterations in the phase III KEYNOTE-042 trial.

PATIENTS AND METHODS

This retrospective exploratory analysis assessed prevalence of tTMB and STK11, KEAP1, and KRAS mutations determined by whole-exome sequencing of tumor tissue and matched normal DNA and their associations with outcomes in KEYNOTE-042. Clinical utility of tTMB was assessed using a prespecified cut point of 175 mutations/exome.

RESULTS

Of 793 patients, 345 (43.5%) had tTMB ≥175 mutations/exome and 448 patients (56.5%) had tTMB <175 mutations/exome. No association was observed between PD-L1 expression and tTMB. Continuous tTMB score was associated with improved overall survival (OS) and progression-free survival among patients receiving pembrolizumab (Wald test, one-sided P < 0.001) but not those receiving chemotherapy (Wald test, two-sided P > 0.05). tTMB ≥175 mutations/exome was associated with improved outcomes for pembrolizumab versus chemotherapy, whereas tTMB <175 mutations/exome was not {OS: hazard ratio, 0.62 [95% confidence interval (CI) 0.48-0.80] and 1.09 (95% CI 0.88-1.36); progression-free survival: 0.75 (0.59-0.95) and 1.27 (1.04-1.55), respectively}. Improved OS [hazard ratio (95% CI)] for pembrolizumab versus chemotherapy was observed regardless of STK11 [STK11 mutant (n = 33): 0.37 (0.16-0.86), STK11 wild-type (n = 396): 0.83 (0.65-1.05)]; KEAP1 [KEAP1 mutant (n = 64): 0.75 (0.42-1.35), KEAP1 wild-type (n = 365): 0.78 (0.61-0.99)], or KRAS [KRAS mutant (n = 69): 0.42 (0.22-0.81); KRAS wild-type (n = 232): 0.86 (0.63-1.18)] mutation status.

CONCLUSION

tTMB with a cut point of ≥175 mutations/exome is a potential predictive biomarker for pembrolizumab monotherapy for advanced/metastatic PD-L1 tumor proportion score ≥1% NSCLC. Pembrolizumab is a standard first-line treatment in this setting regardless of STK11, KEAP1, or KRAS mutation status.

Associations of Tissue Tumor Mutational Burden and Mutational Status With Clinical Outcomes With Pembrolizumab Plus Chemotherapy Versus Chemotherapy For Metastatic NSCLC

Introduction

We evaluated tissue tumor mutational burden (tTMB) and mutations in STK11, KEAP1, and KRAS as biomarkers for outcomes with pembrolizumab plus platinum-based chemotherapy (pembrolizumab-combination) for NSCLC among patients in the phase 3 KEYNOTE-189 (ClinicalTrials.gov, NCT02578680; nonsquamous) and KEYNOTE-407 (ClinicalTrials.gov, NCT02775435; squamous) trials.

Methods

This retrospective exploratory analysis evaluated prevalence of high tTMB and STK11, KEAP1, and KRAS mutations in patients enrolled in KEYNOTE-189 and KEYNOTE-407 and the relationship between these potential biomarkers and clinical outcomes. tTMB and STK11, KEAP1, and KRAS mutation status was assessed using whole-exome sequencing in patients with available tumor and matched normal DNA. The clinical utility of tTMB was assessed using a prespecified cutpoint of 175 mutations/exome.

Results

Among patients with evaluable data from whole-exome sequencing for evaluation of tTMB (KEYNOTE-189, n = 293; KEYNOTE-407, n = 312) and matched normal DNA, no association was found between continuous tTMB score and overall survival (OS) or progression-free survival for pembrolizumab-combination (Wald test, one-sided p > 0.05) or placebo-combination (Wald test, two-sided p > 0.05) in patients with squamous or nonsquamous histology. Pembrolizumab-combination improved outcomes for patients with tTMB greater than or equal to 175 compared with tTMB less than 175 mutations/exome in KEYNOTE-189 (OS, hazard ratio = 0.64 [95% confidence interval (CI): 0.38‒1.07] and 0.64 [95% CI: 0.42‒0.97], respectively) and KEYNOTE-407 (OS, hazard ratio = 0.74 [95% CI: 0.50‒1.08 and 0.86 [95% CI: 0.57‒1.28], respectively) versus placebo-combination. Treatment outcomes were similar regardless of KEAP1, STK11, or KRAS mutation status.

Conclusions

These findings support pembrolizumab-combination as first-line treatment in patients with metastatic NSCLC and do not suggest the utility of tTMB, STK11, KEAP1, or KRAS mutation status as a biomarker for this regimen.

Biomarkers predictive of response to pembrolizumab in head and neck cancer

BACKGROUND

We performed an integrated biomarker evaluation in pembrolizumab-treated patients with R/M HNSCC enrolled in KEYNOTE-012 or KEYNOTE-055. The relationship between biomarkers and HPV status was explored.

METHODS

We evaluated PD-L1 (combined positive score [CPS]), TMB, T-cell-inflamed gene expression profile (Tcell_inf GEP), and HPV status. Associations between biomarkers were evaluated by logistic regression (ORR) and Cox regression (PFS, OS).

RESULTS

Two hundred and fifty-seven patients (KEYNOTE-012, n = 106; KEYNOTE-055, n = 151) had TMB data available; of these, 254 had PD-L1 and 236 had Tcell_inf GEP. TMB, PD-L1, and Tcell_inf GEP were each significantly associated with ORR (p < 0.01). Kaplan-Meier curves at prespecified cutoffs generally showed PFS and OS separation in the anticipated direction for these biomarkers, except for OS and TMB. TMB did not correlate with PD-L1 or Tcell_inf GEP (Spearman ρ = -0.03 and ρ = -0.13, respectively); PD-L1 and Tcell_inf GEP were moderately correlated (Spearman ρ = 0.47). In multivariate models, TMB, PD-L1, and Tcell_inf GEP were each independently predictive for ORR (p < 0.001). ORR was higher in patients with high versus low levels of biomarkers when dichotomized using prespecified cutoffs; patients with higher versus lower levels of TMB and PD-L1 or TMB and Tcell_inf GEP had the highest ORRs. Within HPV subgroups, higher versus lower distributions of biomarkers (PD-L1, TMB, and Tcell_inf GEP) were associated with response. HPV detection by p16-immunohistochemistry and WES showed good concordance (81%); results were generally similar by HPV status, regardless of the detection method.

CONCLUSIONS

TMB and the inflammatory biomarkers PD-L1 and Tcell_inf GEP, assessed alone or together, may be useful for characterizing clinical response to pembrolizumab in R/M HNSCC.

T cell-inflamed gene expression profile and PD-L1 expression and pembrolizumab efficacy in advanced esophageal cancer

Aim: Investigate the relationship between response to pembrolizumab and expression of the 18-gene T cell-inflamed gene expression profile (TcellinfGEP) or PD-L1 combined positive score (CPS) in esophageal cancer. Materials & methods: This analysis included heavily pretreated patients with advanced/metastatic esophageal/gastroesophageal junction adenocarcinoma or squamous cell carcinoma who received pembrolizumab in the single-arm, phase II study KEYNOTE-180. PD-L1 CPS was evaluated with PD-L1 IHC 22C3 pharmDx. Results: In patients with squamous cell carcinoma, trends toward enrichment for responders were observed for patients with PD-L1 CPS ≥10 tumors. In patients with adenocarcinoma, a trend was observed for TcellinfGEP but not for PD-L1. Conclusion: TcellinfGEP and PD-L1 CPS may enrich for responders to pembrolizumab in patients with esophageal cancer. Clinical trial registration: NCT02559687 (ClinicalTrials.gov).

