ARID1A mutations confer intrinsic and acquired resistance to cetuximab treatment in colorectal cancer

Most colorectal (CRC) tumors are dependent on EGFR/KRAS/BRAF/MAPK signaling activation. ARID1A is an epigenetic regulator mutated in approximately 5% of non-hypermutated CRC tumors. Here we show that anti-EGFR but not anti-VEGF treatment enriches for emerging ARID1A mutations in CRC patients. In addition, we find that patients with ARID1A mutations, at baseline, are associated with worse outcome when treated with cetuximab- but not bevacizumab-containing therapies; thus, this suggests that ARID1A mutations may provide both an acquired and intrinsic mechanism of resistance to anti-EGFR therapies. We find that, ARID1A and EGFR-pathway genetic alterations are mutually exclusive across lung and colorectal cancers, further supporting a functional connection between these pathways. Our results not only suggest that ARID1A could be potentially used as a predictive biomarker for cetuximab treatment decisions but also provide a rationale for exploring therapeutic MAPK inhibition in an unexpected but genetically defined segment of CRC patients.

ARID1A is an epigenetic regulator mutated in approximately 5% of non-hypermutated colorectal cancer tumors, however, its relationship with treatment response remains to be explored. Here, the authors suggest that ARID1A mutations may confer intrinsic and acquired resistance to cetuximab treatment.

Abstract 2796: ctDNA prognosis in adjuvant triple-negative breast cancer

Background: Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype, even in early stages. Evidence of molecular residual disease (MRD), after treatment with curative intent (surgery, chemotherapy), predating macroscopic recurrence can provide rationale for early therapeutic intervention, potentially improving patient outcomes. Longitudinal evaluation of circulating tumor DNA (ctDNA) is emerging as a promising early marker of treatment efficacy and recurrence, validated to pre-date recurrence by radiological imaging. However, data in early TNBC (eTNBC) are limited. Here we investigate the prognostic value of longitudinal ctDNA monitoring in eTNBC patients post-surgery and after adjuvant chemotherapy (ACT) using a custom bespoke ctDNA assay.

Methods: Tumor tissue and longitudinal post-surgical plasma samples were collected and analyzed from 186 patients enrolled in the phase 3 BEATRICE clinical study (NCT00528567). Samples from each patient were whole exome sequenced to identify up to 16 SNVs for ctDNA monitoring. ctDNA status was measured longitudinally and correlated with baseline prognostic factors as well as invasive disease free survival (iDFS) and overall survival (OS).

Results: Baseline ctDNA (b-ctDNA), evaluated post-surgery and prior to chemotherapy was detected in 19.9% (36/181) of patients. b-ctDNA was positively associated with large tumors and lymph node (LN) involvement, and negatively correlated with presence of stromal tumor infiltrating lymphocytes (TILs). b-ctDNA presence was a stronger predictor of shorter IDFS and OS compared to LN involvement (HR IDFS: 4.36 [2.47-7.7] vs 1.86 [1.08-3.19]; HR OS: 4.01 [1.6-10.07] vs 2.89 [1.39-6]]), respectively). Remarkably, b-ctDNA prognostic value was restricted to LN+ pts (HR IDFS: 10.94 [3.2-37.41]) vs LN- pts (HR IDFS 1.61 [0.49-5.36]). ctDNA positivity after ACT was observed in 21.5% (40/186) of patients and was associated with reduced IDFS and OS (HR: 8.36 [4.62-15.1] and 18.45 [6.79-50.17]), independent of LN involvement. Upon chemotherapy treatment, the median time to first ctDNA positivity occurrence was 13 months (range 3-42.3 mo) and the median lead time from ctDNA detection to radiographic recurrence was 6.1 months (range 0-30.5 mo). Akaike information criterion (AIC, p<0.05) indicated that ctDNA detected post-surgery or post-chemotherapy identifies patients at the highest risk of disease progression even after adjustment for LN and TILs status as well as the tumor size.

Conclusions: ctDNA, both at post-surgery and post-ACT, provides additional prognostic value beyond the known risk factors of LN involvement, tumor size and TILs. Post-op ctDNA+ provides an independent and stronger indicator of poor prognosis than any other evaluated baseline covariates. Our data show that TNBC pts that are ctDNA+ post-surgery are at the highest risk of recurrence and death and are underserved by current SOC treatment.

Citation Format: Luciana Molinero, Derrick Renner, Hsin-Ta Wu, Nina Qi, Rajesh Patel, Ching-Wei Chang, Himanshu Sethi, Alexey Aleshin, Carlos Bais, David Cameron. ctDNA prognosis in adjuvant triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2796.

Detection of minimal residual disease (MRD) in colorectal cancer (CRC) patients UICC stage II/III by ultra-deep sequencing of cfDNA from post-surgery plasma

26

Background: Detection of primary tumor mutations in cell-free DNA (cfDNA) of post-surgery plasma of patients with R0-resected not-metastasized solid tumors is a strong indicator of recurrence of disease. We explored whether ultra-deep sequencing of cfDNA could improve sensitivity and specificity with respect to time-to-progression. Methods: 84 CRC patients UICC stage II/III were recruited into the prospective, observational study “Molecular Signatures in Colorectal Cancer”. Matched tumor tissue samples, plasma depleted blood cells (PDBC), and cfDNA (drawn 1 to 34 days after R0-resection, median 7 days) were processed with the Roche AVENIO Tumor Tissue and ctDNA Surveillance Kits*. Samples of 79 patients passed all quality controls, in particular cfDNA was sequenced ultra-deep with a median of 180 Mio. instead of 50 Mio. reads/sample. Somatic variants were identified with AVENIO Oncology Analysis software 2.0*. PDBC informed germline variants were removed. If a tissue baseline variant was detected in cfDNA with a significant adjusted p-value, the patient was defined ctDNA+, and ctDNA- otherwise. Results: 8 ctDNA+ patients (28 variants, median AF = 0.15%) were identified of which 4 had a progression of disease at two years. Sensitivity was 44% (95% CI [0.137, 0.788]), specificity was 94% (95% CI [0.86, 0.984]), positive predictive value was 50% (95% CI [0.157, 0.843]), and negative predictive value was 93% (95% CI [0.843, 0.977]). Comparison of time-to-progression of ctDNA+ and ctDNA- patients using the log-rank test resulted in a p-value of 0.0058. Comparison of survival times of ctDNA+ and ctDNA- patients resulted in a p-value of 0.0333. Multivariate analyses of times-to-progression resulted in ctDNA-status (p = 0.0022, hazard ratio (HR) = 7.098) and neoadjuvant therapy (p = 0.0010, HR = 6.618) as significant parameters. Conclusions: Even in this small cohort of CRC UICC stage II/III patients, MRD detection in post-surgery plasma is the strongest predictor of shorter time to progression. Ultra-deep sequencing of cfDNA samples did not influence MRD detection on a patient-level. *for Research Use Only; not for use in diagnostic procedures.

Development of a gene expression-based prognostic signature for IDH wild-type glioblastoma

BACKGROUND

We aimed to develop a gene expression-based prognostic signature for isocitrate dehydrogenase (IDH) wild-type glioblastoma using clinical trial datasets representative of glioblastoma clinical trial populations.

METHODS

Samples were collected from newly diagnosed patients with IDH wild-type glioblastoma in the ARTE, TAMIGA, EORTC 26101 (referred to as "ATE"), AVAglio, and GLARIUS trials, or treated at UCLA. Transcriptional profiling was achieved with the NanoString gene expression platform. To identify genes prognostic for overall survival (OS), we built an elastic net penalized Cox proportional hazards regression model using the discovery ATE dataset. For validation in independent datasets (AVAglio, GLARIUS, UCLA), we combined elastic net-selected genes into a robust z-score signature (ATE score) to overcome gene expression platform differences between discovery and validation cohorts.

