Enhanced Donor Antigen Presentation by B Cells Predicts Acute Cellular Rejection and Late Outcomes After Transplantation

Background

Enhanced B-cell presentation of donor alloantigen relative to presentation of HLA-mismatched reference alloantigen is associated with acute cellular rejection (ACR), when expressed as a ratio called the antigen presenting index (API) in an exploratory cohort of liver and intestine transplant (LT and IT) recipients.

Methods

To test clinical performance, we measured the API using the previously described 6-h assay in 84 LT and 54 IT recipients with median age 3.3 y (0.05-23.96). Recipients experiencing ACR within 60 d after testing were termed rejectors.

Results

We first confirmed that B-cell uptake and presentation of alloantigen induced and thus reflected the alloresponse of T-helper cells, which were incubated without and with cytochalasin and primaquine to inhibit antigen uptake and presentation, respectively. Transplant recipients included 76 males and 62 females. Rejectors were tested at median 3.6 d before diagnosis. The API was higher among rejectors compared with nonrejectors (2.2 ± 0.2 versus 0.6 ± 0.04, P value = 1.7E-09). In logistic regression and receiver-operating-characteristic analysis, API ≥1.1 achieved sensitivity, specificity, and positive and negative predictive values for predicting ACR in 99 training set samples. Corresponding metrics ranged from 80% to 88% in 32 independent posttransplant samples, and 73% to 100% in 20 independent pretransplant samples. In time-to-event analysis, API ≥1.1 predicted higher incidence of late donor-specific anti-HLA antibodies after API measurements in LT recipients (P = 0.011) and graft loss in IT recipients (P = 0.008), compared with recipients with API <1.1, respectively.

Conclusions

Enhanced donor antigen presentation by circulating B cells predicts rejection after liver or intestine transplantation as well as higher incidence of DSA and graft loss late after transplantation.

Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes

BACKGROUND & AIMS

Biliary atresia (BA) is poorly understood and leads to liver transplantation (LT), with the requirement for and associated risks of lifelong immunosuppression, in most children. We performed a genome-wide association study (GWAS) to determine the genetic basis of BA.

METHODS

We performed a GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4,654 genetically matched controls. Whole-genome sequencing of 100 cases evaluated synthetic association with rare variants. Functional studies included whole liver transcriptome analysis of 64 BA cases and perturbations in experimental models.

RESULTS

A GWAS of common single nucleotide polymorphisms (SNPs), i.e. allele frequencies >1%, identified intronic SNPs rs6446628 in AFAP1 with genome-wide significance (p = 3.93E-8) and rs34599046 in TUSC3 at sub-threshold genome-wide significance (p = 1.34E-7), both supported by credible peaks of neighboring SNPs. Like other previously reported BA-associated genes, AFAP1 and TUSC3 are ciliogenesis and planar polarity effectors (CPLANE). In gene-set-based GWAS, BA was associated with 6,005 SNPs in 102 CPLANE genes (p = 5.84E-15). Compared with non-CPLANE genes, more CPLANE genes harbored rare variants (allele frequency <1%) that were assigned Human Phenotype Ontology terms related to hepatobiliary anomalies by predictive algorithms, 87% vs. 40%, p <0.0001. Rare variants were present in multiple genes distinct from those with BA-associated common variants in most BA cases. AFAP1 and TUSC3 knockdown blocked ciliogenesis in mouse tracheal cells. Inhibition of ciliogenesis caused biliary dysgenesis in zebrafish. AFAP1 and TUSC3 were expressed in fetal liver organoids, as well as fetal and BA livers, but not in normal or disease-control livers. Integrative analysis of BA-associated variants and liver transcripts revealed abnormal vasculogenesis and epithelial tube formation, explaining portal vein anomalies that co-exist with BA.

CONCLUSIONS

BA is associated with polygenic susceptibility in CPLANE genes. Rare variants contribute to polygenic risk in vulnerable pathways via unique genes.