Transcriptomic Determinants of Response to Pembrolizumab Monotherapy across Solid Tumor Types

PURPOSE

To explore relationships between biological gene expression signatures and pembrolizumab response.

EXPERIMENTAL DESIGN

RNA-sequencing data on baseline tumor tissue from 1,188 patients across seven tumor types treated with pembrolizumab monotherapy in nine clinical trials were used. A total of 11 prespecified gene expression signatures [18-gene T-cell-inflamed gene expression profile (TcellinfGEP), angiogenesis, hypoxia, glycolysis, proliferation, MYC, RAS, granulocytic myeloid-derived suppressor cell (gMDSC), monocytic myeloid-derived suppressor cell (mMDSC), stroma/epithelial-to-mesenchymal transition (EMT)/TGFβ, and WNT] were evaluated for their relationship to objective response rate (per RECIST, version 1.1). Logistic regression analysis of response for consensus signatures was adjusted for tumor type, Eastern Cooperative Oncology Group performance status, and TcellinfGEP, an approach equivalent to evaluating the association between response and the residuals of consensus signatures after detrending them for their relationship with the TcellinfGEP (previously identified as a determinant of pembrolizumab response) and tumor type. Testing of the 10 prespecified non-TcellinfGEP consensus signatures for negative association [except proliferation (hypothesized positive association)] with response was adjusted for multiplicity.

RESULTS

Covariance patterns of the 11 signatures (including TcellinfGEP) identified in Merck-Moffitt and The Cancer Genome Atlas datasets showed highly concordant coexpression patterns in the RNA-sequencing data from pembrolizumab trials. TcellinfGEP was positively associated with response; signatures for angiogenesis, mMDSC, and stroma/EMT/TGFβ were negatively associated with response to pembrolizumab monotherapy.

CONCLUSIONS

These findings suggest that features beyond IFNγ-related T-cell inflammation may be relevant to anti-programmed death 1 monotherapy response and may define other axes of tumor biology as candidates for pembrolizumab combinations. See related commentary by Cho et al., p. 1479.

Influence of tumor mutational burden, inflammatory gene expression profile, and PD-L1 expression on response to pembrolizumab in head and neck squamous cell carcinoma

Background

To characterize genomic determinants of response to pembrolizumab in recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) in the KEYNOTE-012 study.

Methods

Associations between biomarkers (tumor mutational burden (TMB), neoantigen load (NL), 18-gene T-cell-inflamed gene expression profile (Tcell_infGEP), and PD-L1 combined positive score (CPS)) and clinical outcomes with pembrolizumab were assessed in patients with R/M HNSCC (n=192). Tumor human papillomavirus (HPV) status was also evaluated with the use of p16 immunohistochemistry and whole exome sequencing (WES; HPV⁺, mapping >20 HPV reads) in pretreatment tumor samples (n=106).

Results

TMB, clonality-weighted TMB, and Tcell_infGEP were significantly associated with objective response (p=0.0276, p=0.0201, and p=0.006, respectively), and a positive trend was observed between NL and PD-L1 CPS and clinical response (p=0.0550 and p=0.0682, respectively). No correlation was observed between TMB and Tcell_infGEP (Spearman ρ=–0.026) or TMB and PD-L1 (Spearman ρ=0.009); a correlation was observed between Tcell_infGEP and PD-L1 (Spearman ρ=0.511). HPV status by WES and p16 immunohistochemistry showed concordance (84% ҡ=0.573) among patients whose HPV results were available using both methods.

Conclusions

TMB and inflammatory biomarkers (Tcell_infGEP and PD-L1) may represent distinct and complementary biomarkers predicting response to anti-programmed death 1 therapies in HNSCC; further study of these relationships in randomized clinical trials is needed.

Trial registration number

NCT01848834.

An assessment of animal welfare impacts in wild Norway rat (Rattus norvegicus) management

Norway rats (Rattus norvegicus) are considered one of the most significant vertebrate pests globally, because of their impacts on human and animal health. There are legal and moral obligations to minimise the impacts of wildlife management on animal welfare, yet there are few data on the relative welfare impacts of rat trapping and baiting methods used in the UK with which to inform management decisions. Two stakeholder workshops were facilitated to assess the relative welfare impacts of six lethal rat management methods using a welfare assessment model. Fifteen stakeholders including experts in wildlife management, rodent management, rodent biology, animal welfare science, and veterinary science and medicine, participated. The greatest welfare impacts were associated with three baiting methods, anticoagulants, cholecalciferol and non-toxic cellulose baits (severe to extreme impact for days), and with capture on a glue trap (extreme for hours) with concussive killing (mild to moderate for seconds to minutes); these methods should be considered last resorts from a welfare perspective. Lower impacts were associated with cage trapping (moderate to severe for hours) with concussive killing (moderate for minutes). The impact of snap trapping was highly variable (no impact to extreme for seconds to minutes). Snap traps should be regulated and tested to identify those that cause rapid unconsciousness; such traps might represent the most welfare-friendly option assessed for killing rats. Our results can be used to integrate consideration of rat welfare alongside other factors, including cost, efficacy, safety, non-target animal welfare and public acceptability when selecting management methods. We also highlight ways of reducing welfare impacts and areas where more data are needed.

Protein expression of programmed cell death ligand 1 and ligand 2 and their prognostic values in extensive-stage small cell lung cancer

e20593

Background: The receptor-ligand interaction between programmed cell death protein-1 (PD-1) and its ligands (PD-L1 and PD-L2) plays a critical role in tumor immune evasion and has become a therapeutic target in a number of cancer types, including extensive stage small cell lung cancer (ES-SCLC). While there are some published data on PD-L1 expression in ES-SCLC, the results vary with different laboratory assays or thresholds of positivity employed. Data on PD-L2 expression is very limited in ES-SCLC. The prognostic values of these biomarkers are not well understood. The current study aims to address this data gap. Methods: A retrospective cohort study of patients with ES-SCLC receiving usual care in the clinical setting in Denmark was conducted. Formalin-fixed paraffin embedded (FFPE) tumor tissue samples and data on patient characteristics and clinical outcomes were obtained for the patient population. Protein expression of PD-L1 and PD-L2 was determined by immunohistochemistry (IHC), and a combined positive score (CPS, the percentage of tumor cells and mononuclear inflammatory cells expressing the biomarker at any intensity out of the total number of tumor cells) of ≥1 was used to define biomarker positivity. Kaplan-Meier plots and Cox proportional hazard models were employed to assess the relationship between PD-L1 and PD-L2 protein expression and overall survival (OS). Results: Among the 80 patients with ES-SCLC included in this study, 25 and 29 were positive for PD-L1 and PD-L2, respectively (Table). A total of 68 patients had concordant expression status of PD-L1 and PD-L2 (21 as double positive and 47 as double negative). There was a significant association between PD-L1 positivity and longer OS, which persisted after adjustment for age and stage at SCLC diagnosis, performance score, prior exposure to chemotherapy, and lactate dehydrogenase levels (Table). Similar results were observed for PD-L2 (Table), and the data did not suggest any additional prognostic value of PD-L2 expression independent of PD-L1 expression. Conclusions: PD-L1 and PD-L2 positivity was both observed, and highly correlated with each other, in approximately one third of the ES-SCLC tumor samples tested. Patients with PD-L1 or PD-L2 positive tumors have significantly longer OS than those with negative tumors in this study, independent of other known prognostic factors.[Table: see text]