RESULTS

NanoString data were available from 512 patients in the ATE dataset. Elastic net identified a prognostic signature of 9 genes (CHEK1, GPR17, IGF2BP3, MGMT, MTHFD1L, PTRH2, SOX11, S100A9, and TFRC). Translating weighted elastic net scores to the ATE score conserved the prognostic value of the genes. The ATE score was prognostic for OS in the ATE dataset (P < 0.0001), as expected, and in the validation cohorts (AVAglio, P < 0.0001; GLARIUS, P = 0.02; UCLA, P = 0.004). The ATE score remained prognostic following adjustment for O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status and corticosteroid use at baseline. A positive correlation between ATE score and proneural/proliferative subtypes was observed in patients with MGMT non-methylated promoter status.

CONCLUSIONS

The ATE score showed prognostic value and may enable clinical trial stratification for IDH wild-type glioblastoma.

Abstract LB-063: ARID1A mutations induce an EGFR-like gene expression signature and confer intrinsic and acquired resistance to cetuximab treatment in first line metastatic CRC

Extensive biological and clinical evidence supports the notion many CRC tumors are addicted to EGFR/KRAS/MAPK signaling. For example, mutations in KRAS, BRAF and other MAPK pathway components confer intrinsic or acquired resistance to anti-EGFR therapy. However, a significant proportion of acquired resistance cases have remained unexplained. ARID1A mutations are found in approximately 11% of CRC tumors, but a connection between ARID1A mutations and EGFR/MAPK signaling activation in CRC has not been previously suspected. By leveraging the genomic biomarker data collected from 333 patients at baseline and at progression who participated in the CALGB/SWOG 80405 trial, we found that mutations in ARID1A, a key component of SWI/SNF complex, were enriched in the cell free DNA of 6/16 of the patients whose tumors had become resistant to anti-EGFR therapy with ARID1A mutations detected at either timepoint (adj. p = 0.03, OR = 0.09, two-tailed fisher's exact test). In contrast, there was no evidence of enriched ARID1A mutations in patients treated with bevacizumab. To investigate the potential role of a broader ARID1A deficiency phenotype in resistance to cetuximab therapy, we developed an ARID1A mutant-like signature from TCGA that captures the transcriptional profile characteristic of ARID1A mutants. Using this signature to stratify CALGB patients based on gene expression data collected on tissue at diagnosis, we also found patients with an ARID1A mutant-like gene expression profile had worst outcome in patients treated with cetuximab than bevacizumab with adjustment for established clinical variables for both OS [p = 0.0002, hazard ratio (HR) 6.2, 95% confidence interval (CI) 2.4-16], and PFS [p = 0.0008, HR 4.7 (1.9 -12)], suggesting that ARID1A mutations may be also a mechanism of intrinsic resistance to anti-EGFR therapies. Gene expression analysis demonstrated that ARID1A deficiency leads to re-activation of an EGFR-like signature, suggesting reactivation of this pathway as a possible mechanism of resistance. Furthermore, CRISPR knockout of ARID1A in the cetuximab-sensitive CRC cell line NCI-H508 conferred elevated MAPK signaling relative to parental line and resistance to cetuximab in culture. Consistent with these findings, we also observed strong mutual exclusivity between ARID1A mutations and mutations in the EGFR/MAPK signaling pathway in more than 40,000 lung and colorectal cancer patients profiled in the FoundationCore® database. Strikingly, in lung cancers where EGFR mutations structural variants (SV) are more prevalent, EGFR SV was the top mutually exclusive alteration with ARID1A mutations in lung cancers. Of 5980 lung cancer patients with ARID1A and/or EGFR SVs, only 100 patients (1.7%) had both SVs. Taken together, our data suggest that ARID1A loss-of-function mutations may promote resistance to cetuximab by driving an EGFR-like transcription program in the absence of ligand-dependent activation of EGFR. Our results suggest that ARID1A defects could be potentially used as an exclusion biomarker for cetuximab treatment decisions, and they provide a rationale for exploring therapeutic MAPK inhibition in ARID1A mutant CRC patients.

Citation Format: Radia Marie Johnson, Xueping Qu, Joshua Thomas, Yvonne Kschonsak, Ling-Yuh Huw, Fang-Shu Ou, Ethan Sokol, Nnamdi Ihuegbu, Oliver Zill, Omar Kabbarah, Anneleen Daemen, Richard Bourgon, Alan Venook, Federico Innocenti, Heinz-Josef Lenz, Felipe de Sousa e Melo, Carlos Bais. ARID1A mutations induce an EGFR-like gene expression signature and confer intrinsic and acquired resistance to cetuximab treatment in first line metastatic CRC [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-063.

Abstract 463: Integrated digital pathology and transcriptome analysis identifies molecular mediators of T cell exclusion in ovarian cancer

Background:

Close proximity between cytotoxic T lymphocytes and tumor cells is required for effective immunotherapy. Three tumor-immune (TI) phenotypes, infiltrated, excluded and desert, have been previously described based on the infiltration patterns of CD8+ T cells. However, no quantitative methods exist to define these phenotypes robustly in human solid tumors. Importantly, the molecular features and mechanisms determining these phenotypes are not well understood. Here we report a novel integrated approach to classify and functionally dissect TI phenotypes in human ovarian cancer.

Methods:

CD8 IHC and RNAseq analysis were performed on 370 ovarian tumors from the ICON7 phase III clinical trial, a front-line trial testing the addition of bevacizumab to chemotherapies. A digital image analysis algorithm was developed to quantify the quantity and spatial distribution of CD8+ T cells. Coupling digital pathology with transcriptome analysis, a random forest machine learning algorithm was applied to identify genes associated with these two metrics using a training set (n=155). A gene expression-based classifier was developed for classifying TI phenotypes and validated using testing sets from ICON7 trial and a vendor collection. Functional characterization of key mediators promoting T cell exclusion were carried out by integrating in situ, in vitro and ex vivo analyses on ovarian tumor tissues, cancer associated fibroblasts (CAFs) and ovarian cancer cell lines. Anti-tumor activity of TGFβ blockade in combination with anti-PD-L1 was evaluated in the mouse BrKras ovarian cancer model in FVB background.

Results:

Integrating digital pathology and machine learning on large ovarian tumor cohorts, we developed and validated a 157-gene molecular classifier. We show the TI phenotypes are of biological and clinical importance in ovarian cancer. Two hallmarks of T cell exclusion were identified: 1) loss of MHC I on tumor cells and 2) upregulation of TGFβ/stromal activities. We show that MHC I in ovarian cancer cells is likely regulated by epigenetic mechanisms and TGFβ is a key mediator of T cell exclusion. TGFβ reduced MHC I expression in ovarian cancer cells and induced extracellular matrix and immunosuppressive molecules in human primary fibroblasts. Finally, we demonstrated that combining anti-TGFβ and anti-PD-L1 in the BrKras mouse model improved the anti-tumor efficacy and survival.

Conclusion:

This study provided the first systematic and in-depth characterization of the molecular features and mechanisms underlying the tumor-immune phenotypes in human ovarian cancer. We illuminated a multi-faceted role of TGFβ in mediating crosstalk between tumor cells and CAFs to shape the tumor-immune contexture. Our findings support that targeting the TGFβ pathway represents a promising therapeutic strategy to overcome T cell exclusion and optimize response to cancer immunotherapy.

Citation Format: Melanie Desbois, Akshata Udyavar, Lisa Ryner, Cleopatra Kozlowski, Yinghui Guan, Milena Dürrbaum, Shan Lu, Jean-Philippe Fortin, Hartmut Koeppen, James Ziai, Ching-Wei Chang, Amy Lo, Shilpa Keerthivasan, Marie Plante, Richard Bourgon, Carlos Bais, Priti Hegde, Anneleen Daemen, Shannon Turley, Yulei Wang. Integrated digital pathology and transcriptome analysis identifies molecular mediators of T cell exclusion in ovarian cancer [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 463.

Final Overall Survival of a Randomized Trial of Bevacizumab for Primary Treatment of Ovarian Cancer

PURPOSE

We report the final, protocol-specified analysis of overall survival (OS) in GOG-0218, a phase III, randomized trial of bevacizumab in women with newly diagnosed ovarian, fallopian tube, or primary peritoneal carcinoma.