IMPACT AND IMPLICATIONS

Liver transplantation is needed to cure most children born with biliary atresia, a poorly understood rare disease. Transplant immunosuppression increases the likelihood of life-threatening infections and cancers. To improve care by preventing this disease and its progression to transplantation, we examined its genetic basis. We find that this disease is associated with both common and rare mutations in highly specialized genes which maintain normal communication and movement of cells, and their organization into bile ducts and blood vessels during early development of the human embryo. Because defects in these genes also cause other birth defects, our findings could lead to preventive strategies to lower the incidence of biliary atresia and potentially other birth defects.

Impaired Cellular and Antibody immunity after COVID-19 in Chronically Immunosuppressed Transplant Recipients

Assessment of cellular immunity to the SARS-CoV-2 coronavirus is of great interest in chronically immunosuppressed transplant recipients (Tr), who are predisposed to infections and vaccination failures. We evaluated CD154-expressing T-cells induced by spike (S) antigenic peptides in 204 subjects-103 COVID-19 patients and 101 healthy unexposed subjects. S-reactive CD154+T-cell frequencies were a) higher in 42 healthy unexposed Tr who were sampled pre-pandemic, compared with healthy NT (p=0.02), b) lower in Tr COVID-19 patients compared with healthy Tr (p<0.0001) and were accompanied by lower S-reactive B-cell frequencies (p<0.05), c) lower in Tr with severe COVID-19 (p<0.0001), or COVID-19 requiring hospitalization (p<0.05), compared with healthy Tr. Among Tr with COVID-19, cytomegalovirus co-infection occurred in 34%; further, incidence of anti-receptor-binding-domain IgG (p=0.011) was lower compared with NT COVID-19 patients. Healthy unexposed Tr exhibit pre-existing T-cell immunity to SARS-CoV-2. COVID-19 impairs anti-S T-cell and antibody and predisposes to CMV co-infection in transplant recipients.

DLBCL cell of origin typing and whole transcriptome analysis using single slides with HTG EdgeSeq

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Background: Diffuse large B-cell Lymphoma (DLBCL) is a highly heterogenous disease. Gene microarrays were initially used to classify DLBCL into germinal center B-cell-like (GCB) or activated B-cell-like (ABC) Cell of Origin (COO) subtypes. ABC is associated with shorter overall survival. In newly diagnosed patients, COO classification by RNA profiling is a validated prognostic. A simpler immunohistochemical (IHC) staining of CD10, MUM1 and BCL6 is a proxy used in clinical practice in lieu of transcriptomics due to its expense, complexity and tissue requirements. Recent advances in the HTG EdgeSeq platform allow genome-scale profiling with minimal tissue. We successfully applied this novel technology to perform simultaneous COO classification, immune cell enrichment and tumor pathway analysis using a single FFPE slide. Methods: Accuracy of the HTG EdgeSeq panel (19,000 genes) was assessed in a head-to-head comparison with RNAseq using FFPE tumor samples (n = 8). DLBCL resections and core needle biopsies were commercially sourced and COO typed using Han’s algorithm into GCB or non-GCB (n = 65). Tumor locations included: lymphoid organs, gastrointestinal tract, testes, and the pleural cavity. EdgeSeq was performed on single slides with an average tissue area of 40mm2. Transcriptomic COO classification was performed using a linear combination of genes as described in Wright et al., PNAS 2003, substituting HTG platform-specific weights. Validated COO gene sets from literature and commercial diagnostic assays were tested. Immune cell gene signature enrichment analysis was performed using xCell (Aran et al., Genome Biol 2017); pathway analysis was performed with GSEA (Subramanian et al., PNAS 2005). Results: Gene expression levels estimated from whole transcriptome EdgeSeq on single slides were highly correlated to whole transcriptome RNAseq. Differential expression analysis of GCB vs non-GCB showed that key prognostic genes were detectable and enriched in the expected subtypes. Using these pre-established signatures, subtyping accuracy was ̃93% on the training set and 89% on the test set. Immune cell enrichment analysis identified class-switched memory B-cells as more prevalent in non-GCB subjects. This is consistent with emerging evidence that memory B-cells are the primary source of ABC DLBCL and not plasma cells (Venturutti & Melnick, Blood 2020). Pathway analysis identified genes regulated by the oncogene ic transcription factor MYC were enriched in non-GCB samples; MYC protein was found to be overexpressed in ABC in a large study (Hu et al., Blood 2013). Conclusions: Combined COO typing and whole transcriptome analysis from a single slide efficiently uses precious patient tissue. Longitudinal core needle sampling may yield insights into tumor evolution and therapeutic mechanisms of action across the DLBCL treatment landscape.