Abstract LB-397: Pembrolizumab plus pemetrexed and platinum vs placebo plus pemetrexed and platinum as first-line therapy for metastatic nonsquamous NSCLC: analysis of KEYNOTE-189 by STK11 and KEAP1 status

Background: Mutations in the tumor suppressor genes STK11 (also known as LKB1) and KEAP1 have been associated with poorer clinical outcomes in patients (pts) with NSCLC. In an exploratory analysis, we assessed the prevalence of STK11 and KEAP1 mutations and their association with efficacy in KEYNOTE-189 (NCT02578680). Methods: STK11 and KEAP1 status and tumor mutational burden (TMB) were assessed by whole-exome sequencing (WES) in pts who had available tumor and matched-normal tissue. PD-L1 was assessed by the PD-L1 IHC 22C3 pharmDx assay. The association of STK11 and KEAP1 status with efficacy and their correlation with TMB and PD-L1 expression distributions were evaluated descriptively. Results: WES data from both tumor and normal DNA were evaluable for 289 (47%) of 616 pts, of whom 54 (19%) had an STK11 mutation and 68 (24%) had a KEAP1 mutation; 29 (10%) had both STK11 and KEAP1 mutations. PD-L1 TPS tended to be lower in pts with vs without STK11 mutation (median [IQR] 0% [0-16] vs 15% [0-75]), whereas TMB score tended to be higher in pts with mutation (209 [132-265] vs 146 [89-264]). Similar patterns were seen for pts with vs without KEAP1 mutation (PD-L1 TPS: 1% [0-13] vs 20% [0-75]; TMB: 173 [124-267] vs 147 [89-263]). Although ORR of pembrolizumab plus chemotherapy was lower and PFS and OS shorter in pts with vs without STK11 and KEAP1 mutation, pembrolizumab plus chemotherapy was associated with numerically better outcomes than placebo plus chemotherapy regardless of mutation status (Table). 95% CIs were wide given the modest mutation frequency and the 2:1 randomization in favor of pembrolizumab plus chemotherapy. Conclusions: Data from this exploratory analysis support use of pembrolizumab plus pemetrexed and platinum as standard first-line therapy for pts with metastatic nonsquamous NSCLC regardless of STK11 or KEAP1 status.

STK11KEAP1With MutationWithout MutationWith MutationWithout MutationPembro + ChemoPlacebo + ChemoPembro + ChemoPlacebo + ChemoPembro + ChemoPlacebo + ChemoPembro + ChemoPlacebo + Chemo(n = 36)(n = 18)(n = 168)(n = 67)(n = 45)(n = 23)(n = 159)(n = 62)ORR, % (95% CI)31 (16-48)17 (4-41)49 (41-57)16 (8-27)36 (22-51)17 (5-39)48 (40-56)16 (8-28)PFS, median, mo (95% CI)6 (4-9)5 (5-9)10 (8-14)5 (5-5)5 (4-11)5 (5-9)10 (8-14)5 (5-5)PFS, HR (95% CI)0.81 (0.44-1.47)0.38 (0.27-0.52)0.65 (0.38-1.12)0.38 (0.28-0.53)OS, median, mo (95% CI)17 (5-NR)8 (7-NR)23 (20-NR)12 (8-25)13 (7-NR)9 (7-NR)24 (20-NR)12 (8-NR)OS, HR (95% CI)0.75 (0.37-1.50)0.59 (0.41-0.85)0.81 (0.44-1.49)0.57 (0.39-0.84)

Citation Format: Shirish M. Gadgeel, Delvys Rodriguez-Abreu, Enriqueta Felip, Emilio Esteban, Giovanna Speranza, Martin Reck, Rina Hui, Michael Boyer, Edward B. Garon, Hidehito Horinouchi, Razvan Cristescu, Deepti Aurora-Garg, Andrey Loboda, Jared Lunceford, Julie Kobie, Mark Ayers, Bilal Piperdi, M. Catherine Pietanza, Marina C. Garassino. Pembrolizumab plus pemetrexed and platinum vs placebo plus pemetrexed and platinum as first-line therapy for metastatic nonsquamous NSCLC: analysis of KEYNOTE-189 by STK11 and KEAP1 status [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-397.

Evaluation of blood TMB (bTMB) in KEYNOTE-189: Pembrolizumab (pembro) plus chemotherapy (chemo) with pemetrexed and platinum versus placebo plus chemo as first-line therapy for metastatic nonsquamous NSCLC

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Background: In a previous analysis of KEYNOTE-189 (NCT02578680), we showed that tissue TMB (tTMB) assessed by whole-exome sequencing was not significantly associated with efficacy in either arm and that pembro + chemo improved outcomes vs placebo + chemo in both the tTMB ≥175 and tTMB < 175 mut/exome subgroups. Here, we explored the association of bTMB with efficacy in KEYNOTE-189. Methods: 616 patients (pts) were randomized 2:1 to pembro + chemo or placebo + chemo. bTMB was assessed in cfDNA using the Guardant Health Omni assay. Association of bTMB (continuous square root transformed) with outcomes in each arm was assessed using Cox proportional hazards models (OS, PFS) and logistic regression (ORR) adjusted for ECOG PS; statistical significance was determined at the 0.05 level without multiplicity adjustment. The clinical utility of bTMB on outcomes was assessed using the cutoff that most closely approximated the 175 mut/exome tTMB cutoff as determined by AUROC analysis. Data cutoff was 21 Sep 2018. Results: 235 (38%) treated pts had evaluable tTMB and bTMB: 160 in the pembro + chemo arm and 75 in the placebo + chemo arm. bTMB as a continuous variable was not significantly associated with OS or ORR for pembro + chemo (one-sided P = .229 and .051) or placebo + chemo (two-sided P = .641 and .069); bTMB was significantly associated with PFS in the pembro + chemo arm (one-sided P = .015) but not the placebo + chemo arm (two-sided P = .058). bTMB and tTMB scores were moderately correlated (r = .61). The bTMB cutoff that most closely approximated tTMB 175 mut/exome was 15 mut/Mb (AUROC 0.81, 95% CI 0.75-0.86). 178 (76%) pts had concordant bTMB and tTMB results—101 low and 77 high by both—whereas 57 (24%) had discordant results—21 high bTMB but low tTMB, 36 low bTMB but high tTMB. Pembro + chemo improved OS, PFS, and ORR vs placebo + chemo for bTMB ≥15 and < 15 mut/exome (Table). Conclusions: Similar to previous findings based on tTMB, bTMB has limited clinical utility in the setting of pembro with pemetrexed and platinum given as first-line therapy for metastatic nonsquamous NSCLC. Clinical trial information: NCT02578680 . [Table: see text]

Abstract 2483: An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples

Purpose We built an integrated analytic pipeline to robustly and comprehensively profile molecular features of pembrolizumab-treated tumors using whole exome sequencing (WES) data from clinical trials across different indications.

Experimental design We implemented a computational framework for analysis of WES data generated by different sequencing vendors for 1467 samples from 8 major tumor types. Reads were first processed by BWA-MEM, Picard, and GATK (v2) to generate analysis-ready BAM files. Quality controls (QC) before downstream analysis included Y/X reads ratio for matched normal sample as patient sex prediction and tumor/normal concordance and contamination estimation by Conpair. Key molecular features were evaluated, including tumor mutation burden (TMB) by MuTect (v1) and VEP; HLA-I typing by OptiType; neoantigen burden by NetMHC (v3.4); mutation signature by deconstructSigs; allele-specific copy number by VarScan2 and Sequenza; clonality by PyClone; presence of oncogenic viruses (eg, EBV, HBV, HPV); and LOH score indicating homologous recombination deficiency (HRD-LOH).