METHODS

A total of 1,873 women with incompletely resected stage III to IV disease were randomly assigned 1:1:1 to six 21-day cycles of intravenous carboplatin (area under the concentration v time curve 6) and paclitaxel (175 mg/m²) versus chemotherapy plus concurrent bevacizumab (15 mg/kg, cycles 2 to 6) versus chemotherapy plus concurrent and maintenance bevacizumab (cycles 2 to 22). Inclusion criteria included a Gynecologic Oncology Group performance status of 0 to 2 and no history of clinically significant vascular events or evidence of intestinal obstruction. OS was analyzed in the intention-to-treat population. A total of 1,195 serum and/or tumor specimens were sequenced for BRCA1/2 and damaging mutations in homologous recombination repair (HRR) genes. Intratumoral microvessel density was studied using CD31 immunohistochemistry.

RESULTS

Median follow-up was 102.9 months. Relative to control (n = 625), for patients receiving bevacizumab-concurrent (n = 625), the hazard ratio (HR) of death was 1.06 (95% CI, 0.94 to 1.20); for bevacizumab-concurrent plus maintenance (n = 623), the HR was 0.96 (95% CI, 0.85 to 1.09). Disease-specific survival was not improved in any arm. No survival advantage was observed after censoring patients who received bevacizumab at crossover or as second line. Median OS for stage IV bevacizumab-concurrent plus maintenance was 42.8 v 32.6 months for stage IV control (HR, 0.75; 95% CI, 0.59 to 0.95). Relative to wild type, the HR for death for BRCA1/2 mutated carcinomas was 0.62 (95% CI, 0.52 to 0.73), and for non-BRCA1/2 HRR, the HR was 0.65 (95% CI, 0.51 to 0.85). BRCA1/2, HRR, and CD31 were not predictive of bevacizumab activity.

CONCLUSION

No survival differences were observed for patients who received bevacizumab compared with chemotherapy alone. Testing for BRCA1/2 mutations and homologous recombination deficiency is essential.

Tumor Microvessel Density as a Potential Predictive Marker for Bevacizumab Benefit: GOG-0218 Biomarker Analyses

Background

Combining bevacizumab with frontline chemotherapy statistically significantly improved progression-free survival (PFS) but not overall survival (OS) in the phase III GOG-0218 trial. Evaluation of candidate biomarkers was an exploratory objective.

Methods

Patients with stage III (incompletely resected) or IV ovarian cancer were randomly assigned to receive six chemotherapy cycles with placebo or bevacizumab followed by single-agent placebo or bevacizumab. Five candidate tumor biomarkers were assessed by immunohistochemistry. The biomarker-evaluable population was categorized into high or low biomarker-expressing subgroups using median and quartile cutoffs. Associations between biomarker expression and efficacy were analyzed. All statistical tests were two-sided.

Results

The biomarker-evaluable population (n = 980) comprising 78.5% of the intent-to-treat population had representative baseline characteristics and efficacy outcomes. Neither prognostic nor predictive associations were seen for vascular endothelial growth factor (VEGF) receptor-2, neuropilin-1, or MET. Higher microvessel density (MVD; measured by CD31) showed predictive value for PFS (hazard ratio [HR] for bevacizumab vs placebo = 0.40, 95% confidence interval [CI] = 0.29 to 0.54, vs 0.80, 95% CI = 0.59 to 1.07, for high vs low MVD, respectively, P interaction = .003) and OS (HR = 0.67, 95% CI = 0.51 to 0.88, vs 1.10, 95% CI = 0.84 to 1.44, P interaction = .02). Tumor VEGF-A was not predictive for PFS but showed potential predictive value for OS using a third-quartile cutoff for high VEGF-A expression.

Conclusions

These retrospective tumor biomarker analyses suggest a positive association between density of vascular endothelial cells (the predominant cell type expressing VEGF receptors) and tumor VEGF-A levels and magnitude of bevacizumab effect in ovarian cancer. The potential predictive value of MVD (CD31) and tumor VEGF-A is consistent with a mechanism of action driven by VEGF-A signaling blockade.

Tumor Microvessel Density as a Potential Predictive Marker for Bevacizumab Benefit: GOG-0218 Biomarker Analyses

Background

Combining bevacizumab with frontline chemotherapy statistically significantly improved progression-free survival (PFS) but not overall survival (OS) in the phase III GOG-0218 trial. Evaluation of candidate biomarkers was an exploratory objective.

Methods

Patients with stage III (incompletely resected) or IV ovarian cancer were randomly assigned to receive six chemotherapy cycles with placebo or bevacizumab followed by single-agent placebo or bevacizumab. Five candidate tumor biomarkers were assessed by immunohistochemistry. The biomarker-evaluable population was categorized into high or low biomarker-expressing subgroups using median and quartile cutoffs. Associations between biomarker expression and efficacy were analyzed. All statistical tests were two-sided.

Results

The biomarker-evaluable population (n = 980) comprising 78.5% of the intent-to-treat population had representative baseline characteristics and efficacy outcomes. Neither prognostic nor predictive associations were seen for vascular endothelial growth factor (VEGF) receptor-2, neuropilin-1, or MET. Higher microvessel density (MVD; measured by CD31) showed predictive value for PFS (hazard ratio [HR] for bevacizumab vs placebo = 0.40, 95% confidence interval [CI] = 0.29 to 0.54, vs 0.80, 95% CI = 0.59 to 1.07, for high vs low MVD, respectively, P interaction = .003) and OS (HR = 0.67, 95% CI = 0.51 to 0.88, vs 1.10, 95% CI = 0.84 to 1.44, P interaction = .02). Tumor VEGF-A was not predictive for PFS but showed potential predictive value for OS using a third-quartile cutoff for high VEGF-A expression.

Conclusions

These retrospective tumor biomarker analyses suggest a positive association between density of vascular endothelial cells (the predominant cell type expressing VEGF receptors) and tumor VEGF-A levels and magnitude of bevacizumab effect in ovarian cancer. The potential predictive value of MVD (CD31) and tumor VEGF-A is consistent with a mechanism of action driven by VEGF-A signaling blockade.

Tumor Microvessel Density as a Potential Predictive Marker for Bevacizumab Benefit: GOG-0218 Biomarker Analyses

Background

Combining bevacizumab with frontline chemotherapy statistically significantly improved progression-free survival (PFS) but not overall survival (OS) in the phase III GOG-0218 trial. Evaluation of candidate biomarkers was an exploratory objective.

Methods

Patients with stage III (incompletely resected) or IV ovarian cancer were randomly assigned to receive six chemotherapy cycles with placebo or bevacizumab followed by single-agent placebo or bevacizumab. Five candidate tumor biomarkers were assessed by immunohistochemistry. The biomarker-evaluable population was categorized into high or low biomarker-expressing subgroups using median and quartile cutoffs. Associations between biomarker expression and efficacy were analyzed. All statistical tests were two-sided.

Results

The biomarker-evaluable population (n = 980) comprising 78.5% of the intent-to-treat population had representative baseline characteristics and efficacy outcomes. Neither prognostic nor predictive associations were seen for vascular endothelial growth factor (VEGF) receptor-2, neuropilin-1, or MET. Higher microvessel density (MVD; measured by CD31) showed predictive value for PFS (hazard ratio [HR] for bevacizumab vs placebo = 0.40, 95% confidence interval [CI] = 0.29 to 0.54, vs 0.80, 95% CI = 0.59 to 1.07, for high vs low MVD, respectively, P interaction = .003) and OS (HR = 0.67, 95% CI = 0.51 to 0.88, vs 1.10, 95% CI = 0.84 to 1.44, P interaction = .02). Tumor VEGF-A was not predictive for PFS but showed potential predictive value for OS using a third-quartile cutoff for high VEGF-A expression.