A network-based approach to identify expression modules underlying rejection in pediatric liver transplantation

Selecting the right immunosuppressant to ensure rejection-free outcomes poses unique challenges in pediatric liver transplant (LT) recipients. A molecular predictor can comprehensively address these challenges. Currently, there are no well-validated blood-based biomarkers for pediatric LT recipients before or after LT. Here, we discover and validate separate pre- and post-LT transcriptomic signatures of rejection. Using an integrative machine learning approach, we combine transcriptomics data with the reference high-quality human protein interactome to identify network module signatures, which underlie rejection. Unlike gene signatures, our approach is inherently multivariate and more robust to replication and captures the structure of the underlying network, encapsulating additive effects. We also identify, in an individual-specific manner, signatures that can be targeted by current anti-rejection drugs and other drugs that can be repurposed. Our approach can enable personalized adjustment of drug regimens for the dominant targetable pathways before and after LT in children.

The Combiome Hypothesis: Selecting Optimal Treatment for Cancer Patients

Existing approaches for cancer diagnosis are inefficient in the use of diagnostic tissue, and decision-making is often sequential, typically resulting in delayed treatment initiation. Future diagnostic testing needs to be faster and optimize increasingly complex treatment decisions. We envision a future where comprehensive testing is routine. Our approach, termed the "combiome," combines holistic information from the tumor, and the patient's immune system. The combiome model proposed here advocates synchronized up-front testing with a panel of sensitive assays, revealing a more complete understanding of the patient phenotype and improved targeting and sequencing of treatments. Development and eventual adoption of the combiome model for diagnostic testing may provide better outcomes for all cancer patients, but will require significant changes in workflows, technology, regulations, and administration. In this review, we discuss the current and future testing landscape, targeting of personalized treatments, and technological and regulatory advances necessary to achieve the combiome.

Impaired T-cell and antibody immunity after COVID-19 infection in chronically immunosuppressed transplant recipients

Assessment of T-cell immunity to the COVID-19 coronavirus requires reliable assays and is of great interest, given the uncertain longevity of the antibody response. Some recent reports have used immunodominant spike (S) antigenic peptides and anti-CD28 co-stimulation in varying combinations to assess T-cell immunity to SARS-CoV-2. These assays may cause T-cell hyperstimulation and could overestimate antiviral immunity in chronically immunosuppressed transplant recipients, who are predisposed to infections and vaccination failures. Here, we evaluate CD154-expressing T-cells induced by unselected S antigenic peptides in 204 subjects-103 COVID-19 patients and 101 healthy unexposed subjects. Subjects included 72 transplanted and 130 non-transplanted subjects. S-reactive CD154+T-cells co-express and can thus substitute for IFNγ (n=3). Assay reproducibility in a variety of conditions was acceptable with coefficient of variation of 2-10.6%. S-reactive CD154+T-cell frequencies were a) higher in 42 healthy unexposed transplant recipients who were sampled pre-pandemic, compared with 59 healthy non-transplanted subjects (p=0.02), b) lower in Tr COVID-19 patients compared with healthy transplant patients (p<0.0001), c) lower in Tr patients with severe COVID-19 (p<0.0001), or COVID-19 requiring hospitalization (p<0.05), compared with healthy Tr recipients. S-reactive T-cells were not significantly different between the various COVID-19 disease categories in NT recipients. Among transplant recipients with COVID-19, cytomegalovirus co-infection occurred in 34%; further, CMV-specific T-cells (p<0.001) and incidence of anti-receptor-binding-domain IgG (p=0.011) were lower compared with non-transplanted COVID-19 patients. Healthy unexposed transplant recipients exhibit pre-existing T-cell immunity to SARS-CoV-2. COVID-19 infection leads to impaired T-cell and antibody responses to SARS-CoV-2 and increased risk of CMV co-infection in transplant recipients.