Results Concordance rate between predicted and clinical sex was 1446/1464 (98.8%), and 1420/1467 (96.8%) samples passed tumor-normal alignment QC. Highest TMB (median [range]) was detected in melanoma (245 [2-6246]) and urothelial carcinoma (UC) (124 [4-1579]), with lowest TMB in metastatic castration-resistant prostate cancer (52 [1-6143]) and ovarian cancer (OvCa) (49.5 [8-272]). The correlation of median TMB across 7 cancer types in our data and TCGA was Spearman R = 0.957. Within indications, there was no difference in TMB distribution for sequencing data originating from different sequencing vendors and TCGA data, which demonstrated concordance across data sets and robust TMB calling by our integrated pipeline. Neoantigen burden strongly correlated with TMB (N = 1420; Spearman R = 0.890). HPV was detected in 20/129 (15.5%) head and neck squamous cell carcinomas (HNSCC) and 4/6 (66.7%) anal cancers; EBV was detected in 8/129 (6.2%) HNSCC and 18/318 (5.7%) gastric cancers (GC). The dominant mutation signatures by disease included APOBEC for UC (135/236) and HNSCC (22/122), alcohol for HCC (19/35), HRD for OvCa (12/64) and triple-negative breast cancer (51/175), UV exposure for melanoma (145/176), and dMMR for GC (84/287) and CRPC (16/155). Samples with deleterious BRCA mutations showed significantly higher HRD-LOH score (N = 1420; AUROC = 0.61 [95% CI, 0.53-0.69]) and HRD mutational signature (N = 1316; DOR = 6.4 [95% CI, 3.7-11.1]).

Conclusion We assembled heterogeneous computational modules into an integrated pipeline to reliably profile diverse molecular features from WES data of nearly 1500 clinical samples across different tumor types. These data serve as a foundation for translational research efforts supporting pembrolizumab development.

Citation Format: Xiaoqiao Liu, Xinwei Sher, Hongchao Lu, Jun Zhuang, Weilong Zhao, Andrew Albright, Cinthia Umemoto, Christen Wudarski, Maureen Lane, Mark Ayers, Andrea L. Webber, Sandra C. Souza, Ping Qiu, Diane Levitan, Jennifer Cho, Deepti Aurora-Garg, Matthew Marton, Alexandra Snyder, Michael Morrissey, Andrey Loboda, Ronghua Chen, Razvan Cristescu. An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2483.

T-Cell-Inflamed Gene-Expression Profile, Programmed Death Ligand 1 Expression, and Tumor Mutational Burden Predict Efficacy in Patients Treated With Pembrolizumab Across 20 Cancers: KEYNOTE-028

PURPOSE

Biomarkers that can predict response to anti-programmed cell death 1 (PD-1) therapy across multiple tumor types include a T-cell-inflamed gene-expression profile (GEP), programmed death ligand 1 (PD-L1) expression, and tumor mutational burden (TMB). Associations between these biomarkers and the clinical efficacy of pembrolizumab were evaluated in a clinical trial that encompassed 20 cohorts of patients with advanced solid tumors.

METHODS

KEYNOTE-028 ( ClinicalTrials.gov identifier: NCT02054806) is a nonrandomized, phase Ib trial that enrolled 475 patients with PD-L1-positive advanced solid tumors who were treated with pembrolizumab 10 mg/kg every 2 weeks for 2 years or until confirmed disease progression or unacceptable toxicity occurred. The primary end point was objective response rate (ORR; by RECIST v1.1, investigator review). Secondary end points included safety, progression-free survival (PFS), and overall survival (OS). Relationships between T-cell-inflamed GEP, PD-L1 expression, and TMB and antitumor activity were exploratory end points.

RESULTS

ORRs (with 95% CIs) ranged from 0% (0.0% to 14.2%) in pancreatic cancer to 33% (15.6% to 55.3%) in small-cell lung cancer. Across cohorts, median (95% CI) PFS ranged from 1.7 months (1.5 to 2.9 months) to 6.8 months (1.9 to 14.1 months) in pancreatic and thyroid cancers, respectively, and median OS from 3.9 months (2.8 to 5.5 months) to 21.1 months (9.1 to 22.4 months) in vulvar and carcinoid tumors, respectively. Higher response rates and longer PFS were demonstrated in tumors with higher T-cell-inflamed GEP, PD-L1 expression, and/or TMB. Correlations of TMB with GEP and PD-L1 were low. Response patterns indicate that patients with tumors that had high levels of both TMB and inflammatory markers (GEP or PD-L1) represent a population with the highest likelihood of response. Safety was similar and consistent with prior pembrolizumab reports.

CONCLUSION

A T-cell--inflamed GEP, PD-L1 expression, and TMB predicted response to pembrolizumab in multiple tumor types. These biomarkers (alone/in combination) may help identify patients who have a higher likelihood of response to anti-PD-1 therapies across a broad spectrum of cancers.

T-Cell-Inflamed Gene-Expression Profile, Programmed Death Ligand 1 Expression, and Tumor Mutational Burden Predict Efficacy in Patients Treated With Pembrolizumab Across 20 Cancers: KEYNOTE-028

PURPOSE

Biomarkers that can predict response to anti-programmed cell death 1 (PD-1) therapy across multiple tumor types include a T-cell-inflamed gene-expression profile (GEP), programmed death ligand 1 (PD-L1) expression, and tumor mutational burden (TMB). Associations between these biomarkers and the clinical efficacy of pembrolizumab were evaluated in a clinical trial that encompassed 20 cohorts of patients with advanced solid tumors.

METHODS

KEYNOTE-028 ( ClinicalTrials.gov identifier: NCT02054806) is a nonrandomized, phase Ib trial that enrolled 475 patients with PD-L1-positive advanced solid tumors who were treated with pembrolizumab 10 mg/kg every 2 weeks for 2 years or until confirmed disease progression or unacceptable toxicity occurred. The primary end point was objective response rate (ORR; by RECIST v1.1, investigator review). Secondary end points included safety, progression-free survival (PFS), and overall survival (OS). Relationships between T-cell-inflamed GEP, PD-L1 expression, and TMB and antitumor activity were exploratory end points.

RESULTS

ORRs (with 95% CIs) ranged from 0% (0.0% to 14.2%) in pancreatic cancer to 33% (15.6% to 55.3%) in small-cell lung cancer. Across cohorts, median (95% CI) PFS ranged from 1.7 months (1.5 to 2.9 months) to 6.8 months (1.9 to 14.1 months) in pancreatic and thyroid cancers, respectively, and median OS from 3.9 months (2.8 to 5.5 months) to 21.1 months (9.1 to 22.4 months) in vulvar and carcinoid tumors, respectively. Higher response rates and longer PFS were demonstrated in tumors with higher T-cell-inflamed GEP, PD-L1 expression, and/or TMB. Correlations of TMB with GEP and PD-L1 were low. Response patterns indicate that patients with tumors that had high levels of both TMB and inflammatory markers (GEP or PD-L1) represent a population with the highest likelihood of response. Safety was similar and consistent with prior pembrolizumab reports.

CONCLUSION

A T-cell--inflamed GEP, PD-L1 expression, and TMB predicted response to pembrolizumab in multiple tumor types. These biomarkers (alone/in combination) may help identify patients who have a higher likelihood of response to anti-PD-1 therapies across a broad spectrum of cancers.