Conclusions

These retrospective tumor biomarker analyses suggest a positive association between density of vascular endothelial cells (the predominant cell type expressing VEGF receptors) and tumor VEGF-A levels and magnitude of bevacizumab effect in ovarian cancer. The potential predictive value of MVD (CD31) and tumor VEGF-A is consistent with a mechanism of action driven by VEGF-A signaling blockade.

Abstract 1773: A baseline IFNG gene expression signature correlates with clinical outcomes in durvalumab-treated advanced NSCLC cancer patients

Durvalumab (D) is a human IgG1 monoclonal antibody which inhibits PDL1 binding to PD-1 and CD80, restoring antitumor immunity. In D-treated (tx) NSCLC patients (pts), we previously reported high baseline levels of tumoral PD-L1 protein and IFNγ mRNA expression associated with improved ORRs, PFS and OS. Here, a gene expression signature of baseline tumors associates with improved outcomes on D. CP1108/NCT01693562 was a nonrandomized phase 1/2 trial evaluating D in advanced previously tx NSCLC or other solid tumors. By 29APR2016, 304 NSCLC pts received 10 mg/kg Q2W of D ≤12 months with median 18.8 months follow up. RNA sequencing of frozen biopsies was conducted on 97 NSCLC tumors of sufficient quality with matched IHC for tumoral PD-L1 on 92 fresh or archival biopsies. Among 21 pre-identified immune-related genes, mRNAs for IFNG, LAG3, CXCL9, and PDL1 individually correlated best with outcomes in NSCLC after adjustment for sex, age, prior therapy, histology, ECOG and smoking. A signature was developed as mean mRNA levels of the four genes; signatures &gt;upper tertile were IFNG signature positive (IFNGS+). Analysis was performed on NSCLC, then applied to 30 available urothelial bladder cancer (UBC) biopsies. NSCLC with ≥25% tumor cells stained for PD-L1 at any intensity were PD-L1+. 29 NSCLC had pre/post-treatment tumors for mRNA analysis. KM and Cox PH models were used. IFNGS+ D-tx NSCLC pts had higher ORR, median PFS and OS compared to PDL1+, PDL1-, and IFNGS- pts (Table 1); IFNGS+ UBC D-tx pts also correlated with these outcomes. Following D treatment, IFNGS was induced in NSCLC pts (FC=2; p=0.0046) regardless of clinical response. High levels of pre-treatment IFNGS in NSCLC pts associated with greater benefit from D. D induces IFNGS within the tumor microenvironment. Observations from other tumor types will be presented. Table 1. Clinical outcomes by IFNGS or PD-L1 status

# Pts (# events [OS;PFS])ORR % (95% CI)Median OS months (95% CI)OS adjusted HRa; pMedian PFS months (95% CI)PFS adjusted HRa; pNSCLCIFNGS+32 (16;21)37.5 (21.7,56.3)24.6 (10.3,NA)0.42; 0.00827.5 (3.6,NA)0.32; 0.00028IFNGS-65 (40;51)6.2 (2.0,15.8)6.5 (4.8,15.7)1.4 (1.4,2.6)PDL1 TPS&gt;=25%38 (18;25)28.9 (16.0,46.1)20.5 (6.6,NA)0.53; 0.07883.6 (1.7,14.6)0.60; 0.0823PDL1 TPS&lt;25%54 (35;43)7.4 (5.8,25.5)9.1 (5.4,21.1)1.5 (1.4,3.9)NR=Not Reached; NA=Not Applicable; aAdjusted for covariates. TPS= tumor proportion score Ventana SP263 assay

Citation Format: Brandon W. Higgs, Chris A. Morehouse, Katie Streicher, Philp Z. Brohawn, Keith Steele, Marlon Rebelatto, Fernanda Pilataxi, Carlos Bais, Li Shi, Xiaoping Jin, Joyce Antal, Ashok Gupta, Koustubh Ranade. A baseline IFNG gene expression signature correlates with clinical outcomes in durvalumab-treated advanced NSCLC cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1773. doi:10.1158/1538-7445.AM2017-1773

Abstract 3720: Biological and clinical relevance of PD-L1 expression in tumor and inflammatory cells in NSCLC

Background: High PD-L1 expression has been shown to be associated with improved clinical outcomes to anti-PD-1/L1 therapies in NSCLC and other indications. However, only a fraction of the PD-L1 high patients (pts) respond. PD-L1 can be induced by IFNG and expressed in tumor cells (TC) and inflammatory cells (IC). Improving our ability to predict patient benefit from anti-PD-1/L1 therapies requires a better understanding of associations between PD-L1 expression in TC and/or IC and outcome. Here we explore the relationship between patterns of IHC PD-L1 expression in TC and IC, gene expression, and clinical outcome.

Methods: CP1108/NCT01693562 was a nonrandomized phase 1/2 trial evaluating durvalumab in pts with advanced NSCLC or other solid tumors. As of 29 APR 2016, 368 previously treated NSCLC pts received durvalumab ≤12 months with a median 18.8 months follow up. Pts with ≥25% TC or IC were scored TC+ and/or IC+, respectively.

Results: TC+ PD-L1 pts (includes IC+ and IC- PD-L1 pts) had improved survival compared to TC- PD-L1 pts. TC+ and IC+ PD-L1 pts had: improved survival compared to TC+/IC-, TC-/IC+, or TC-/IC- PD-L1 pts. However, prevalence of TC+/IC+ was lower than TC+. Twenty-one genes significantly differed between TC+/IC+, TC+/IC-, TC-/IC+, and TC-/IC- PD-L1 patient subsets, the vast majority being well-known IFNG-inducible genes and mostly over-expressed in the TC+/IC+ subset.

Conclusions: TC+ and IC+ PD-L1 pts had the highest levels of IFNG-inducible gene expression, a key biological feature that distinguishes PD-L1 IHC positive from negative pts. Thus, in addition to PD-L1 IHC, the predictive value of IFNG should be investigated in additional relevant studies

Selection CriteriaPrevalence of Biomarker Positive BiomarkerPositive/negative median OSlog-rank pHRcox pTC+158/276 (57%)15.67/7.730.00910.690.046TC+/IC+70/276 (25%)25.63/8.377.46E-060.345.24E-05TC+/IC-88/276 (32%)10.5/13.970.0941.50.032TC-/IC+50/276 (18%)9.07/13.230.830.960.84TC-/IC-68/276 (25%)5.77/14.030.000841.660.012

All comers: median OS: 11.2 months (N=304)

Citation Format: Carlos Bais, Chris Morehouse, Brandon W. Higgs, Rebelatto Marlon, Keith Steele, Xiaoping Jin, Li Shi, Susana Korolevich, Ashok Gupta, Koustubh Ranade. Biological and clinical relevance of PD-L1 expression in tumor and inflammatory cells in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3720. doi:10.1158/1538-7445.AM2017-3720

Association of early reduction in circulating tumor DNA (ctDNA) with improved progression-free survival (PFS) and overall survival (OS) of patients (pts) with urothelial bladder cancer (UBC) treated with durvalumab (D)