Durvalumab With or Without Tremelimumab vs Standard Chemotherapy in First-line Treatment of Metastatic Non-Small Cell Lung Cancer: The MYSTIC Phase 3 Randomized Clinical Trial

Question

Does first-line durvalumab treatment with or without tremelimumab improve survival outcomes vs chemotherapy in patients with metastatic non–small cell lung cancer?

Findings

In this phase 3 randomized clinical trial including 1118 patients with non–small cell lung cancer, although the trial did not meet its primary end points, treatment with durvalumab resulted in a numerically reduced risk of death vs chemotherapy in patients with programmed cell death ligand 1 expression on at least 25% of tumor cells. In exploratory analyses, a blood tumor mutational burden threshold of at least 20 mutations per megabase was identified for optimal clinical benefit with durvalumab plus tremelimumab vs chemotherapy.

Meaning

These findings highlight the need for further investigation and prospective validation of blood tumor mutational burden as a predictive biomarker for immunotherapy.

Importance

Checkpoint inhibitors targeting programmed cell death 1 or its ligand (PD-L1) as monotherapies or in combination with anti–cytotoxic T-lymphocyte–associated antigen 4 have shown clinical activity in patients with metastatic non–small cell lung cancer.

Objective

To compare durvalumab, with or without tremelimumab, with chemotherapy as a first-line treatment for patients with metastatic non–small cell lung cancer.

Design, Setting, and Participants

This open-label, phase 3 randomized clinical trial (MYSTIC) was conducted at 203 cancer treatment centers in 17 countries. Patients with treatment-naive, metastatic non–small cell lung cancer who had no sensitizing EGFR or ALK genetic alterations were randomized to receive treatment with durvalumab, durvalumab plus tremelimumab, or chemotherapy. Data were collected from July 21, 2015, to October 30, 2018.

Interventions

Patients were randomized (1:1:1) to receive treatment with durvalumab (20 mg/kg every 4 weeks), durvalumab (20 mg/kg every 4 weeks) plus tremelimumab (1 mg/kg every 4 weeks, up to 4 doses), or platinum-based doublet chemotherapy.

Main Outcomes and Measures

The primary end points, assessed in patients with ≥25% of tumor cells expressing PD-L1, were overall survival (OS) for durvalumab vs chemotherapy, and OS and progression-free survival (PFS) for durvalumab plus tremelimumab vs chemotherapy. Analysis of blood tumor mutational burden (bTMB) was exploratory.

Results

Between July 21, 2015, and June 8, 2016, 1118 patients were randomized. Baseline demographic and disease characteristics were balanced between treatment groups. Among 488 patients with ≥25% of tumor cells expressing PD-L1, median OS was 16.3 months (95% CI, 12.2-20.8) with durvalumab vs 12.9 months (95% CI, 10.5-15.0) with chemotherapy (hazard ratio [HR], 0.76; 97.54% CI, 0.56-1.02; P = .04 [nonsignificant]). Median OS was 11.9 months (95% CI, 9.0-17.7) with durvalumab plus tremelimumab (HR vs chemotherapy, 0.85; 98.77% CI, 0.61-1.17; P = .20). Median PFS was 3.9 months (95% CI, 2.8-5.0) with durvalumab plus tremelimumab vs 5.4 months (95% CI, 4.6-5.8) with chemotherapy (HR, 1.05; 99.5% CI, 0.72-1.53; P = .71). Among 809 patients with evaluable bTMB, those with a bTMB ≥20 mutations per megabase showed improved OS for durvalumab plus tremelimumab vs chemotherapy (median OS, 21.9 months [95% CI, 11.4-32.8] vs 10.0 months [95% CI, 8.1-11.7]; HR, 0.49; 95% CI, 0.32-0.74). Treatment-related adverse events of grade 3 or higher occurred in 55 (14.9%) of 369 patients who received treatment with durvalumab, 85 (22.9%) of 371 patients who received treatment with durvalumab plus tremelimumab, and 119 (33.8%) of 352 patients who received treatment with chemotherapy. These adverse events led to death in 2 (0.5%), 6 (1.6%), and 3 (0.9%) patients, respectively.