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy

Programmed cell death protein-1 (PD-1) and programmed cell death ligand-1 (PD-L1) checkpoint blockade immunotherapy elicits durable antitumor effects in multiple cancers, yet not all patients respond. We report the evaluation of >300 patient samples across 22 tumor types from four KEYNOTE clinical trials. Tumor mutational burden (TMB) and a T cell-inflamed gene expression profile (GEP) exhibited joint predictive utility in identifying responders and nonresponders to the PD-1 antibody pembrolizumab. TMB and GEP were independently predictive of response and demonstrated low correlation, suggesting that they capture distinct features of neoantigenicity and T cell activation. Analysis of The Cancer Genome Atlas database showed TMB and GEP to have a low correlation, and analysis by joint stratification revealed biomarker-defined patterns of targetable-resistance biology. These biomarkers may have utility in clinical trial design by guiding rational selection of anti-PD-1 monotherapy and combination immunotherapy regimens.

Molecular Profiling of Cohorts of Tumor Samples to Guide Clinical Development of Pembrolizumab as Monotherapy

PURPOSE

Molecular profiling of large databases of human tumor gene expression profiles offers novel opportunities for informing decisions in clinical development programs.

EXPERIMENTAL DESIGN

Gene expression profile of programmed death ligand 1 (PD-L1) was explored in a dataset of 16,000 samples, including approximately 4,000 metastatic tumors, across >25 tumor types prevalent in the United States, looking for new indications for the programmed death 1 (PD-1) inhibitor pembrolizumab. PD-L1 expression was highly concordant with several genomic signatures indicative of immune-inflamed tumor microenvironment. Prevalence of activated immune-inflamed tumors across all tumor types was explored and used to rank tumor types for potential response to pembrolizumab monotherapy.

RESULTS

The analysis yielded 3 tiers of indications in which high levels of PD-L1 and immune-inflamed signatures were found in up to 40% to 60%, 20% to 40%, and 0% to 20% of tumors. Tier 1 contained novel indications known at the time of analysis to be responsive to PD-1 checkpoint blockade in the clinic (such as melanoma and non-small cell lung cancer), as well as indications not studied in the clinic previously, including microsatellite instability-high colorectal, head and neck, bladder, and triple-negative breast cancers. Complementary analysis of an Asian/Pacific cancer dataset (gastric cancer) revealed high prevalence of immune-inflamed tumors in gastric cancer. These data contributed to prioritization of these indications for clinical development of pembrolizumab as monotherapy.

CONCLUSIONS

Data highlight the value of molecular profiling in identifying populations with high unmet needs with potentially favorable response characteristics and accelerating development of novel therapies for these patients.See related commentary by Mansfield and Jen, p. 1443.

Genomic biomarkers in relation to PD-1 checkpoint blockade response

25

Background: Somatic tumor mutational burden (TMB) and a T-cell inflamed gene expression profile (GEP) predict response to anti-PD-1/PD-L1 immunotherapies in multiple tumor types. We assessed the potential for GEP and TMB to jointly predict clinical response to pembrolizumab and to identify distinct, targetable patterns of biology that may modulate response/resistance. Methods: To assess the individual and joint clinical utility of TMB and GEP in a pan-tumor context, pembrolizumab-treated patients with advanced solid tumors and melanoma were stratified as 4 biomarker-defined clinical response groups (GEP low/TMB low, GEP low/TMB high, GEP high/TMB low, GEP high/TMB high; N > 300) based on cutoffs for TMB (ROC Youden Index associated) and GEP (selected via analysis of pan cancer data). TMB and GEP were used to guide transcriptome and exome analysis of tumors in 2 large databases (Moffitt, n = 2944; TCGA, n = 6978). Results: TMB and GEP had a low, but significant, correlation in these clinical datasets. ORR was highest in GEP high/TMB high (37-57%), modest in GEP high/TMB low (12-35%) and GEP low/TMB high (11-42%), and lowest in GEP low/TMB low (0-9%) groups. Within the Moffitt and TCGA databases, GEP and TMB again had a low correlation, demonstrating their potential joint utility for stratifying additional transcriptomic and genomic features of these datasets. Specific gene modules showed strong positive or negative and highly statistically significant associations with TMB, GEP or both in each dataset, and patterns were consistent between datasets. In particular, gene set enrichment analysis identified proliferative, stromal and vascular biology corresponding to specific TMB-defined subgroups within GEP high tumors. In TMB-high tumors, indication-dependent somatic DNA alterations in key cancer driver genes showed a strong negative association ( P< 1e-5) with GEP. Conclusions: This analysis shows that TMB and T-cell inflamed GEP score can stratify human cancers into groups with different response rates to pembrolizumab monotherapy, and identify patterns of underlying, targetable biology related to these groups. This approach may provide a precision medicine framework for evaluating anti-PD-1/L1-based combination therapy regimens. Clinical trial information: NCT01848834; NCT02054806; NCT01295827; NCT01866319.

IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade

Programmed death-1-directed (PD-1-directed) immune checkpoint blockade results in durable antitumor activity in many advanced malignancies. Recent studies suggest that IFN-γ is a critical driver of programmed death ligand-1 (PD-L1) expression in cancer and host cells, and baseline intratumoral T cell infiltration may improve response likelihood to anti-PD-1 therapies, including pembrolizumab. However, whether quantifying T cell-inflamed microenvironment is a useful pan-tumor determinant of PD-1-directed therapy response has not been rigorously evaluated. Here, we analyzed gene expression profiles (GEPs) using RNA from baseline tumor samples of pembrolizumab-treated patients. We identified immune-related signatures correlating with clinical benefit using a learn-and-confirm paradigm based on data from different clinical studies of pembrolizumab, starting with a small pilot of 19 melanoma patients and eventually defining a pan-tumor T cell-inflamed GEP in 220 patients with 9 cancers. Predictive value was independently confirmed and compared with that of PD-L1 immunohistochemistry in 96 patients with head and neck squamous cell carcinoma. The T cell-inflamed GEP contained IFN-γ-responsive genes related to antigen presentation, chemokine expression, cytotoxic activity, and adaptive immune resistance, and these features were necessary, but not always sufficient, for clinical benefit. The T cell-inflamed GEP has been developed into a clinical-grade assay that is currently being evaluated in ongoing pembrolizumab trials.

IFN-γ-related mRNA profile predicts clinical response to PD-1 blockade

Programmed death-1-directed (PD-1-directed) immune checkpoint blockade results in durable antitumor activity in many advanced malignancies. Recent studies suggest that IFN-γ is a critical driver of programmed death ligand-1 (PD-L1) expression in cancer and host cells, and baseline intratumoral T cell infiltration may improve response likelihood to anti-PD-1 therapies, including pembrolizumab. However, whether quantifying T cell-inflamed microenvironment is a useful pan-tumor determinant of PD-1-directed therapy response has not been rigorously evaluated. Here, we analyzed gene expression profiles (GEPs) using RNA from baseline tumor samples of pembrolizumab-treated patients. We identified immune-related signatures correlating with clinical benefit using a learn-and-confirm paradigm based on data from different clinical studies of pembrolizumab, starting with a small pilot of 19 melanoma patients and eventually defining a pan-tumor T cell-inflamed GEP in 220 patients with 9 cancers. Predictive value was independently confirmed and compared with that of PD-L1 immunohistochemistry in 96 patients with head and neck squamous cell carcinoma. The T cell-inflamed GEP contained IFN-γ-responsive genes related to antigen presentation, chemokine expression, cytotoxic activity, and adaptive immune resistance, and these features were necessary, but not always sufficient, for clinical benefit. The T cell-inflamed GEP has been developed into a clinical-grade assay that is currently being evaluated in ongoing pembrolizumab trials.

