Primary Colorectal Tumor Displays Differential Genomic Expression Profiles Associated with Hepatic and Peritoneal Metastases

BACKGROUND

Despite improvements in characterization of CRC heterogeneity, appropriate risk stratification tools are still lacking in clinical practice. This study aimed to elucidate the primary tumor transcriptomic signatures associated with distinct metastatic routes.

METHODS

Primary tumor specimens obtained from CRC patients with either isolated LM (CRC-Liver) or PM (CRC-Peritoneum) were analyzed by transcriptomic mRNA sequencing, gene set enrichment analyses (GSEA) and immunohistochemistry. We further assessed the clinico-pathological associations and prognostic value of our signature in the COAD-TCGA independent cohort.

RESULTS

We identified a significantly different distribution of Consensus Molecular Subtypes between CRC-Liver and CRC-peritoneum groups. A transcriptomic signature based on 61 genes discriminated between liver and peritoneal metastatic routes. GSEA showed a higher expression of immune response and epithelial invasion pathways in CRC-Peritoneum samples and activation of proliferation and metabolic pathways in CRC-Liver samples. The biological relevance of RNA-Seq results was validated by the immunohistochemical expression of three significantly differentially expressed genes (ACE2, CLDN18 and DUSP4) in our signature. In silico analysis of the COAD-TCGA showed that the CRC-Peritoneum signature was associated with negative prognostic factors and poor overall and disease-free survivals.

CONCLUSIONS

CRC primary tumors spreading to the liver and peritoneum display significantly different transcriptomic profiles. The implementation of this signature in clinical practice could contribute to identify new therapeutic targets for stage IV CRC and to define individualized follow-up programs in stage II-III CRC.

Safety and clinical activity of intratumoral MEDI9197 alone and in combination with durvalumab and/or palliative radiation therapy in patients with advanced solid tumors

Background

MEDI9197 is an intratumorally administered toll-like receptor 7 and 8 agonist. In mice, MEDI9197 modulated antitumor immune responses, inhibited tumor growth and increased survival. This first-time-in-human, phase 1 study evaluated MEDI9197 with or without the programmed cell death ligand-1 (PD-L1) inhibitor durvalumab and/or palliative radiation therapy (RT) for advanced solid tumors.

Patients and methods

Eligible patients had at least one cutaneous, subcutaneous, or deep-seated lesion suitable for intratumoral (IT) injection. Dose escalation used a standard 3+3 design. Patients received IT MEDI9197 0.005–0.055 mg with or without RT (part 1), or IT MEDI9197 0.005 or 0.012 mg plus durvalumab 1500 mg intravenous with or without RT (part 3), in 4-week cycles. Primary endpoints were safety and tolerability. Secondary endpoints included pharmacokinetics, pharmacodynamics, and objective response based on Response Evaluation Criteria for Solid Tumors version 1.1. Exploratory endpoints included tumor and peripheral biomarkers that correlate with biological activity or predict response.

Results

From November 2015 to March 2018, part 1 enrolled 35 patients and part 3 enrolled 17 patients; five in part 1 and 2 in part 3 received RT. The maximum tolerated dose of MEDI9197 monotherapy was 0.037 mg, with dose-limiting toxicity (DLT) of cytokine release syndrome in two patients (one grade 3, one grade 4) and 0.012 mg in combination with durvalumab 1500 mg with DLT of MEDI9197-related hemorrhagic shock in one patient (grade 5) following liver metastasis rupture after two cycles of MEDI9197. Across parts 1 and 3, the most frequent MEDI9197-related adverse events (AEs) of any grade were fever (56%), fatigue (31%), and nausea (21%). The most frequent MEDI9197-related grade ≥3 events were decreased lymphocytes (15%), neutrophils (10%), and white cell counts (10%). MEDI9197 increased tumoral CD8+ and PD-L1+ cells, inducing type 1 and 2 interferons and Th1 response. There were no objective clinical responses; 10 patients in part 1 and 3 patients in part 3 had stable disease ≥8 weeks.

Conclusion

IT MEDI9197 was feasible for subcutaneous/cutaneous lesions but AEs precluded its use in deep-seated lesions. Although no patients responded, MEDI9197 induced systemic and intratumoral immune activation, indicating potential value in combination regimens in other patient populations.

Trial registration number

NCT02556463.

Radiomics to predict outcomes and abscopal response of patients with cancer treated with immunotherapy combined with radiotherapy using a validated signature of CD8 cells

BACKGROUND

Combining radiotherapy (RT) with immuno-oncology (IO) therapy (IORT) may enhance IO-induced antitumor response. Quantitative imaging biomarkers can be used to provide prognosis, predict tumor response in a non-invasive fashion and improve patient selection for IORT. A biologically inspired CD8 T-cells-associated radiomics signature has been developed on previous cohorts. We evaluated here whether this CD8 radiomic signature is associated with lesion response, whether it may help to assess disease spatial heterogeneity for predicting outcomes of patients treated with IORT. We also evaluated differences between irradiated and non-irradiated lesions.

METHODS

Clinical data from patients with advanced solid tumors in six independent clinical studies of IORT were investigated. Immunotherapy consisted of 4 different drugs (antiprogrammed death-ligand 1 or anticytotoxic T-lymphocyte-associated protein 4 in monotherapy). Most patients received stereotactic RT to one lesion. Irradiated and non-irradiated lesions were delineated from baseline and the first evaluation CT scans. Radiomic features were extracted from contrast-enhanced CT images and the CD8 radiomics signature was applied. A responding lesion was defined by a decrease in lesion size of at least 30%. Dispersion metrices of the radiomics signature were estimated to evaluate the impact of tumor heterogeneity in patient's response.

RESULTS

A total of 94 patients involving multiple lesions (100 irradiated and 189 non-irradiated lesions) were considered for a statistical interpretation. Lesions with high CD8 radiomics score at baseline were associated with significantly higher tumor response (area under the receiving operating characteristic curve (AUC)=0.63, p=0.0020). Entropy of the radiomics scores distribution on all lesions was shown to be associated with progression-free survival (HR=1.67, p=0.040), out-of-field abscopal response (AUC=0.70, p=0.014) and overall survival (HR=2.08, p=0.023), which remained significant in a multivariate analysis including clinical and biological variables.