Conclusions and Relevance

The phase 3 MYSTIC study did not meet its primary end points of improved OS with durvalumab vs chemotherapy or improved OS or PFS with durvalumab plus tremelimumab vs chemotherapy in patients with ≥25% of tumor cells expressing PD-L1. Exploratory analyses identified a bTMB threshold of ≥20 mutations per megabase for optimal OS benefit with durvalumab plus tremelimumab.

Trial Registration

ClinicalT rials.gov Identifier: NCT02453282

A Blood-based Assay for Assessment of Tumor Mutational Burden in First-line Metastatic NSCLC Treatment: Results from the MYSTIC Study

PURPOSE

Tumor mutational burden (TMB) has been shown to be predictive of survival benefit in patients with non-small cell lung cancer (NSCLC) treated with immune checkpoint inhibitors. Measuring TMB in the blood (bTMB) using circulating cell-free tumor DNA (ctDNA) offers practical advantages compared with TMB measurement in tissue (tTMB); however, there is a need for validated assays and identification of optimal cutoffs. We describe the analytic validation of a new bTMB algorithm and its clinical utility using data from the phase III MYSTIC trial.

PATIENTS AND METHODS

The dataset used for the clinical validation was from MYSTIC, which evaluated first-line durvalumab (anti-PD-L1 antibody) ± tremelimumab (anticytotoxic T-lymphocyte-associated antigen-4 antibody) or chemotherapy for metastatic NSCLC. bTMB and tTMB were evaluated using the GuardantOMNI and FoundationOne CDx assays, respectively. A Cox proportional hazards model and minimal P value cross-validation approach were used to identify the optimal bTMB cutoff.

RESULTS

In MYSTIC, somatic mutations could be detected in ctDNA extracted from plasma samples in a majority of patients, allowing subsequent calculation of bTMB. The success rate for obtaining valid TMB scores was higher for bTMB (809/1,001; 81%) than for tTMB (460/735; 63%). Minimal P value cross-validation analysis confirmed the selection of bTMB ≥20 mutations per megabase (mut/Mb) as the optimal cutoff for clinical benefit with durvalumab + tremelimumab.

CONCLUSIONS

Our study demonstrates the feasibility, accuracy, and reproducibility of the GuardantOMNI ctDNA platform for quantifying bTMB from plasma samples. Using the new bTMB algorithm and an optimal bTMB cutoff of ≥20 mut/Mb, high bTMB was predictive of clinical benefit with durvalumab + tremelimumab versus chemotherapy.

Prognostic and Predictive Impact of Circulating Tumor DNA in Patients with Advanced Cancers Treated with Immune Checkpoint Blockade

The utility of circulating tumor DNA (ctDNA) as a biomarker in patients with advanced cancers receiving immunotherapy is uncertain. We therefore analyzed pretreatment (n = 978) and on-treatment (n = 171) ctDNA samples across 16 advanced-stage tumor types from three phase I/II trials of durvalumab (± the anti-CTLA4 therapy tremelimumab). Higher pretreatment variant allele frequencies (VAF) were associated with poorer overall survival (OS) and other known prognostic factors, but not objective response, suggesting a prognostic role for patient outcomes. On-treatment reductions in VAF and lower on-treatment VAF were independently associated with longer progression-free survival and OS and increased objective response rate, but not prognostic variables, suggesting that on-treatment ctDNA dynamics are predictive of benefit from immune checkpoint blockade. Accordingly, we propose a concept of "molecular response" using ctDNA, incorporating both pretreatment and on-treatment VAF, that predicted long-term survival similarly to initial radiologic response while also permitting early differentiation of responders among patients with initially radiologically stable disease. SIGNIFICANCE: In a pan-cancer analysis of immune checkpoint blockade, pretreatment ctDNA levels appeared prognostic and on-treatment dynamics predictive. A "molecular response" metric identified long-term responders and adjudicated benefit among patients with initially radiologically stable disease. Changes in ctDNA may be more dynamic than radiographic changes and could complement existing trial endpoints.This article is highlighted in the In This Issue feature, p. 1775.