Genomic determinants of response to pembrolizumab in head and neck squamous cell carcinoma (HNSCC)

6009

Background: Somatic mutational load (ML) is associated with response to anti CTLA-4 and PD-1/-L1 immunotherapies in select tumors, due to formation of neoepitopes not subject to central immune tolerance. Neoepitopes specific to HPV, EBV virus infection are also present in some HNSCC. An IFNγ gene expression profile (GEP) characteristic of tumor inflammation is also related to response to anti PD-1/-L1 therapy. This study evaluated relationships between ML and clinical outcome and independent predictive values of ML and GEP in patients with HNSCC treated with pembrolizumab. Methods: Whole exome sequencing (WES) and GEP were assessed in FFPE tumor specimens of patients with HNSCC (KEYNOTE 012; subsets of B1 [PD-L1+, n = 34] and B2 [PD-L1+/‒, n = 73] cohorts). ML, neoantigen load (NL), HPV/EBV status and clonality were assessed by standard WES analytical methods. GEP score is a weighted sum of normalized expression values of 18 genes. Statistical testing of ML and response, and ML and GEP relationship by HPV/EBV status was prespecified. Results: There were 73 patients identified as HPV‒ and EBV‒ (n = 25 in B1; n = 48 in B2). In HPV‒ and EBV‒ patients in B1 and B2 cohorts, respectively, associations between ML and objective response (OR) (P = 0.029 and 0.055; AUROC 0.89 and 0.63), and GEP and OR (P = 0.064 and 0.01; AUROC 0.82 and 0.74) were statistically significant. In combined cohorts of HPV‒ and EBV‒ patients, ML and GEP were significantly associated with OR (P = 0.009 and 0.002; AUROC 0.70 and 0.76, respectively). ML and GEP were only weakly correlated (r = 0.173). In a joint model, ML was significantly associated with response (p = 0.020) after adjusting for GEP (also significant, p = 0.006). NL and clonality weighted ML were also significantly associated with response (P = 0.026 and 0.006, respectively). In HPV+ or EBV+subjects, OR association was not significant for ML, possibly due to a dominance of viral vs somatic neoepitopes; GEP was significant, likely due to tumor inflammation. Conclusions: ML and GEP are independently predictive of response to pembrolizumab in HPV‒/EBV‒ patients with HNSCC; GEP was predictive regardless of viral status. ML and GEP may have utility in characterizing responses to anti PD-1 therapies and novel cancer regimens in HNSCC. Clinical trial information: NCT01848834.

Mutational load (ML) and T-cell-inflamed microenvironment as predictors of response to pembrolizumab

1

Background: ML is associated with response to anti CTLA-4 and PD-1/L1 immunotherapies in some cancers, likely due to increased tumor antigenicity via generation of neoepitopes not subject to central immune tolerance. An IFNγ centric gene expression profile (GEP), characteristic of a T cell inflamed microenvironment, is also related to response to PD-1/PD-L1 therapies. The association between ML and outcome, and independent predictive values of ML and GEP in pembrolizumab treated patients across 21 tumor types were assessed. Methods: Whole exome and RNA sequencing were performed on FFPE specimens pooled from 2 multicohort advanced solid tumor trials (KEYNOTE 012 [n = 39] and 028 [n = 80]). The previously defined GEP score is a weighted sum of normalized expression values for 18 genes. ML and neoantigen analysis tools included GATK, MuTect and NetMHC. Statistical testing was adjusted for multiple testing. ML and GEP association was also explored in Moffitt and TCGA datasets. Results: ML and neoantigen load were significantly associated with objective response (OR) (AUROC = 0.76 and 0.78; p = 0.0036 and 0.0083, respectively). Median numbers of mutations were 180 in responders and 61 in nonresponders. The overall response rate (ORR) in all patients was 15%. At a ML cutoff of 102 (based on ROC Curve YoudenIndex), the ORR was 32.3% (prevalence 31.0%; NPV 92.8%). GEP was also significantly associated with OR (AUROC = 0.76; p = 0.0071). ML and GEP were modestly correlated (r = 0.28), consistent with associations between ML and GEP in Moffitt (r = 0.11) and TCGA databases (r = 0.29). When jointly modeled, ML was significantly associated with response (p = 0.0078) after adjusting for GEP (also significant; p = 0.0251). Data from additional patients will also be presented. Conclusions: These data show that ML and GEP are independently predictive biomarkers of response to pembrolizumab in multiple tumor types, suggesting that tumor antigenicity and T cell infiltration may provide complementary information for expected pembrolizumab activity. As measures of distinct, yet common features of a PD-1 checkpoint blockade responsive tumor, ML and GEP may have utility in characterizing responses to anti PD-1 and other cancer immunotherapies. Clinical trial information: NCT01848834; NCT02054806.

Dalotuzumab in chemorefractory KRAS exon 2 mutant colorectal cancer: Results from a randomised phase II/III trial

Limited data are available on the efficacy of anti-IGF-1R agents in KRAS mutant colorectal cancer (CRC). We analysed the outcome of 69 chemorefractory, KRAS exon 2 mutant CRC patients who were enrolled in a double-blind, randomised, phase II/III study of irinotecan and cetuximab plus dalotuzumab 10 mg/kg once weekly (arm A), dalotuzumab 7.5 mg/kg every second week (arm B) or placebo (arm C). Objective response rate (5.6% vs. 3.1% vs. 4.8%), median progression-free survival (2.7 vs. 2.6 vs. 1.4 months) and overall survival (7.8 vs. 10.3 vs. 7.8 months) were not statistically significantly different between treatment groups. Most common grade ≥3 treatment-related toxicities included neutropenia, diarrhoea, hyperglycaemia, fatigue and dermatitis acneiform. Expression of IGF-1R, IGF-1, IGF-2 and EREG by quantitative real-time polymerase chain reaction was assessed in 351 patients from the same study with available data on KRAS exon 2 mutational status. Median cycle threshold values for all biomarkers were significantly lower (i.e., higher expression, p < 0.05) among patients with KRAS wild-type compared to those with KRAS exon 2 mutant tumours. No significant changes were found according to location of the primary tumour with only a trend towards lower expression of IGF-1 in colon compared to rectal cancers (p = 0.06). Albeit limited by the small sample size, this study does not appear to support a potential role for anti-IGF-1R agents in KRAS exon 2 mutant CRC. Data on IGF-1R, IGF-1 and IGF-2 expression here reported may be useful for patient stratification in future trials with inhibitors of the IGF pathway.

A phase II study of clinical activity of SCH 717454 (robatumumab) in patients with relapsed osteosarcoma and Ewing sarcoma

BACKGROUND

Robatumumab (19D12; MK-7454 otherwise known as SCH717454) is a fully human antibody that binds to and inhibits insulin-like growth factor receptor-1 (IGF-1R). This multiinstitutional study (P04720) determined the safety and clinical efficacy of robatumumab in three separate patient groups with resectable osteosarcoma metastases (Group 1), unresectable osteosarcoma metastases (Group 2), and Ewing sarcoma metastases (Group 3).

PROCEDURE

Robatumumab infusions were administered every 2 weeks and were well tolerated with minimal toxicity. Centrally reviewed response data were available for 144 patients.