CONCLUSIONS

These results enhance the predictive value of the biologically inspired CD8 radiomics score and suggests that tumor heterogeneity should be systematically considered in patients treated with IORT. This CD8 radiomics signature may help select patients who are most likely to benefit from IORT.

Comparison of Fast-Progression, Hyperprogressive Disease, and Early Deaths in Advanced Non–Small-Cell Lung Cancer Treated With PD-1/PD-L1 Inhibitors or Chemotherapy

PURPOSE

Hyperprogressive disease (HPD), fast progression (FP), and early death (ED) have been described in 13.8%, 4.7%, and 5.6% and in 5.1%, 2.8%, and 6.8%, respectively, of patients with non–small-cell lung cancer (NSCLC) treated with single-agent programmed cell death ligand 1 inhibitors (ICI) or chemotherapy, respectively. Whether FP/ED and HPD represent overlapping patterns is unknown.

PATIENTS AND METHODS

FP, ED, and HPD were retrospectively assessed in patients with NSCLC treated with single-agent ICI or chemotherapy. Eligibility required 2 computed tomography (CT) scans before and 1 CT scan during treatment. (1) HPD, (2) FP, (3) ED were defined as (1) RECIST version 1.1 progression at first CT scan and tumor growth rate variation per month > 50%, (2) ≥ 50% increase in the sum of the longest diameters of target lesions within 6 weeks from baseline, and (3) death as a result of radiologic progression within 12 weeks from baseline CT scan, respectively.

RESULTS

Of 406 ICI-treated NSCLC, 56 patients (13.8%), 9 patients (2.2%), and 36 patients (8.8%) were HPD, FP, and ED, respectively. Eight (14.2%) and 20 (35.7%) of 56 patients with HPD were also FP and ED. ED significantly correlated with baseline Eastern Cooperative Oncology Group performance status ≥ 2 compared with HPD (33% v 13%, P = .02). Overall survival was significantly longer for HPD (3.4 months [95% CI, 2.7 to 4.0 months]) compared with FP (0.7 months [95% CI, 0.6 to 0.8 months]); HR, 0.18 [95% CI, 0.08 to 0.42]; P < .0001) and ED (1.4 months [95% CI, 1.3 to 1.6 months]); HR, 0.19 [95% CI, 0.11 to 0.34]); P < .0001), whereas it did not differ between FP and ED (HR, 1.3 [95% CI, 0.56 to 3.0]; P = .55). Of 59 patients with NSCLC treated with single-agent chemotherapy, the HPD, FP, and ED rates were 5.1%, 1.7%, and 6.7%, respectively.

CONCLUSION

FP, ED, and HPD represent distinct progression patterns with limited overlap and different survival outcomes.

Evidence of pseudoprogression in patients treated with PD1/PDL1 antibodies across tumor types

Background

PD(L)1 antibodies (anti‐PD(L)‐1) have been a major breakthrough in several types of cancer. Novel patterns of response and progression have been described with anti‐PD(L)‐1. We aimed at characterizing pseudoprogression (PSPD) among patients with various solid tumor types treated by anti‐PD(L)‐1.

Methods

All consecutive patients (pts) enrolled in phase 1 trials with advanced solid tumors and lymphomas treated in phase I clinical trials evaluating monotherapy by anti‐PD(L)‐1 at Gustave Roussy were analyzed. We aimed to assess prevalence and outcome of PSPD across tumor types. We also intended to describe potential clinical and pathological factors associated with PSPD.

Results

A total of 169 patients treated with anti‐PD(L)‐1 were included in the study. Most frequent tumor types included melanoma (n = 57) and non‐small cell lung cancer (n = 19). At first tumor evaluation 77 patients (46%) presented with immune unconfirmed progressive disease. Six patients (8%) experienced PSPD: 2 patients with partial response; 4 patients with stable disease. Increase in target lesions in the first CT‐scan was more frequently associated to PSPD (67% vs 33%; P = .04). Patients with a PSPD had a superior survival when compared to patients progressing (median OS: 10.7 months vs 8.7 months; P = .07).

Conclusions

A small subset of PSPD patients may experience response after an initial progression. Assessment of the current strategy for immune‐related response evaluations may require further attention.

Hyperprogressive Disease in Patients With Advanced Non-Small Cell Lung Cancer Treated With PD-1/PD-L1 Inhibitors or With Single-Agent Chemotherapy

Importance

Hyperprogressive disease (HPD) is a new pattern of progression recently described in patients with cancer treated with programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors. The rate and outcome of HPD in advanced non-small cell lung cancer (NSCLC) are unknown.

Objectives

To investigate whether HPD is observed in patients with advanced NSCLC treated with PD-1/PD-L1 inhibitors compared with single-agent chemotherapy and whether there is an association between treatment and HPD.

Design, Setting, and Participants

In this multicenter retrospective study that included patients treated between August 4, 2011, and April 5, 2017, the setting was pretreated patients with advanced NSCLC who received PD-1/PD-L1 inhibitors (8 institutions) or single-agent chemotherapy (4 institutions) in France. Measurable disease defined by Response Evaluation Criteria in Solid Tumors (RECIST version 1.1) on at least 2 computed tomographic scans before treatment and 1 computed tomographic scan during treatment was required.

Interventions

The tumor growth rate (TGR) before and during treatment and variation per month (ΔTGR) were calculated. Hyperprogressive disease was defined as disease progression at the first evaluation with ΔTGR exceeding 50%.

Main Outcomes and Measures

The primary end point was assessment of the HPD rate in patients treated with IO or chemotherapy.