11538

Background: Mutation variant allele frequencies (VAFs) in ctDNA indicate the frequency of cancer clones harboring the specific variant in the primary lesion and metastases, thus providing a surrogate for tumor burden. We previously reported that early reduction in VAF in ctDNA was associated with improved survival on durvalumab in NSCLC subjects. Here we replicated this association in UBC pts treated with durvalumab. Methods: CP1108/NCT01693562 was a nonrandomized phase 1/2 trial evaluating D in pts with advanced UBC or other solid tumors. By 24OCT2016, 103 UBC pts received 10 mg/kg Q2W of D with median 8.4 mos follow up. A panel of 70 genes was assayed for DNA variants using the Guardant360 cancer panel in plasma ctDNA from 33 UBC pts pre-treatment and 29 pts pre and 6 wks on-treatment. The mean VAF pre or on treatment of patient single nucleotide variants (SNVs) and insertion/deletions was correlated with clinical outcomes. Objective response rate (ORR) was calculated according to RECIST v1.1 and a Cox proportional hazard ratio (HR) was calculated adjusting for baseline ECOG, sex, age, and smoking status. Results: Complete and partial responders (CR/PRs) showed a significant decrease (Δ = -2.4%, p = 0.02) in ctDNA mean VAF post-treatment with D (i.e. reduction in tumor burden) compared to an increase in mean VAF (i.e. increase in tumor burden) in progressive disease (PD) pts (Δ = +2.7%, p = 0.31). This correlation was also observed in total mutation count in CR/PR (Δ = -4.6, p = 0.003) compared to PD pts (Δ = +2.8, p = 0.44). Pts with a decrease in ctDNA VAF at week 6 had longer median PFS (9.3 mos, 95%CI = [3.0, not reached(NR)] and OS (median NR, 95% CI = [20.3,NR]) compared to those with an increase in VAF (median PFS = 1.4 mos, 95%CI = [1.3,NR];HR = 0.29; p = 0.05 and median OS = 8.2 mos, 95% CI = [2.3,NR]; HR = 0.12; adjusted p = 0.04). DCR was 85%/14% for pts with a decrease/increase in VAF (p = 0.002). Conclusions: CtDNA VAFs were reduced in responders but not non-responders after six wks of D. A decrease in VAFs 6 wks following treatment with D correlated with longer PFS and OS, suggesting utility as an early indicator of clinical benefit. Clinical trial information: NCT01693562.

Biologic and clinical relevance of an IFNG mRNA signature (IFNGS) and PD-L1 protein expression in tumor and immune cells in urothelial cancer (UC) patients (pts) treated with durvalumab (D)

3037

Background: PD-L1 can be induced by IFNG in tumor cells (TC) and immune cells (IC). TC PD-L1 expression prevalence in UC is low and the relevance of scoring TC (in addition to IC) is not fully understood. We recently reported a positive correlation between high levels of an IFNGS and outcome in a cohort of 30 UC pts treated with D. Here, we assessed the potential predictive value of the IFNGS in an additional 32 pts (total N = 62) and further explored the relationship between the IFNGS and TC and/or IC PD-L1 IHC expression patterns. Methods: Study CP1108 was a phase 1/2 trial evaluating D in pts with solid tumors; 191 UC pts received 10 mg/kg D with median follow up of 8.4 mo. 144 of these pts have available ORR and PD-L1 data and 62 pts have ORR, PD-L1 and IFNGS data. Pts with ≥25% TC or IC were scored as PD-L1 high (TC+ or IC+). Pts within the top tertile of IFNGS ( LAG3, PDL1, CXCL9, and IFNG mRNAs) tumor expression were scored positive. Cox proportional hazards models were used adjusting for age, gender, ECOG, smoking status, line of therapy, and liver metastasis at baseline. ORR was evaluated using RECIST v1.1. Results: IFNGS+ pts had increased ORR (45 vs 16%) and improved PFS (adj HR 0.3; p = 0.005) and OS (adj HR 0.18; p = 0.016) over IFNGS- pts. IFNGS expression was significantly higher in pts who were PD-L1 high (TC+/IC+) compared with TC-/IC- (low/negative) pts (mean IFNGS expression 3.5 vs 1.1; p = 0.0155) and also in TC+ or IC+ vs TC-/IC- (mean IFNGS 2.2 vs 1.1; p = 0.000127). TC-/IC+ and TC+/IC- groups had a mean IFNGS expression of 2 and 2.2 respectively. ORR in all 1108 UC pts with available IHC and ORR data (N = 144) was 29% for TC+/- pts, 36% in TC-/IC+ pts, and 7% in the TC-/IC- pts. Conclusions: IFNGS predicted improved outcomes in a cohort of 62 2L+ UC pts treated with D. TC-/IC- PD-L1 pts had lowest levels of IFNGS expression. Observations that TC+ (and IC+) pts contribute to IFNGS enrichment and that TC+/IC-, and TC-/IC+ pts have increased response vs TC-/IC-pts provides rationale for TC+ inclusion (in addition to IC+) in the SP263 PD-L1 scoring algorithm for UC. IFNGS is an additional potential predictive biomarker in UC pts that warrants further investigation.

Randomized, Double-Blind, Placebo-Controlled, Multicenter Phase II Study of Onartuzumab Plus Bevacizumab Versus Placebo Plus Bevacizumab in Patients With Recurrent Glioblastoma: Efficacy, Safety, and Hepatocyte Growth Factor and O6-Methylguanine–DNA Methyltransferase Biomarker Analyses

Purpose

Bevacizumab regimens are approved for the treatment of recurrent glioblastoma in many countries. Aberrant mesenchymal-epithelial transition factor (MET) expression has been reported in glioblastoma and may contribute to bevacizumab resistance. The phase II study GO27819 investigated the monovalent MET inhibitor onartuzumab plus bevacizumab (Ona + Bev) versus placebo plus bevacizumab (Pla + Bev) in recurrent glioblastoma.

Methods

At first recurrence after chemoradiation, bevacizumab-naïve patients with glioblastoma were randomly assigned 1:1 to receive Ona (15 mg/kg, once every 3 weeks) + Bev (15 mg/kg, once every 3 weeks) or Pla + Bev until disease progression. The primary end point was progression-free survival by response assessment in neuro-oncology criteria. Secondary end points were overall survival, objective response rate, duration of response, and safety. Exploratory biomarker analyses correlated efficacy with expression levels of MET ligand hepatocyte growth factor, O6-methylguanine–DNA methyltransferase promoter methylation, and glioblastoma subtype.

Results

Among 129 patients enrolled (Ona + Bev, n = 64; Pla + Bev, n = 65), baseline characteristics were balanced. The median progression-free survival was 3.9 months for Ona + Bev versus 2.9 months for Pla + Bev (hazard ratio, 1.06; 95% CI, 0.72 to 1.56; P = .7444). The median overall survival was 8.8 months for Ona + Bev and 12.6 months for Pla + Bev (hazard ratio, 1.45; 95% CI, 0.88 to 2.37; P = .1389). Grade ≥ 3 adverse events were reported in 38.5% of patients who received Ona + Bev and 35.9% of patients who received Pla + Bev. Exploratory biomarker analyses suggested that patients with high expression of hepatocyte growth factor or unmethylated O6-methylguanine–DNA methyltransferase may benefit from Ona + Bev.

Conclusion

There was no evidence of further clinical benefit with the addition of onartuzumab to bevacizumab compared with bevacizumab plus placebo in unselected patients with recurrent glioblastoma in this phase II study; however, further investigation into biomarker subgroups is warranted.

Abstract P5-08-18: Biomarker (BM) results from MERiDiAN, a double-blind placebo (PLA)-controlled randomized phase 3 trial of 1st-line paclitaxel (PAC) with or without bevacizumab (BEV) for HER2-negative metastatic breast cancer (mBC)

Background: In the MERiDiAN trial, progression-free survival (PFS) was significantly improved with the addition of BEV to 1st-line PAC for mBC in both the ITT population and the subgroup with high baseline plasma (p) vascular endothelial growth factor (VEGF)-A, meeting both co-primary objectives. However, a predictive effect of pVEGF-A was not seen (PFS pVEGF-A-by-treatment interaction p=0.46; secondary endpoint). We report exploratory analyses of additional candidate BMs.

Methods: Patients (pts) with HER2-negative mBC previously untreated with chemotherapy for mBC were randomized to receive PAC (90 mg/m2, days 1, 8 & 15 q4w) combined with either PLA or BEV 10 mg/kg q2w until disease progression or unacceptable toxicity. Plasma, blood and archival tumor sampling was mandatory. The BM-evaluable population (BEP) comprised all ITT pts with a baseline sample for ≥1 BM. Prespecified exploratory BM analyses included: tumor (t) CD31 (marker of microvascular density) and tVEGF-A (molecular target of BEV) by immunohistochemistry; tPAM50 gene expression; and pVEGF receptor (R)-2 by ELISA. For CD31, tVEGF-A and pVEGFR-2 analyses, the BEP was dichotomized using the median of each BM as the cutoff between low and high subgroups. BEV effect on PFS was assessed within these subgroups (unstratified analyses). Similar subgroup analyses were done for each tPAM50 molecular subtype. No adjustment was made for multiplicity of testing as the analyses were exploratory.