RESULTS

Low disease burden was important for osteosarcoma response: three of 31 patients had complete response or partial response (PR) by Response Evaluation Criteria in Solid Tumors (RECIST) in resectable patients (Group 1) versus zero of 29 in unresectable patients (Group 2); median overall survival was 20 months in Group 1 versus 8.2 months in Group 2. In centrally reviewed patients with Ewing sarcoma with PET-CT data (N = 84/115), there were six PR, 23 stable disease, and 55 progression of disease by RECIST at 2 months. Patients with Ewing sarcoma had a median overall survival of 6.9 months. However, responding patients with Ewing sarcoma were allowed to continue on treatment after study closure. A minority of patients with metastatic Ewing sarcoma showed clinical responses and have remained healthy after receiving 25-115 doses of robatumumab with remissions of >4 years duration (N = 6).

CONCLUSIONS

These findings show that although the IGF-1R remains an attractive treatment target, additional research is needed to identify responders and/or means to achieve durable remissions in order to successfully exploit IGF-1R signal blockade in Ewing sarcoma (clinicaltrials.gov: NCT00617890).

A Randomized Phase II/III Study of Dalotuzumab in Combination With Cetuximab and Irinotecan in Chemorefractory, KRAS Wild-Type, Metastatic Colorectal Cancer

BACKGROUND

Insulin-like growth factor type 1 receptor (IGF-1R) mediates resistance to epidermal growth factor receptor (EGFR) inhibition and may represent a therapeutic target. We conducted a multicenter, randomized, double blind, phase II/III trial of dalotuzumab, an anti-IGF-1R monoclonal antibody, with standard therapy in chemo-refractory, KRAS wild-type metastatic colorectal cancer.

METHODS

Eligible patients were randomly assigned to dalotuzumab 10mg/kg weekly (arm A), dalotuzumab 7.5mg/kg every alternate week (arm B), or placebo (arm C) in combination with cetuximab and irinotecan. Primary endpoints were progression-free survival (PFS) and overall survival (OS). Secondary endpoints included exploratory biomarker analyses. All statistical tests were two-sided.

RESULTS

The trial was prematurely discontinued for futility after 344 eligible KRAS wild-type patients were included in the primary efficacy population (arm A = 116, arm B = 117, arm C = 111). Median PFS was 3.9 months in arm A (hazard ratio [HR] = 1.33, 95% confidence interval [CI] = 0.98 to 1.83, P = .07) and 5.4 months in arm B (HR = 1.13, 95% CI = 0.83 to 1.55, P = .44) compared with 5.6 months in arm C. Median OS was 10.8 months in arm A (HR = 1.41, 95% CI = 0.99 to 2.00, P = .06) and 11.6 months in arm B (HR = 1.26, 95% CI = 0.89 to 1.79, P = .18) compared with 14.0 months in arm C. Grade 3 or higher asthenia and hyperglycaemia occurred more frequently with dalotuzumab compared with placebo. In exploratory biomarker analyses, patients with high IGF-1 mRNA tumors in arm A had numerically better PFS (5.6 vs 3.6 months, HR = 0.59, 95% CI = 0.28 to 1.23, P = .16) and OS (17.9 vs 9.4 months, HR = 0.67, 95% CI = 0.31 to 1.45, P = .31) compared with those with high IGF-1 mRNA tumors in arm C. In contrast, in arm C high IGF-1 mRNA expression predicted lower response rate (17.6% vs 37.3%, P = .04), shorter PFS (3.6 vs 6.6 months, HR = 2.15, 95% CI = 1.15 to 4.02, P = .02), and shorter OS (9.4 vs 15.5 months, HR = 2.42, 95% CI = 1.21 to 4.82, P = .01).

CONCLUSIONS

Adding dalotuzumab to irinotecan and cetuximab was feasible but did not improve survival outcome. IGF-1R ligands are promising biomarkers for differential response to anti-EGFR and anti-IGF-1R therapies.

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

Gastric cancer, a leading cause of cancer-related deaths, is a heterogeneous disease. We aim to establish clinically relevant molecular subtypes that would encompass this heterogeneity and provide useful clinical information. We use gene expression data to describe four molecular subtypes linked to distinct patterns of molecular alterations, disease progression and prognosis. The mesenchymal-like type includes diffuse-subtype tumors with the worst prognosis, the tendency to occur at an earlier age and the highest recurrence frequency (63%) of the four subtypes. Microsatellite-unstable tumors are hyper-mutated intestinal-subtype tumors occurring in the antrum; these have the best overall prognosis and the lowest frequency of recurrence (22%) of the four subtypes. The tumor protein 53 (TP53)-active and TP53-inactive types include patients with intermediate prognosis and recurrence rates (with respect to the other two subtypes), with the TP53-active group showing better prognosis. We describe key molecular alterations in each of the four subtypes using targeted sequencing and genome-wide copy number microarrays. We validate these subtypes in independent cohorts in order to provide a consistent and unified framework for further clinical and preclinical translational research.

Breast cancer biomarkers and molecular medicine: part II

In this second part of the two-part review of breast cancer biomarkers and molecular medicine, the first section will consider additional breast cancer prognostic factors, including oncogenes, tumor suppressor genes, cell adhesion molecules, invasion-associated proteins and proteases, hormone receptor proteins, drug resistance proteins, apoptosis regulators, transcription factors, telomerase, DNA repair and methylation and transcriptional profiling using high-density genomic microarrays. The second section will consider the prediction of therapy response using the techniques of pharmacogenetics and pharmacogenomics.

Abstract 699: Optimized dosing strategies resulting in prolonged pathway inhibition enhance dinaciclib anti-tumor activity in preclinical xenograft models

Dinaciclib is a novel CDK1, 2, 5, and 9 inhibitor currently in clinical development for CLL. Preclinical studies indicate that dinaciclib may have activity in a wide variety of indications including hematologic malignancies and solid tumors. Clinically, dinaciclib is administered by 2 hour intravenous (iv) infusion and achieves plasma concentrations above 100nM for ∼6 hours; a concentration and duration of treatment which in vitro provides complete target engagement and induces apoptosis. Pre-clinically, dinaciclib is administered by intraperitoneal (ip) bolus injections and achieves plasma concentrations above 100nM for less than 2 hours. To determine whether prolonged plasma concentrations would enhance dinaciclib activity, we administered dinaciclib to COLO-320DM tumor bearing mice either as a 40 mg/kg single dose, or as two doses of 20 mg/kg separated by 2 hours. This 20-20 split dosing resulted in prolonged target engagement, phospho-RNA-Polymerase-2 reduction, decreased MCL-1, and increased apoptosis relative to the 40mg/kg single dose. Comparing the in vivo anti-tumor activity of dinaciclib dosed at 40 mg/kg ip every 4 days (q4d) vs. 20 mg/kg bid separated by 2 hours q4d demonstrated that the 20-20 split dose increased the anti-tumor activity of dinaciclib (25% Tumor Growth Inhibition (TGI) versus 66% TGI). Dinaciclib single vs. split dosing was further evaluated in 8 lung cancer xenograft models, 5 of which were insensitive to dinaciclib single dose (TGI &gt;50%) and 3 of which were sensitive. 20-20 split dosing resulted in increased anti-tumor activity in all models tested. Split dosing resulted in &lt;50% TGI in 4 of 5 insensitive models. Split dosing also increased anti-tumor activities in all 3 sensitive models tested resulting in stasis in 2 models, and sustained complete regressions in one lung cancer xenograft model. Body weight measurements revealed that split dosing increased body weight loss indicating that prolonged pathway inhibition can affect both anti-tumor activity and tolerability. Taken together, these data suggest that dinaciclib dosing paradigms that prolong pathway inhibition enhanced anti-tumor activity in pre-clinical xenograft models.