Results

Among 406 eligible patients treated with PD-1/PD-L1 inhibitors (63.8% male), 46.3% (n = 188) were 65 years or older, 72.4% (n = 294) had nonsquamous histology, and 92.9% (n = 377) received a PD-1 inhibitor as monotherapy in second-line therapy or later. The median follow-up was 12.1 months (95% CI, 10.1-13.8 months), and the median overall survival (OS) was 13.4 months (95% CI, 10.2-17.0 months). Fifty-six patients (13.8%) were classified as having HPD. Pseudoprogression was observed in 4.7% (n = 19) of the population. Hyperprogressive disease was significantly associated with more than 2 metastatic sites before PD-1/PD-L1 inhibitors compared with non-HPD (62.5% [35 of 56] vs 42.6% [149 of 350]; P = .006). Patients experiencing HPD within the first 6 weeks of PD-1/PD-L1 inhibitor treatment had significantly lower OS compared with patients with progressive disease (median OS, 3.4 months [95% CI, 2.8-7.5 months] vs 6.2 months [95% CI, 5.3-7.9 months]; hazard ratio, 2.18 [95% CI, 1.29-3.69]; P = .003). Among 59 eligible patients treated with chemotherapy, 3 (5.1%) were classified as having HPD.

Conclusions and Relevance

Our study suggests that HPD is more common with PD-1/PD-L1 inhibitors compared with chemotherapy in pretreated patients with NSCLC and is also associated with high metastatic burden and poor prognosis in patients treated with PD-1/PD-L1 inhibitors. Additional studies are needed to determine the molecular mechanisms involved in HPD.

Hyperprogressive Disease in Patients With Advanced Non-Small Cell Lung Cancer Treated With PD-1/PD-L1 Inhibitors or With Single-Agent Chemotherapy

Importance

Hyperprogressive disease (HPD) is a new pattern of progression recently described in patients with cancer treated with programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors. The rate and outcome of HPD in advanced non-small cell lung cancer (NSCLC) are unknown.

Objectives

To investigate whether HPD is observed in patients with advanced NSCLC treated with PD-1/PD-L1 inhibitors compared with single-agent chemotherapy and whether there is an association between treatment and HPD.

Design, Setting, and Participants

In this multicenter retrospective study that included patients treated between August 4, 2011, and April 5, 2017, the setting was pretreated patients with advanced NSCLC who received PD-1/PD-L1 inhibitors (8 institutions) or single-agent chemotherapy (4 institutions) in France. Measurable disease defined by Response Evaluation Criteria in Solid Tumors (RECIST version 1.1) on at least 2 computed tomographic scans before treatment and 1 computed tomographic scan during treatment was required.

Interventions

The tumor growth rate (TGR) before and during treatment and variation per month (ΔTGR) were calculated. Hyperprogressive disease was defined as disease progression at the first evaluation with ΔTGR exceeding 50%.

Main Outcomes and Measures

The primary end point was assessment of the HPD rate in patients treated with IO or chemotherapy.

Results

Among 406 eligible patients treated with PD-1/PD-L1 inhibitors (63.8% male), 46.3% (n = 188) were 65 years or older, 72.4% (n = 294) had nonsquamous histology, and 92.9% (n = 377) received a PD-1 inhibitor as monotherapy in second-line therapy or later. The median follow-up was 12.1 months (95% CI, 10.1-13.8 months), and the median overall survival (OS) was 13.4 months (95% CI, 10.2-17.0 months). Fifty-six patients (13.8%) were classified as having HPD. Pseudoprogression was observed in 4.7% (n = 19) of the population. Hyperprogressive disease was significantly associated with more than 2 metastatic sites before PD-1/PD-L1 inhibitors compared with non-HPD (62.5% [35 of 56] vs 42.6% [149 of 350]; P = .006). Patients experiencing HPD within the first 6 weeks of PD-1/PD-L1 inhibitor treatment had significantly lower OS compared with patients with progressive disease (median OS, 3.4 months [95% CI, 2.8-7.5 months] vs 6.2 months [95% CI, 5.3-7.9 months]; hazard ratio, 2.18 [95% CI, 1.29-3.69]; P = .003). Among 59 eligible patients treated with chemotherapy, 3 (5.1%) were classified as having HPD.

Conclusions and Relevance

Our study suggests that HPD is more common with PD-1/PD-L1 inhibitors compared with chemotherapy in pretreated patients with NSCLC and is also associated with high metastatic burden and poor prognosis in patients treated with PD-1/PD-L1 inhibitors. Additional studies are needed to determine the molecular mechanisms involved in HPD.

Hyperprogressive disease: recognizing a novel pattern to improve patient management

Anti-PD-1/PD-L1 monoclonal antibodies have substantially improved the overall survival of a subset of patients across multiple solid tumour types, but other patients can have a deterioration of their disease as a result of such therapies. This paradoxical phenomenon is defined as hyperprogression. In this Review, we present the available evidence of hyperprogressive disease following immune-checkpoint inhibition, the pathophysiological hypotheses that might explain hyperprogressive disease and the current challenges for patient management in routine clinical settings. Finally, we also discuss how the risk of hyperprogressive disease should be taken into account in clinical decisions involving immune-checkpoint inhibition.

A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study

BACKGROUND

Because responses of patients with cancer to immunotherapy can vary in success, innovative predictors of response to treatment are urgently needed to improve treatment outcomes. We aimed to develop and independently validate a radiomics-based biomarker of tumour-infiltrating CD8 cells in patients included in phase 1 trials of anti-programmed cell death protein (PD)-1 or anti-programmed cell death ligand 1 (PD-L1) monotherapy. We also aimed to evaluate the association between the biomarker, and tumour immune phenotype and clinical outcomes of these patients.

METHODS

In this retrospective multicohort study, we used four independent cohorts of patients with advanced solid tumours to develop and validate a radiomic signature predictive of immunotherapy response by combining contrast-enhanced CT images and RNA-seq genomic data from tumour biopsies to assess CD8 cell tumour infiltration. To develop the radiomic signature of CD8 cells, we used the CT images and RNA sequencing data of 135 patients with advanced solid malignant tumours who had been enrolled into the MOSCATO trial between May 1, 2012, and March 31, 2016, in France (training set). The genomic data, which are based on the CD8B gene, were used to estimate the abundance of CD8 cells in the samples and data were then aligned with the images to generate the radiomic signatures. The concordance of the radiomic signature (primary endpoint) was validated in a Cancer Genome Atlas [TGCA] database dataset including 119 patients who had available baseline preoperative imaging data and corresponding transcriptomic data on June 30, 2017. From 84 input variables used for the machine-learning method (78 radiomic features, five location variables, and one technical variable), a radiomics-based predictor of the CD8 cell expression signature was built by use of machine learning (elastic-net regularised regression method). Two other independent cohorts of patients with advanced solid tumours were used to evaluate this predictor. The immune phenotype internal cohort (n=100), were randomly selected from the Gustave Roussy Cancer Campus database of patient medical records based on previously described, extreme tumour-immune phenotypes: immune-inflamed (with dense CD8 cell infiltration) or immune-desert (with low CD8 cell infiltration), irrespective of treatment delivered; these data were used to analyse the correlation of the immune phenotype with this biomarker. Finally, the immunotherapy-treated dataset (n=137) of patients recruited from Dec 1, 2011, to Jan 31, 2014, at the Gustave Roussy Cancer Campus, who had been treated with anti-PD-1 and anti-PD-L1 monotherapy in phase 1 trials, was used to assess the predictive value of this biomarker in terms of clinical outcome.