Results: The BEP included 467 (97%) of the 481 randomized pts. There was no correlation between CD31, tVEGF-A and pVEGFR-2. Correlations between BMs and PFS are shown below. The hazard ratio (HR) point estimate for BEV effect was lower in luminal B (0.59) than luminal A (0.96) or other smaller tPAM50 subgroups, but 95% CIs overlapped. pVEGFR-2 showed borderline significance for predictive potential using the median (10.2 ng/mL) as the cutoff. In further exploratory analyses using the 1st quartile (Q1; 8.7 ng/mL) as the cutoff, the PFS HR was 1.19 (95% CI 0.75–1.89) in the low (≤Q1) subgroup vs 0.60 (95% CI 0.46–0.79) in the high (&gt;Q1) subgroup (interaction p=0.01).

BMSubgroupNo. of events/ptsMedian PFS, mosPFS HR (95% Wald CI)Interaction p-value  PAC–PLAPAC–BEVPAC–PLAPAC–BEV  tPAM50 (N=421)Luminal A65/10367/10610.911.20.96 (0.68-1.35)Not applicable Luminal B46/6332/569.011.00.59 (0.38-0.93)  HER2 enriched8/119/105.58.30.88 (0.33-2.32)  Basal like29/3727/355.68.50.67 (0.39-1.14) tCD31 (N=410)Low69/9969/1067.610.80.71 (0.51-0.99)0.40 High78/11164/949.211.00.87 (0.62-1.22) tVEGF-A (N=434)Low78/10777/1107.411.00.68 (0.49-0.93)0.23 High76/11165/1069.210.90.89 (0.64-1.24) pVEGFR-2 (N=436)Low70/10773/1119.210.60.90 (0.64-1.25)0.06 High83/10968/1097.912.20.58 (0.42-0.81) 

Conclusions: Of the 4 candidate BMs explored here, potential predictive value was suggested only for pVEGFR-2. Correlations between pVEGFR-2 levels and outcome have been observed in previous retrospective analyses of breast cancer trials. However, similar levels in healthy donors and breast cancer pts, as well as the narrow dynamic range, may limit the utility of pVEGFR-2 as a potential predictive BM for BEV efficacy.

Citation Format: Das Thakur M, Bais C, Estay I, Vaidyanathan R, O'Shaughnessy J, Cameron D, Hubeaux S, Quah C, Miles D. Biomarker (BM) results from MERiDiAN, a double-blind placebo (PLA)-controlled randomized phase 3 trial of 1st-line paclitaxel (PAC) with or without bevacizumab (BEV) for HER2-negative metastatic breast cancer (mBC). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-08-18.

Abstract S1-01: Analysis of molecular prognostic factors associated with tumor immune and stromal microenvironment in BEATRICE, an open-label phase 3 trial in early triple-negative breast cancer (eTNBC)

Background: TNBC is a mutationally complex heterogeneous breast cancer subtype. In BEATRICE, adding bevacizumab to standard adjuvant chemotherapy for eTNBC improved neither invasive disease-free survival (IDFS; primary endpoint) nor overall survival (OS) [Cameron 2013; Bell SABCS 2014]. We explored prognostic effects of tumor-associated immune and stromal gene signatures.

Methods: Gene expression (RNA) was assessed in pretreatment archival tumor tissue using an 800-gene nanostring platform. Given the low event rates and lack of bevacizumab effect in BEATRICE, treatment arms were pooled. The biomarker-evaluable population (BEP; all patients with an evaluable biomarker sample and ≥1 postbaseline efficacy assessment) was dichotomized using median gene expression level as the cutoff. Prognostic associations between IDFS/OS and prespecified candidate gene sets/de novo identified clusters were assessed using univariate Cox proportional hazards models.

Results: Baseline characteristics and efficacy were similar in the BEP (988/2591 randomized pts; 38%) and the overall study population. In hierarchical cluster analysis based exclusively on immune gene expression, immune genes were enriched in 33% of samples, intermediate in 38%, and weak in 28%. Further characterization suggested differential prognostic value of distinct immune and stromal cell gene sets (Table). A significant prognostic effect for IDFS and OS was seen for CD8 effector T cell (Teff) and regulatory T cell (Treg) gene signatures, but not for the Teff:Treg ratio. A less pronounced positive prognostic effect was seen for other gene sets representing immune cells, including macrophages, CD4 T cells, and B cells (data not shown). Activated T helper (Th)-1 cell-derived chemokines and negative immune modulators of T cell activity (eg PD-L1) were highly prognostic for IDFS and OS. Both the cytokine IL-8 and ESM1 (target of VEGF-A pathway activation) were associated with worse IDFS and OS. No association was seen between outcome and markers for classic microvasculature (CD31, CD34), cancer-associated fibroblasts (FAP, BGN, DCN), VEGF-A, or VEGF-C.

 IDFSOSGene signatureHR (95% CI)Interaction p-valueHR (95% CI)Interaction p-valueTeff0.40 (0.28-0.57)7.2x10-70.29 (0.17-0.49)4.2x10-6Treg0.38 (0.26-0.54)1.6x10-70.23 (0.13-0.40)2.9x10-7Teff:Treg ratio0.80 (0.58-1.12)0.20.89 (0.57-1.39)0.6Th10.45 (0.31-0.64)8.1x10-60.43 (0.27-0.70)5.8x10-4PD-L10.42 (0.29-0.60)1.8x10-60.24 (0.14-0.41)3.4x10-7IL-81.48 (1.06-2.08)0.0221.89 (1.18-3.01)0.0076ESM11.73 (1.23-2.43)0.00172.22 (1.38-3.58)0.001

Conclusions: These molecular gene signature analyses in eTNBC confirm that markers of cytotoxic CD8 T cells are associated with good prognosis. This is the first report of a positive prognostic effect of regulatory T cell markers, immune checkpoint modulators, and macrophage-associated markers in the adjuvant TNBC setting. High VEGF-A activity, but not its expression, was associated with worse prognosis. The strong prognostic effect of immune checkpoint modulators suggests equilibrium between cytotoxic T cells and their inhibitors in eTNBC, supporting further exploration of immune checkpoint inhibitors in this therapeutic context.

Citation Format: Molinero L, Yu J, Li C, Deurloo R, Dent RA, Bell R, Brown J, Parmar M, Toi M, Suter T, Steger G, Pivot X, Mackey J, Jackisch C, Hall P, Hegde P, Bais C, Cameron D. Analysis of molecular prognostic factors associated with tumor immune and stromal microenvironment in BEATRICE, an open-label phase 3 trial in early triple-negative breast cancer (eTNBC). [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S1-01.

Patients With Proneural Glioblastoma May Derive Overall Survival Benefit From the Addition of Bevacizumab to First-Line Radiotherapy and Temozolomide: Retrospective Analysis of the AVAglio Trial

PURPOSE

The AVAglio (Avastin in Glioblastoma) and RTOG-0825 randomized, placebo-controlled phase III trials in newly diagnosed glioblastoma reported prolonged progression-free survival (PFS), but not overall survival (OS), with the addition of bevacizumab to radiotherapy plus temozolomide. To establish whether certain patient subgroups derived an OS benefit from the addition of bevacizumab to first-line standard-of-care therapy, AVAglio patients were retrospectively evaluated for molecular subtype, and bevacizumab efficacy was assessed for each patient subgroup.

PATIENTS AND METHODS

A total of 349 pretreatment specimens (bevacizumab arm, n = 171; placebo arm, n = 178) from AVAglio patients (total, N = 921) were available for biomarker analysis. Samples were profiled for gene expression and isocitrate dehydrogenase 1 (IDH1) mutation status and classified into previously identified molecular subtypes. PFS and OS were assessed within each subtype.