Citation Format: Alwin Schuller, Robert Booher, Louise Cadzow, Minilik Angagaw, Lauren Harmonay, Xianlu Qu, Nathan Miselis, Vincenzo Pucci, Mark Ayers, Thorsten Graef, Ellie Im, Rebecca Blanchard, Brian Long, Leigh Zawel, peter strack. Optimized dosing strategies resulting in prolonged pathway inhibition enhance dinaciclib anti-tumor activity in preclinical xenograft models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 699. doi:10.1158/1538-7445.AM2013-699

Abstract 698: MCL1 dependent cells are sensitive to the CDK inhibitor Dinaciclib

Dinaciclib is a potent inhibitor of cyclin dependent kinases (CDKs) 1, 2, 5, and 9 and is currently in Phase 3 for the treatment of refractory chronic lymphocytic leukemia (CLL). To further understand the mechanism of action, identify predictive biomarkers, and find additional cancer types which may benefit from dinaciclib, we evaluated cell viability following 24 hours treatment across a panel of ∼500 cells lines. Hematopoietic cell lines were on average 3-times more sensitive than solid tumor lines. In agreement with previous findings, mRNA expression of the anti-apoptotic family member BCL-xL or the ratio of MCL1-to-BCL-xL continue to be the best predictor of dinaciclib sensitivity in both hematopoietic and solid tumor cell lines. MCL1 appears to be an important target of dinaciclib particularly in MCL1 amplified cell lines. Dependence on MCL1 was established in a panel of 19 breast, NSCLC and SCLC cell lines by depletion of the protein by either dinaciclib treatment or MCL1 RNAi. The NSCLC line H23 was highly dependent on MCL1, as RNAi knockdown decreased viability to &lt;20% and could be rescued by introduction of a non-targeted MCL1 expression construct. In the H23 xenograft, dinaciclib diminished MCL1 levels and induced tumor apoptosis resulting in &gt;80% tumor regression. Cell lines which lacked pro-apoptotic proteins BAX / BAK or harbored a BAX mutation were insensitive to the inhibitor. Using apoptosis defective lines we demonstrate that 24 hours of dinaciclib treatment still impacted cell count by blocking cell cycle progression as measured by FACS. These data demonstrate that both cell cycle block and induction of apoptosis contribute to dinaciclib's mechanism of action. However, the observation that MCL1 and BCL-xL were top genes associated with sensitivity suggests that induction of apoptosis is the predominant mechanism of dinaciclib's anti-tumor effect and warrants further investigation of MCL1 amplification as a predictive biomarker in future clinical studies.

Citation Format: Harold Hatch, Robert Booher, Samanthi Perera, Thi Nguyen, Brian Dolinski, Samer Al-Assaad, Lauren Harmonay, Alwin Schuller, Minilik Angagaw, Brian Long, Xianlu Qu, Nathan Miselis, Mark Ayers, Michael Nebozhyn, Heather Hirsch, Danielle Greenawalt, Andrey Loboda, Thorseten Graef, Ellie Im, Rebecca Blanchard, Leigh Zawel, Peter Strack. MCL1 dependent cells are sensitive to the CDK inhibitor Dinaciclib. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 698. doi:10.1158/1538-7445.AM2013-698

Ki67 expression in the primary tumor predicts for clinical benefit and time to progression on first-line endocrine therapy in estrogen receptor-positive metastatic breast cancer

We examined whether baseline Ki67 expression in estrogen receptor-positive (ER+) primary breast cancer correlates with clinical benefit and time to progression on first-line endocrine therapy and survival in metastatic disease. Ki67 values and outcome information were retrieved from a prospectively maintained clinical database and validated against the medical records; 241 patients with metastatic breast cancer were included--who had ER+ primary cancer with known Ki67 expression level--and received first-line endocrine therapy for metastatic disease. Patients were assigned to low (<10 %), intermediate (10-25 %), or high (>25 %) Ki67 expression groups. Kaplan-Meier survival curves were plotted and multivariate analysis was performed to assess association between clinical and immunohistochemical variables and outcome. The clinical benefit rates were 81, 65, and 55 % in the low (n = 32), intermediate (n = 103), and high (n = 106) Ki67 expression groups (P = 0.001). The median times to progression on first-line endocrine therapy were 20.3 (95 % CI, 17.5-38.5), 10.8 (95 % CI, 8.9-18.8), and 8 (95 % CI, 6.1-11.1) months, respectively (P = 0.0002). The median survival times after diagnosis of metastatic disease were also longer for the low/intermediate compared to the high Ki67 group, 52 versus 30 months (P < 0.0001). In multivariate analysis, high Ki67 expression in the primary tumor remained an independent adverse prognostic factor in metastatic disease (P = 0.001). Low Ki67 expression in the primary tumor is associated with higher clinical benefit and longer time to progression on first-line endocrine therapy and longer survival after metastatic recurrence.

Tumor IGF-1 expression as a predictive biomarker for IGF1R-directed therapy in advanced pancreatic cancer (APC)

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Background: IGF-1 up-regulates PC proliferation and invasiveness through activation of PI3K/Akt signaling pathway and down-regulates PTEN. We investigated IGF-1 expression in tissue and blood as potential predictive markers in phase II study of IGF1R-directed monoclonal antibody, MK-0646 in APC. Prior phase I established the MTD of MK0646 at 5 mg/kg with gemcitabine (G) and erlotinib (E) and 10 mg/kg with G alone. Methods: Patients (pts) with stage IV, previously untreated APC, ECOG PS 0-1, adequate hematologic and organ function were enrolled. Arm A: G 1,000 mg/m2 over 100 min, weekly x 3, MK-0646 weekly x 4; Arm B: G 1000 mg/m2 and MK-0646 + E 100 mg daily. Arm C (control) was G 1,000 mg/m2 + E 100 mg. Cycles were repeated every 4 weeks. Pts were equally randomized in the 3 arms. Primary study objective was progression-free survival (PFS). Pre-treatment peripheral blood samples were measured for IGF-1 level by ELISA; archival core biopsies were analyzed for IGF-1 mRNA expression. RNA extraction from FFPE samples used Roche Transcriptor First Strand cDNA Synthesis Kit. TaqMan PreAmp technique was used to amplify target cDNA prior to TaqMan RT-PCR analysis. Cox proportional hazards model for PFS analyzed the interaction between tissue IGF-1 expression and treatment. Results: 50 pts were enrolled (A=15, B=16,C=16 pts, 3 ineligible). Median PFS of arms A, B and C were 5.5 months (95% CI: 3.9 – NA), 3.0 months (95% CI:1.8 – 5.6) and 2.0 months (95% CI: 1.8 – NA), respectively (log-rank test; p = 0.17). Median OS of A was 11.3 months (95% CI: 8.9 – NA), B 8.9 months (95% CI: 5.3 – NA) and C 5.7 months (95% CI: 2.0 – NA) (log-rank test; p = 0.44). 35 archival core biopsies were analyzed, 21 had adequate tissue for analysis. Using a Multivariable Cox proportional hazards model for PFS, where IGF-1 was dichotomized at the median, there was a 76% reduction in the risk of disease progression or death in arm A as compared with the control (arm C) at high IGF-1 level (p = 0.16). When IGF-1 was fitted as a continuous variable, this reduction was 96% (p = 0.08). There was no correlation between tissue and serum IGF-1. Conclusions: Tissue expression of IGF-1 level may represent a promising predictive biomarker for IGF1R-directed therapy in APC.