FINDINGS

We developed a radiomic signature for CD8 cells that included eight variables, which was validated with the gene expression signature of CD8 cells in the TCGA dataset (area under the curve [AUC]=0·67; 95% CI 0·57-0·77; p=0·0019). In the cohort with assumed immune phenotypes, the signature was also able to discriminate inflamed tumours from immune-desert tumours (0·76; 0·66-0·86; p<0·0001). In patients treated with anti-PD-1 and PD-L1, a high baseline radiomic score (relative to the median) was associated with a higher proportion of patients who achieved an objective response at 3 months (vs those with progressive disease or stable disease; p=0·049) and a higher proportion of patients who had an objective response (vs those with progressive disease or stable disease; p=0·025) or stable disease (vs those with progressive disease; p=0·013) at 6 months. A high baseline radiomic score was also associated with improved overall survival in univariate (median overall survival 24·3 months in the high radiomic score group, 95% CI 18·63-42·1; vs 11·5 months in the low radiomic score group, 7·98-15·6; hazard ratio 0·58, 95% CI 0·39-0·87; p=0·0081) and multivariate analyses (0·52, 0·35-0·79; p=0·0022).

INTERPRETATION

The radiomic signature of CD8 cells was validated in three independent cohorts. This imaging predictor provided a promising way to predict the immune phenotype of tumours and to infer clinical outcomes for patients with cancer who had been treated with anti-PD-1 and PD-L1. Our imaging biomarker could be useful in estimating CD8 cell count and predicting clinical outcomes of patients treated with immunotherapy, when validated by further prospective randomised trials.

FUNDING

Fondation pour la Recherche Médicale, and SIRIC-SOCRATE 2.0, French Society of Radiation Oncology.

High incidence of cetuximab-related infusion reactions in head and neck patients

Background

Cetuximab is crucial in the management of squamous cell carcinoma of the head and neck of patients. Grade 3-4 cetuximab-induced infusion reactions (CI-IRs) occur in 2% of patients with colorectal cancer. Despite the 2.7% CI-IR rate in the EXTREME trial, higher rates were reported in small series of patients with head and neck squamous cell carcinoma (HNSCC) (6%-18%). There is an urgent need to better appraise the natural history and the predictive factors for CI-IRs in patients with HNSCC exposed to cetuximab.

Methods

The medical records from patients with HNSCC (n=428) treated by cetuximab at Gustave Roussy from January 2013 to December 2015 were reviewed. The impact of potential risk factors was analysed.

Results

Out of 428 patients, 24 patients (5.4%) presented CI-IR, including grade 3-4 (95.7%); about 21% (5/24) requiring intensive care unit referral and quasi all occurred within the first cycle (21/24). In a multivariate analysis, the occurrence of grade 3-4 CI-IR was associated with tobacco and alcohol history (p=8.5e-3) and with prior allergy history (p=2.9e-3). CI-IRs tended to be associated with poor overall survival in patients with recurrent and metastatic HNSCC and with a higher number of further lines of chemotherapy.

Conclusion

In real life, CI-IRs appear far more common in patients with HNSCC (5.4%) than reported in prospective trials. This is the largest series of patients ever focusing on the risk of CI-IR in patients with HNSCC. Prior allergy history and tobacco history are associated with CI-IR and could be used to better allocate treatment. Further prospective data are required to confirm these findings.

Promises and challenges for the implementation of computational medical imaging (radiomics) in oncology

Medical image processing and analysis (also known as Radiomics) is a rapidly growing discipline that maps digital medical images into quantitative data, with the end goal of generating imaging biomarkers as decision support tools for clinical practice. The use of imaging data from routine clinical work-up has tremendous potential in improving cancer care by heightening understanding of tumor biology and aiding in the implementation of precision medicine. As a noninvasive method of assessing the tumor and its microenvironment in their entirety, radiomics allows the evaluation and monitoring of tumor characteristics such as temporal and spatial heterogeneity. One can observe a rapid increase in the number of computational medical imaging publications-milestones that have highlighted the utility of imaging biomarkers in oncology. Nevertheless, the use of radiomics as clinical biomarkers still necessitates amelioration and standardization in order to achieve routine clinical adoption. This Review addresses the critical issues to ensure the proper development of radiomics as a biomarker and facilitate its implementation in clinical practice.

Abstract A051: Prediction of clinical outcomes of cancer patients treated with anti-PD-1/PD-L1 using a radiomics-based imaging score of immune infiltrate

Background: The discovery of biomarkers identifying responders to immunotherapy is a major challenge. Tumor and peritumoral immune infiltration has been shown to be associated with response to anti-PD-1/PD-L1. The aim of this study was to develop a radiomics-based imaging tool of tumor immune infiltrate and to assess whether such a tool could predict clinical outcomes of patients treated with anti-PD1/PDL1.

Methods: A predictive radiomics-based model of tumor-infiltrating CD8+ T cells was trained using data from the head and neck cohort of The Cancer Imaging Archive (HNSC-TCIA). Two cohorts from our institute were used for validation. Contrast-enhanced CTs of 57 patients from the HNSC-TCIA were manually segmented (tumor and surrounding tissue) and 76 radiomics features extracted. A radiomics-based score was build using radiomics features to predict tumor-infiltrating CD8+ T-cells' abundance, which was estimated using RNA-sequencing data from The Cancer Genome Atlas, and the Microenvironment Cell Populations-counter signature. As a first validation, this signature was applied to an independent cohort of 100 patients for whom the pathologic tumor immune infiltrate was postulated as either favorable (lymphoma, melanoma, lung, bladder, renal, MSI+ cancers, and adenopathy; 70 patients) or unfavorable (adenoid cystic carcinoma, low-grade neuroendocrine tumors, uterine leiomyoma; 30 patients). The signature was then applied on baseline-CTs of a second external cohort of 139 patients prospectively enrolled in anti PD-1/PD-L1 phase 1 trials. The median of the radiomics-based CD8+ score was used to separate patients into two groups (high and low score). Survival was estimated using Cox-proportional hazards model.