RESULTS

A multivariable analysis accounting for prognostic covariates revealed that bevacizumab conferred a significant OS advantage versus placebo for patients with proneural IDH1 wild-type tumors (17.1 v 12.8 months, respectively; hazard ratio, 0.43; 95% CI, 0.26 to 0.73; P = .002). This analysis also revealed an interaction between the proneural subtype biomarker and treatment arm (P = .023). The group of patients with mesenchymal and proneural tumors derived a PFS benefit from bevacizumab compared with placebo; however, this translated to an OS benefit in the proneural subset only.

CONCLUSION

Retrospective analysis of AVAglio data suggests that patients with IDH1 wild-type proneural glioblastoma may derive an OS benefit from first-line bevacizumab treatment. The predictive value of the proneural subtype observed in AVAglio should be validated in an independent data set.

Upregulation of Periostin and Reactive Stroma Is Associated with Primary Chemoresistance and Predicts Clinical Outcomes in Epithelial Ovarian Cancer

PURPOSE

Up to one third of ovarian cancer patients are intrinsically resistant to platinum-based treatment. However, predictive and therapeutic strategies are lacking due to a poor understanding of the underlying molecular mechanisms. This study aimed to identify key molecular characteristics that are associated with primary chemoresistance in epithelial ovarian cancers.

EXPERIMENTAL DESIGN

Gene expression profiling was performed on a discovery set of 85 ovarian tumors with clinically well-defined response to chemotherapies as well as on an independent validation dataset containing 138 ovarian patients from the chemotreatment arm of the ICON7 trial.

RESULTS

We identified a distinct "reactive stroma" gene signature that is specifically associated with primary chemoresistant tumors and was further upregulated in posttreatment recurrent tumors. Immunohistochemistry (IHC) and RNA in situ hybridization (RNA ISH) analyses on three of the highest-ranked signature genes (POSTN, LOX, and FAP) confirmed that modulation of the reactive stroma signature genes within the peritumoral stromal compartments was specifically associated with the clinical chemoresistance. Consistent with these findings, chemosensitive ovarian cells grown in the presence of recombinant POSTN promoted resistance to carboplatin and paclitaxel treatment in vitro. Finally, we validated the reactive stroma signature in an independent dataset and demonstrated that a high POSTN expression level predicts shorter progression-free survival following first-line chemotherapy.

CONCLUSIONS

Our findings highlight the important interplay between cancer and the tumor microenvironment in ovarian cancer biology and treatment. The identified reactive stromal components in this study provide a molecular basis to the further development of novel diagnostic and therapeutic strategies for overcoming chemoresistance in ovarian cancer.

Glycosylation-dependent lectin-receptor interactions preserve angiogenesis in anti-VEGF refractory tumors

The clinical benefit conferred by vascular endothelial growth factors (VEGF)-targeted therapies is variable, and tumors from treated patients eventually reinitiate growth. Here, we identify a glycosylation-dependent pathway that compensates for the absence of cognate ligand and preserves angiogenesis in response to VEGF blockade. Remodeling of the endothelial cell (EC) surface glycome selectively regulated binding of galectin-1 (Gal1), which upon recognition of complex N-glycans on VEGFR2, activated VEGF-like signaling. Vessels within anti-VEGF-sensitive tumors exhibited high levels of α2-6-linked sialic acid, which prevented Gal1 binding. In contrast, anti-VEGF refractory tumors secreted increased Gal1 and their associated vasculature displayed glycosylation patterns that facilitated Gal1-EC interactions. Interruption of β1-6GlcNAc branching in ECs or silencing of tumor-derived Gal1 converted refractory into anti-VEGF-sensitive tumors, whereas elimination of α2-6-linked sialic acid conferred resistance to anti-VEGF. Disruption of the Gal1-N-glycan axis promoted vascular remodeling, immune cell influx and tumor growth inhibition. Thus, targeting glycosylation-dependent lectin-receptor interactions may increase the efficacy of anti-VEGF treatment.

Identification and analysis of in vivo VEGF downstream markers link VEGF pathway activity with efficacy of anti-VEGF therapies

PURPOSE

The aim of this study was to identify conserved pharmacodynamic and potential predictive biomarkers of response to anti-VEGF therapy using gene expression profiling in preclinical tumor models and in patients.

EXPERIMENTAL DESIGN

Surrogate markers of VEGF inhibition [VEGF-dependent genes or VEGF-dependent vasculature (VDV)] were identified by profiling gene expression changes induced in response to VEGF blockade in preclinical tumor models and in human biopsies from patients treated with anti-VEGF monoclonal antibodies. The potential value of VDV genes as candidate predictive biomarkers was tested by correlating high or low VDV gene expression levels in pretreatment clinical samples with the subsequent clinical efficacy of bevacizumab (anti-VEGF)-containing therapy.

RESULTS

We show that VDV genes, including direct and more distal VEGF downstream endothelial targets, enable detection of VEGF signaling inhibition in mouse tumor models and human tumor biopsies. Retrospective analyses of clinical trial data indicate that patients with higher VDV expression in pretreatment tumor samples exhibited improved clinical outcome when treated with bevacizumab-containing therapies.

CONCLUSIONS

In this work, we identified surrogate markers (VDV genes) for in vivo VEGF signaling in tumors and showed clinical data supporting a correlation between pretreatment VEGF bioactivity and the subsequent efficacy of anti-VEGF therapy. We propose that VDV genes are candidate biomarkers with the potential to aid the selection of novel indications as well as patients likely to respond to anti-VEGF therapy. The data presented here define a diagnostic biomarker hypothesis based on translational research that warrants further evaluation in additional retrospective and prospective trials.

Targeting placental growth factor/neuropilin 1 pathway inhibits growth and spread of medulloblastoma

Medulloblastoma is the most common pediatric malignant brain tumor. Although current therapies improve survival, these regimens are highly toxic and are associated with significant morbidity. Here, we report that placental growth factor (PlGF) is expressed in the majority of medulloblastomas, independent of their subtype. Moreover, high expression of PlGF receptor neuropilin 1 (Nrp1) correlates with poor overall survival in patients. We demonstrate that PlGF and Nrp1 are required for the growth and spread of medulloblastoma: PlGF/Nrp1 blockade results in direct antitumor effects in vivo, resulting in medulloblastoma regression, decreased metastasis, and increased mouse survival. We reveal that PlGF is produced in the cerebellar stroma via tumor-derived Sonic hedgehog (Shh) and show that PlGF acts through Nrp1-and not vascular endothelial growth factor receptor 1-to promote tumor cell survival. This critical tumor-stroma interaction-mediated by Shh, PlGF, and Nrp1 across medulloblastoma subtypes-supports the development of therapies targeting PlGF/Nrp1 pathway.

Phosphoproteomic analysis implicates the mTORC2-FoxO1 axis in VEGF signaling and feedback activation of receptor tyrosine kinases

The vascular endothelial growth factor (VEGF) signaling pathway plays a pivotal role in normal development and also represents a major therapeutic target for tumors and intraocular neovascular disorders. The VEGF receptor tyrosine kinases promote angiogenesis by phosphorylating downstream proteins in endothelial cells. We applied a large-scale proteomic approach to define the VEGF-regulated phosphoproteome and its temporal dynamics in human umbilical vein endothelial cells and then used siRNA (small interfering RNA) screens to investigate the function of a subset of these phosphorylated proteins in VEGF responses. The PI3K (phosphatidylinositol 3-kinase)-mTORC2 (mammalian target of rapamycin complex 2) axis emerged as central in activating VEGF-regulated phosphorylation and increasing endothelial cell viability by suppressing the activity of the transcription factor FoxO1 (forkhead box protein O1), an effect that limited cellular apoptosis and feedback activation of receptor tyrosine kinases. This FoxO1-mediated feedback loop not only reduced the effectiveness of mTOR inhibitors at decreasing protein phosphorylation and cell survival but also rendered cells more susceptible to PI3K inhibition. Collectively, our study provides a global and dynamic view of VEGF-regulated phosphorylation events and implicates the mTORC2-FoxO1 axis in VEGF receptor signaling and reprogramming of receptor tyrosine kinases in human endothelial cells.

Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development

The Caenorhabditis elegans vulva is an important paradigm for cell-cell interactions in animal development. The fates of six vulval precursor cells are patterned through the action of the epidermal growth factor receptor-mitogen-activated protein kinase (EGFR-MAPK) inductive signaling pathway, which specifies the 1 degrees fate, and the LIN-12/Notch lateral signaling pathway, which specifies the 2 degrees fate. Here, we provide evidence that the inductive signal is spatially graded and initially activates the EGFR-MAPK pathway in the prospective 2 degrees cells. Subsequently, this effect is counteracted by the expression of multiple new negative regulators of the EGFR-MAPK pathway, under direct transcriptional control of the LIN-12-mediated lateral signal.

Kaposi's sarcoma associated herpesvirus G protein-coupled receptor immortalizes human endothelial cells by activation of the VEGF receptor-2/ KDR

The G protein-coupled receptor oncogene (vGPCR) of the Kaposi's sarcoma (KS) associated herpesvirus (KSHV), an oncovirus implicated in angioproliferative neoplasms, induces angiogenesis by VEGF secretion. Accordingly, we found that expression of vGPCR in human umbilical vein endothelial cells (HUVEC) leads to immortalization with constitutive VEGF receptor-2/ KDR expression and activation. vGPCR immortalization was associated with anti-senescence mediated by alternative lengthening of telomeres and an anti-apoptotic response mediated by vGPCR constitutive signaling and KDR autocrine signaling leading to activation of the PI3K/AKT pathway. In the presence of the KS growth factor VEGF, this mechanism can sustain suppression of signaling by the immortalizing gene. We conclude that vGPCR can cause an oncogenic immortalizing event and recapitulate aspects of the KS angiogenic phenotype in human endothelial cells, pointing to this gene as a pathogenic determinant of KSHV.

Activated fibroblast growth factor receptor 3 is an oncogene that contributes to tumor progression in multiple myeloma

The t(4;14) translocation occurs frequently in multiple myeloma (MM) and results in the simultaneous dysregulated expression of 2 potential oncogenes, FGFR3 (fibroblast growth factor receptor 3) from der(14) and multiple myeloma SET domain protein/Wolf-Hirschhorn syndrome candidate gene 1 from der(4). It is now shown that myeloma cells carrying a t(4;14) translocation express a functional FGFR3 that in some cases is constitutively activated by the same mutations that cause thanatophoric dysplasia. As with activating mutations of K-ras and N-ras, which are reported in approximately 40% of patients with MM, activating mutations of FGFR3 occur during tumor progression. However, the constitutive activation of ras and FGFR3 does not occur in the same myeloma cells. Thus the activated forms of these proteins appear to share an overlapping role in tumor progression, suggesting that they also share the signaling cascade. Consistent with this prediction, it is shown that activated FGFR3-when expressed at levels similar to those seen in t(4;14) myeloma-is an oncogene that acts through the MAP kinase pathway to transform NIH 3T3 cells, which can then generate tumors in nude mice. Thus, FGFR3, when overexpressed in MM, may be not only oncogenic when stimulated by FGF ligands in the bone marrow microenvironment, but is also a target for activating mutations that enable FGFR3 to play a ras-like role in tumor progression.

The Kaposi's sarcoma-associated herpes virus G protein-coupled receptor up-regulates vascular endothelial growth factor expression and secretion through mitogen-activated protein kinase and p38 pathways acting on hypoxia-inducible factor 1alpha

The elucidation of the molecular mechanisms governing the transition from a nonangiogenic to an angiogenic phenotype is central for understanding and controlling malignancies. Viral oncogenes represent powerful tools for disclosing transforming mechanisms, and they may also afford the possibility of investigating the relationship between transforming pathways and angiogenesis. In this regard, we have recently observed that a constitutively active G protein-coupled receptor (GPCR) encoded by the Kaposi's sarcoma-associated herpes virus (KSHV)/human herpes virus 8 is oncogenic and stimulates angiogenesis by increasing the secretion of vascular endothelial growth factor (VEGF), which is a key angiogenic stimulator and a critical mitogen for the development of Kaposi's sarcoma. Here we show that the KSHV GPCR enhances the expression of VEGF by stimulating the activity of the transcription factor hypoxia-inducible factor (HIF)-1alpha, which activates transcription from a hypoxia response element within the 5'-flanking region of the VEGF promoter. Stimulation of HIF-1alpha by the KSHV GPCR involves the phosphorylation of its regulatory/inhibitory domain by the p38 and mitogen-activated protein kinase (MAPK) signaling pathways, thereby enhancing its transcriptional activity. Moreover, specific inhibitors of the p38 (SKF86002) and MAPK (PD98059) pathways are able to inhibit the activation of the transactivating activity of HIF-1alpha induced by the KSHV GPCR, as well as the VEGF expression and secretion in cells overexpressing this receptor. These findings suggest that the KSHV GPCR oncogene subverts convergent physiological pathways leading to angiogenesis and provide the first insight into a mechanism whereby growth factors and oncogenes acting upstream from MAPK, as well as inflammatory cytokines and cellular stresses that activate p38, can interact with the hypoxia-dependent machinery of angiogenesis. These results may also help to identify novel targets for the development of antiangiogenic therapies aimed at the treatment of Kaposi's sarcoma and other neoplastic diseases.

Inhibition of constitutive signaling of Kaposi's sarcoma-associated herpesvirus G protein-coupled receptor by protein kinases in mammalian cells in culture

Kaposi's sarcoma-associated herpesvirus (KSHV)/human herpesvirus 8, which is consistently present in tissues of patients with Kaposi's sarcoma and primary effusion lymphomas, contains a gene that encodes a G protein-coupled receptor (KSHV-GPCR). We recently showed that KSHV-GPCR exhibits constitutive signaling via activation of phosphoinositide-specific phospholipase C and stimulates cell proliferation and transformation. In this study, we determined whether normal cellular mechanisms could inhibit constitutive signaling by KSHV-GPCR and thereby KSHV-GPCR-stimulated proliferation. We show that coexpression of GPCR-specific kinases (GRKs) and activation of protein kinase C inhibit constitutive signaling by KSHV-GPCR in COS-1 monkey kidney cells and in mouse NIH 3T3 cells. Moreover, GRK-5 but not GRK-2 inhibits KSHV-GPCR-stimulated proliferation of rodent fibroblasts. These data provide evidence that cell regulatory pathways of receptor desensitization may be therapeutic targets in human diseases involving constitutively active receptors.

G-protein-coupled receptor of Kaposi's sarcoma-associated herpesvirus is a viral oncogene and angiogenesis activator

The Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) is a gamma-2 herpesvirus that is implicated in the pathogenesis of Kaposi's sarcoma and of primary effusion B-cell lymphomas (PELs). KSHV infects malignant and progenitor cells of Kaposi's sarcoma and PEL, it encodes putative oncogenes and genes that may cause Kaposi's sarcoma pathogenesis by stimulating angiogenesis. The G-protein-coupled receptor encoded by an open reading frame (ORF 74) of KSHV is expressed in Kaposi's sarcoma lesions and in PEL and stimulates signalling pathways linked to cell proliferation in a constitutive (agonist-independent) way. Here we show that signalling by this KSHV G-protein-coupled receptor leads to cell transformation and tumorigenicity, and induces a switch to an angiogenic phenotype mediated by vascular endothelial growth factor, an angiogenesis and Kaposi's-spindle-cell growth factor. We find that this receptor can activate two protein kinases, JNK/SAPK and p38MAPK, by triggering signalling cascades like those induced by inflammatory cytokines that are angiogenesis activators and mitogens for Kaposi's sarcoma cells and B cells. We conclude that the KSHV G-protein-coupled receptor is a viral oncogene that can exploit cell signalling pathways to induce transformation and angiogenesis in KSHV-mediated oncogenesis.