Results: We developed a radiomics-based CD8+ signature using the six radiomics features that had highest performance on random forest. In the first external cohort, the radiomics-based CD8 T-cells score was associated with the postulated tumor immune infiltrate (Wilcoxon test, P &lt; 0.001). In the second external cohort of patients treated with anti-PD-1/anti-PD-L1, median (±SD) radiomics score was 109.6±61.3. Patients with high-predicted score had significantly better OS (HR= 0.55, 95%CI=0.36-0.86, P= 0.009). The radiomics-based CD8+ predicted score remained significant in a multivariate Cox regression analysis including RMH score (HR= 0.50, 95%CI=0.32-0.78, P= 0.003).

Conclusions: The radiomics-based signature of CD8+ T cells appears as a promising tool to estimate tumor immune infiltrate and to infer the outcome of patients treated with anti-PD-1/PD-L1.

Citation Format: Roger Sun, Elaine Johanna Limkin, Laurent Dercle, Sylvain Reuzé, Stéphane Champiat, David Brandao, Loic Verlingue, Samy Ammari, Sandrine Aspeslagh, Antoine Hollebecque, Christophe Massard, Aurélien Marabelle, Jean-Yves Scoazec, Charlotte Robert, Jean-Charles Soria, Eric Deutsch, Charles Ferté. Prediction of clinical outcomes of cancer patients treated with anti-PD-1/PD-L1 using a radiomics-based imaging score of immune infiltrate [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A051.

Precision medicine for patients with advanced biliary tract cancers: An effective strategy within the prospective MOSCATO-01 trial

BACKGROUND

Recommended treatments of patients with advanced biliary tract cancer (aBTC) are limited to one chemotherapy doublet. Nevertheless, efficacy of treatment personalisation for aBTCs is supported by accumulating evidences but remains to be evaluated.

PATIENTS AND METHODS

Patients with aBTCs included in the prospective clinical trial MOSCATO-01 were treated by at least one previous systemic treatment, had an ECOG performance status of 0-1, and at least one tumour site accessible to biopsy. Multiple high-throughput molecular analysis was performed on biopsies to drive the administration of molecular targeted agents (MTAs).

RESULTS

From November 2011 to March 2016, 43 patients (4%) of the 1035 adult patients included in MOSCATO-01 had aBTCs with a majority of intrahepatic localisation (67%). Successful biopsy procedures and DNA extractions led to molecular portraits for 34 patients (79%). Orientation to an appropriate early clinical trial or accessible MTA(s) was possible for 23 of these patients (68%), and 18 (53%) have received matched MTA(s). Among them, the overall response rate was 33% and the disease control rate was 88%. A PFS ≥6 months was observed in 37% and the PFS ratio was >1.3 for 50% of the patients. These patients had a lower risk for death as compared to the 20 patients not orientated to a matched MTA (HR, 0.29; 95% CI, 0.11-0.76; p = 0.008).

CONCLUSIONS

Within the MOSCATO-01 trial, patients with aBTCs had the highest rate of orientation to matched MTAs and derived a clear clinical benefit. A broader evaluation of these findings may improve future treatments strategies for aBTCs.

TRIAL REGISTRATION

NCT01566019.

Limits of radiomic-based entropy as a surrogate of tumor heterogeneity: ROI-area, acquisition protocol and tissue site exert substantial influence

Entropy is a promising quantitative imaging biomarker for characterizing cancer imaging phenotype. Entropy has been associated with tumor gene expression, tumor metabolism, tumor stage, patient prognosis, and treatment response. Our hypothesis states that tumor-specific biomarkers such as entropy should be correlated between synchronous metastases. Therefore, a significant proportion of the variance of entropy should be attributed to the malignant process. We analyzed 112 patients with matched/paired synchronous metastases (SM#1 and SM#2) prospectively enrolled in the MOSCATO-01 clinical trial. Imaging features were extracted from Regions Of Interest (ROI) delineated on CT-scan using TexRAD software. We showed that synchronous metastasis entropy was correlated across 5 Spatial Scale Filters: Spearman's Rho ranged between 0.41 and 0.59 (P = 0.0001, Bonferroni correction). Multivariate linear analysis revealed that entropy in SM#1 is significantly associated with (i) primary tumor type; (ii) entropy in SM#2 (same malignant process); (iii) ROI area size; (iv) metastasis site; and (v) entropy in the psoas muscle (reference tissue). Entropy was a logarithmic function of ROI area in normal control tissues (aorta, psoas) and in mathematical models (P < 0.01). We concluded that entropy is a tumor-specific metric only if confounding factors are corrected.

Predictive and prognostic value of CT based radiomics signature in locally advanced head and neck cancers patients treated with concurrent chemoradiotherapy or bioradiotherapy and its added value to Human Papillomavirus status

OBJECTIVES

To explore prognostic and predictive value of radiomics in patients with locally advanced head and neck squamous cell carcinomas (LAHNSCC) treated with concurrent chemoradiotherapy (CRT) or bioradiotherapy (BRT).

MATERIALS AND METHODS

Data of 120 patients (CRT vs. BRT matched 2:1) were retrospectively analyzed. A total of 544 radiomics features of the primary tumor were extracted from radiotherapy planning computed tomography scans. Cox proportional hazards models were used to examine the association between survival and radiomics features with false discovery rate correction. The discriminatory performance was evaluated using receiver operating characteristic curve analysis.

RESULTS

Multivariate analysis showed a 24-feature based signature significantly predicted for OS (HR=0.3, P=0.02) and progression-free survival (PFS) (HR=0.3, P=0.01). Combining the radiomics signature with p16 status showed a significant improvement of prognostic performance compared with p16 (AUC=0.78vs. AUC=0.64 at 5years, P=0.01) or radiomics signature (AUC=0.78vs. AUC=0.67, P=0.01) alone. When patients were stratified according to this combination, OS and PFS were significantly different according to the 4 sub-types (p16+ with low/high signature score; p16- with low/high signature score) (P<0.001). Patients with high signature score significantly benefited from CRT (vs. BRT) in terms of OS (P=0.004), while no benefit from CRT in patients with low signature score.

CONCLUSION

Our analysis suggests an added value of radiomics features as prognostic and predictive biomarker in HNSCC treated with CRT/BRT. Moreover, the radiomics signature provided additional information to HPV/p16 status to further stratify patients. External validation of such findings is mandatory given the risk of overfitting.

The MET/AXL/FGFR Inhibitor S49076 Impairs Aurora B Activity and Improves the Antitumor Efficacy of Radiotherapy

Several therapeutic agents targeting HGF/MET signaling are under clinical development as single agents or in combination, notably with anti-EGFR therapies in non-small cell lung cancer (NSCLC). However, despite increasing data supporting a link between MET, irradiation, and cancer progression, no data regarding the combination of MET-targeting agents and radiotherapy are available from the clinic. S49076 is an oral ATP-competitive inhibitor of MET, AXL, and FGFR1-3 receptors that is currently in phase I/II clinical trials in combination with gefitinib in NSCLC patients whose tumors show resistance to EGFR inhibitors. Here, we studied the impact of S49076 on MET signaling, cell proliferation, and clonogenic survival in MET-dependent (GTL16 and U87-MG) and MET-independent (H441, H460, and A549) cells. Our data show that S49076 exerts its cytotoxic activity at low doses on MET-dependent cells through MET inhibition, whereas it inhibits growth of MET-independent cells at higher but clinically relevant doses by targeting Aurora B. Furthermore, we found that S49076 improves the antitumor efficacy of radiotherapy in both MET-dependent and MET-independent cell lines in vitro and in subcutaneous and orthotopic tumor models in vivo In conclusion, our study demonstrates that S49076 has dual antitumor activity and can be used in combination with radiotherapy for the treatment of both MET-dependent and MET-independent tumors. These results support the evaluation of combined treatment of S49076 with radiation in clinical trials without patient selection based on the tumor MET dependency status. Mol Cancer Ther; 16(10); 2107-19. ©2017 AACR.

Hyperprogressive Disease Is a New Pattern of Progression in Cancer Patients Treated by Anti-PD-1/PD-L1

Purpose: While immune checkpoint inhibitors are disrupting the management of patients with cancer, anecdotal occurrences of rapid progression (i.e., hyperprogressive disease or HPD) under these agents have been described, suggesting potentially deleterious effects of these drugs. The prevalence, the natural history, and the predictive factors of HPD in patients with cancer treated by anti-PD-1/PD-L1 remain unknown.Experimental Design: Medical records from all patients (N = 218) prospectively treated in Gustave Roussy by anti-PD-1/PD-L1 within phase I clinical trials were analyzed. The tumor growth rate (TGR) prior ("REFERENCE"; REF) and upon ("EXPERIMENTAL"; EXP) anti-PD-1/PD-L1 therapy was compared to identify patients with accelerated tumor growth. Associations between TGR, clinicopathologic characteristics, and overall survival (OS) were computed.Results: HPD was defined as a RECIST progression at the first evaluation and as a ≥2-fold increase of the TGR between the REF and the EXP periods. Of 131 evaluable patients, 12 patients (9%) were considered as having HPD. HPD was not associated with higher tumor burden at baseline, nor with any specific tumor type. At progression, patients with HPD had a lower rate of new lesions than patients with disease progression without HPD (P < 0.05). HPD is associated with a higher age (P < 0.05) and a worse outcome (overall survival). Interestingly, REF TGR (before treatment) was inversely correlated with response to anti-PD-1/PD-L1 (P < 0.05) therapy.Conclusions: A novel aggressive pattern of hyperprogression exists in a fraction of patients treated with anti-PD-1/PD-L1. This observation raises some concerns about treating elderly patients (>65 years old) with anti-PD-1/PD-L1 monotherapy and suggests further study of this phenomenon. Clin Cancer Res; 23(8); 1920-8. ©2016 AACRSee related commentary by Sharon, p. 1879.

rCGH: a comprehensive array-based genomic profile platform for precision medicine

Summary: We present rCGH, a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine. rCGH supports the major microarray platforms, ensures a full traceability and facilitates profiles interpretation and decision-making through sharable interactive visualizations.

Availability and implementation: The rCGH R package is available on bioconductor (under Artistic-2.0). The aCGH-viewer is available at https://fredcommo.shinyapps.io/aCGH_viewer, and the application implementation is freely available for installation at https://github.com/fredcommo/aCGH_viewer.

Contact:frederic.commo@gustaveroussy.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

BACKGROUND

A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2) frequencies of the 96 classes of single-nucleotide substitution determined by the flanking bases, and 3) copy number profiles, if available.

METHODS

We used publicly available somatic mutation data from the COSMIC database to train random forest classifiers to distinguish among those tissues of origin for which sufficient data was available. We selected feature sets using cross-validation and then derived two final classifiers (with or without copy number profiles) using 80 % of the available tumors. We evaluated the accuracy using the remaining 20 %. For further validation, we assessed accuracy of the without-copy-number classifier on three independent data sets: 1669 newly available public tumors of various types, a cohort of 91 breast metastases, and a set of 24 specimens from 9 lung cancer patients subjected to multiregion sequencing.

RESULTS

The cross-validation accuracy was highest when all three types of information were used. On the left-out COSMIC data not used for training, we achieved a classification accuracy of 85 % across 6 primary sites (with copy numbers), and 69 % across 10 primary sites (without copy numbers). Importantly, a derived confidence score could distinguish tumors that could be identified with 95 % accuracy (32 %/75 % of tumors with/without copy numbers) from those that were less certain. Accuracy in the independent data sets was 46 %, 53 % and 89 % respectively, similar to the accuracy expected from the training data.

CONCLUSIONS

Identification of primary site from point mutation and/or copy number data may be accurate enough to aid clinical diagnosis of cancers of unknown primary origin.

Abstract 2401: Circulating cell-free tumor DNA (cfDNA) analysis of 50-genes by next-generation sequencing (NGS) in the prospective MOSCATO trial

Background

Precision-medicine initiatives are driven by the molecular analysis of tumor samples (fresh or FFPE material). Such an approach is limited by the availability of the tumor material and the challenges related to on-purpose tumor biopsies. A very appealing alternative to advance precision-medicine initiatives is the development of liquid biopsies using cfDNA.

Methods

We investigated the use of NGS on tumor biopsy and plasma, and evaluated the consistency between the tissue biopsy (tDNA) and cfDNA analysis on a prospective cohort of patients with metastatic or locally advanced solid tumors enrolled in the MOSCATO 01 trial (NCT01566019).

Blood samples were collected at inclusion before tumor biopsy and cfDNA was extracted from 500μl plasma. Hot-spot mutations from 50 genes were screened with Ampliseq CHP2 panel (IonTorrent, Life Technologies, Dramstadt). Only variants reported by the Torrent Suite Variant Caller v4.2 were retained for the analysis. Paired results in tumor and plasma were described using Cohen's Kappa agreement coefficient (κ).

Results

From November 2011 to May 2014, among the 516 patients enrolled in the MOSCATO 01 trial, 190 patients (37%) were analyzed for tDNA and cfDNA. In addition, cfDNA was evaluated in 43 patients for whom no tumor analysis was performed because of low cellularity (&lt; 10% of tumor cells).

Patient characteristics were as follows: median age at biopsy: 57 years (range, 18-78); main tumor types: lung (19%), ENT (14%), colorectal (10%), breast (10%); median of 3 previous lines of treatment.

Overall, 325 mutations were identified in the tDNA of 184 patients: 146 mutations were identified both in tumor and plasma and 179 in tumor, but not in plasma. 15 mutations were only found in cfDNA, thereby providing additional information. The κ.was 59% (95%CI, 0.54-0.64). The sensibility of using NGS for 50 targeted hot-spot genes analysis in cfDNA compared to tDNA was 44.9% and the specificity was 99.8%, with a positive predictive value of 90.7% and negative predictive value of 98.1%.

The ten most frequent pathogenic mutations found in the tDNA or cfDNA (&gt;5 cases each) included KRAS (33 cases), PIK3CA (22 cases) and TP53 genes (22 cases). When considering only these ten most frequent mutations, 77 mutations were identified in 71 patients: 39 in tumor and plasma, 36 in tumor, but not in plasma and 2 mutations only in plasma, with a κ of 66% (95%CI, 56-76%). The p.H1047R PIK3CA mutation, was found only in tumor (5 cases); for the other nine mutations, the κ coefficient varied from 56% to 89%, with a median of 75%.

The cfDNA analysis of the 43 patients without tDNA analysis revealed at least one mutation in 24 patients (56%), including 11 pathogenic variants of therapeutic interest.

Conclusion

The analysis of cfDNA using NGS represents an attractive and noninvasive alternative to tumor biopsies, and can be used as a surrogate method to screen for mutations. Further prospective validation is warranted.

Citation Format: Ecaterina Ileana, Cécile Jovelet, Marie-Cécile Le Deley, Christophe Massard, Nelly Motté, Antoine Hollebecque, Amélie Boichard, Charles Ferté, Sophie Postel-Vinay, Silvia Rosellini, Maud Ngo-Camus, Thierry De Baere, Philippe Vielh, Catherine Richon, Mélanie Laporte, Siham Gouissem, Yohann Loriot, Rastilav Bahleda, Anas Gazzah, Andrea Varga, Gilles Vassal, Alexander Eggermont, Fabrice André, Jean-Charles Soria, Ludovic Lacroix. Circulating cell-free tumor DNA (cfDNA) analysis of 50-genes by next-generation sequencing (NGS) in the prospective MOSCATO trial. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2401. doi:10.1158/1538-7445.AM2015-2401

Abstract 2568: S49076, a MET, AXL, FGFR inhibitor, potentiates radiation therapy in subcutaneous and orthotopic models of lung cancer

S49076 is an oral ATP-competitive inhibitor of the receptor tyrosine kinases MET, AXL, and FGFR1-3 currently in phase I/II clinical development in patients with advanced solid tumors. Here, we investigated the effect of S49076 on both MET- and non-MET- dependent cell lines alone and in association with ionizing radiation (IR) both in vitro and in vivo. We performed proliferation and clonogenic survival assays using the low MET-expressing H460 and A549 non-small-cell lung cancer (NSCLC) cell lines, the high MET-expressing H441 NSCLC cell line and the MET-dependent GTL16 gastric cancer cell line. Activity against the MET receptor and Aurora B kinase was assessed by analyzing the phosphorylation status of MET Tyr1234/1235 and Histone H3 Ser10 residues. Pharmacologic and RNA interference approaches against Aurora B and MET were used to determine the molecular mechanism of the cell response to S49076.

S49076 inhibited MET activity in the nanomolar range (1 - 100 nM). At higher, but still clinically-relevant concentrations (0.5 - 1 μM), S49076 was also found to inhibit Aurora B kinase activity in all cell lines tested. In non MET-dependent cell lines, the antiproliferative and anti-clonogenic effects of the drug correlated with its activity against Aurora B, whereas in the MET-dependent cell line, these effects could be attributed to direct inhibition of the MET receptor. When treatment with S49076 was combined with IR, an enhancement of IR effects was observed in all cell lines tested in vitro. In vivo, a significant growth delay of subcutaneous tumors was observed at 50 mg/kg bid oral S49076 in non-MET dependent models and at 3 mg/kg bid oral S49076 in the GTL16 MET-dependent model. For non MET-dependent models, immunohistochemistry revealed that treatment with S49076 reduced Histone H3 phosphorylation on Ser10. This is consistent with the finding that S49076 concentrations above 1 μM were attained in the tumors, as determined by LC-MS/MS analysis. In all tumors tested, S49076 treatment significantly delayed tumor growth when combined to a fractionated IR (4 fractions of 2.5 Gy) compared to IR alone. An orthotopic model of lung cancer using luciferase-expressing H460 NSCLC cells was also used to evaluate the combination of S49076 (50mg/kg bid) and locally fractionated thoracic IR (4*2.5 Gy). In this model, the median survival after cell implantation was 22 days for control mice, 29.5 and 29 days for S49076 treated and irradiated mice respectively and 41 days for mice receiving the combined treatment (p&lt;0.002 for combined treatment versus the irradiated arm or the S49076 treated arm).

Our findings indicate that S49076 improves the efficacy of radiotherapy in both MET- and non-MET- dependent cell, supporting the use of combined treatment with S49076 and radiation in clinical trials without patient selection.

Citation Format: Céline Clémenson, Cyrus Chargari, Michele Mondini, Charles Ferté, Winchygn Liu, Mike Burbridge, Valérie Cattan, Anne Jacquet-Bescond, Eric Deutsch. S49076, a MET, AXL, FGFR inhibitor, potentiates radiation therapy in subcutaneous and orthotopic models of lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2568. doi:10.1158/1538-7445.AM2015-2568

Systemic treatment of advanced hepatocellular carcinoma: from disillusions to new horizons

Hepatocellular carcinoma (HCC) is an aggressive malignancy, which accounts for a third of all cancer deaths globally each year. The management of patients with HCC is complex, as both the tumour stage and any underlying liver disease must be considered conjointly. Since the approval of sorafenib in advanced HCC, several phase III clinical trials have failed to demonstrate any superiority over sorafenib in the frontline setting, and no agent has been shown to impact outcomes after sorafenib failure. This review will focus on the range of experimental therapeutics for patients with advanced HCC and highlight the successes and failures of these treatments as well as areas for future development. Specifics such as dose limiting toxicity and safety profile in patients with liver dysfunction related to the underlying chronic liver disease should be considered when developing therapies in HCC. Finally, robust validated and reproducible surrogate end-points as well as predictive biomarkers should be defined in future randomised trials.

Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology

BACKGROUND

Comparative genomic hybridization (CGH) arrays are increasingly used in personalized medicine programs to identify gene copy number aberrations (CNAs) that may be used to guide clinical decisions made during molecular tumor boards. However, analytical processes such as the centralization step may profoundly affect CGH array results and therefore may adversely affect outcomes in the precision medicine context.

PATIENTS AND METHODS

The effect of three different centralization methods: median, maximum peak, alternative peak, were evaluated on three datasets: (i) the NCI60 cell lines panel, (ii) the Cancer Cell Line Encyclopedia (CCLE) panel, and (iii) the patients enrolled in prospective molecular screening trials (SAFIR-01 n = 283, MOSCATO-01 n = 309), and compared with karyotyping, drug sensitivity, and patient-drug matching, respectively.

RESULTS

Using the NCI60 cell lines panel, the profiles generated by the alternative peak method were significantly closer to the cell karyotypes than those generated by the other centralization strategies (P < 0.05). Using the CCLE dataset, selected genes (ERBB2, EGFR) were better or equally correlated to the IC50 of their companion drug (lapatinib, erlotinib), when applying the alternative centralization. Finally, focusing on 24 actionable genes, we observed as many as 7.1% (SAFIR-01) and 6.8% (MOSCATO-01) of patients originally not oriented to a specific treatment, but who could have been proposed a treatment based on the alternative peak centralization method.

CONCLUSION

The centralization method substantially affects the call detection of CGH profiles and may thus impact precision medicine approaches. Among the three methods described, the alternative peak method addresses limitations associated with existing approaches.

Social interactomes for enabling research communities

SUMMARY

Data-driven analyses of scientific abstracts with web apps such as "abstract interactomes" provide a new visualization tool for the biomedical research community to interactively navigate a rich assembly of investigators and identify common research topics. Alternative conference formats such as "social interactomes," with structured, albeit informal, discussions among attendees, are able to engage fellows and top investigators, facilitate the exchange of ideas, and encourage data sharing and future collaborations.

Exomics and immunogenics: Bridging mutational load and immune checkpoints efficacy

Anti-PD-1/PD-L1 antibodies are emerging as promising anticancer therapeutics. Interestingly, elevated response rates to these agents are mostly documented among patients with tumors that bear high level of somatic mutations, like melanoma or non-small cell lung carcinoma. We herein formulate the hypothesis that high levels of mutational heterogeneity in the tumor could be the key for the success of immune checkpoint-targeting therapies.

Modeling RAS phenotype in colorectal cancer uncovers novel molecular traits of RAS dependency and improves prediction of response to targeted agents in patients

PURPOSE

KRAS wild-type status is an imperfect predictor of sensitivity to anti-EGF receptor (EGFR) monoclonal antibodies in colorectal cancer, motivating efforts to identify novel molecular aberrations driving RAS. This study aimed to build a quantitative readout of RAS pathway activity to (i) uncover molecular surrogates of RAS activity specific to colorectal cancer, (ii) improve the prediction of cetuximab response in patients, and (iii) suggest new treatment strategies.

EXPERIMENTAL DESIGN

A model of RAS pathway activity was trained in a large colorectal cancer dataset and validated in three independent colorectal cancer patient datasets. Novel molecular traits were inferred from The Cancer Genome Atlas colorectal cancer data. The ability of the RAS model to predict resistance to cetuximab was tested in mouse xenografts and three independent patient cohorts. Drug sensitivity correlations between our model and large cell line compendiums were performed.

RESULTS

The performance of the RAS model was remarkably robust across three validation datasets. (i) Our model confirmed the heterogeneity of the RAS phenotype in KRAS wild-type patients, and suggests novel molecular traits driving its phenotype (e.g., MED12 loss, FBXW7 mutation, MAP2K4 mutation). (ii) It improved the prediction of response and progression-free survival (HR, 2.0; P < 0.01) to cetuximab compared with KRAS mutation (xenograft and patient cohorts). (iii) Our model consistently predicted sensitivity to MAP-ERK kinase (MEK) inhibitors (P < 0.01) in two cell panel screens.

CONCLUSIONS

Modeling the RAS phenotype in colorectal cancer allows for the robust interrogation of RAS pathway activity across cell lines, xenografts, and patient cohorts. It demonstrates clinical utility in predicting response to anti-EGFR agents and MEK inhibitors.