A New Pipeline to Predict and Confirm Tumor Neoantigens Predict Better Response to Immune Checkpoint Blockade

Mutations that drive oncogenesis in cancer can generate neoantigens that may be recognized by the immune system. Identification of these neoantigens remains challenging due to the complexity of the MHC antigen and T-cell receptor interaction. Here, we describe the development of a systematic approach to efficiently identify and validate immunogenic neoantigens. Whole-exome sequencing of tissue from a patient with melanoma was used to identify nonsynonymous mutations, followed by MHC binding prediction and identification of tumor clonal architecture. The top 18 putative class I neoantigens were selected for immunogenicity testing via a novel in vitro pipeline in HLA-A201 healthy donor blood. Naïve CD8 T cells from donors were stimulated with allogeneic dendritic cells pulsed with peptide pools and then with individual peptides. The presence of antigen-specific T cells was determined via functional assays. We identified one putative neoantigen that expanded T cells specific to the mutant form of the peptide and validated this pipeline in a subset of patients with bladder tumors treated with durvalumab (n = 5). Within this cohort, the top predicted neoantigens from all patients were immunogenic in vitro. Finally, we looked at overall survival in the whole durvalumab-treated bladder cohort (N = 37) by stratifying patients by tertile measure of tumor mutation burden (TMB) or neoantigen load. Patients with higher neoantigen and TMB load tended to show better overall survival. IMPLICATIONS: This pipeline can enable accurate and rapid identification of personalized neoantigens that may help to identify patients who will survive longer on durvalumab.

Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR

DNA methylation biomarkers are increasingly utilized for the detection, prognosis and monitoring of cancer. Here we use publicly-available whole genome bisulfite sequencing data to identify differentially methylated regions (cDMRs) in diverse tumor types and further define a set of genomic target regions that have optimal characteristics for Methylation Sensitive Restriction Enzyme-PCR (MSRE-PCR)-based detection: conserved hypermethylation in tumors, abundant MSRE sites and low methylation levels in normal tissues. The identified MSRE-PCR target regions (n = 1,294) were primarily encompassed within CpG islands (97%) and promoters (81%) with 39% of the target regions overlapping the transcription start site. Gene set enrichment analysis of the target regions identified significant enrichment of genes involved in neuronal development. A multiplexed MSRE-PCR assay was developed interrogating 47 target regions and was tested on a set of genomic DNAs (n = 100) from diverse tumor and normal tissue types including colon, breast, lung, stomach and blood. A logistic regression model containing seven target region amplicons distinguished between tumor and normal tissue in the training (n = 50) with a ROC AUC of 0.97 (95% CI [0.92, 1]) and independent test set (n = 50) with an AUC of 0.93 (95% CI [0.84, 1]). These findings show that genomic regions with conserved hypermethylation across diverse tumor types, abundant MSRE sites and low methylation levels in normal tissues provide target regions for the detection of tumor DNA via MSRE-PCR. The selective amplification of tumor-derived DNA via MSRE-PCR may have utility in the development of non-invasive cancer detection and surveillance strategies.

Biliary-Atresia-Associated Mannosidase-1-Alpha-2 Gene Regulates Biliary and Ciliary Morphogenesis and Laterality

Background/Aims

Infectious and genetic factors are invoked, respectively in isolated biliary atresia (BA), or syndromic BA, with major extrahepatic anomalies. However, isolated BA is also associated with minor extrahepatic gut and cardiovascular anomalies and multiple susceptibility genes, suggesting common origins.

Methods

We investigated novel susceptibility genes with genome-wide association, targeted sequencing and tissue staining in BA requiring liver transplantation, independent of BA subtype. Candidate gene effects on morphogenesis, developmental pathways, and ciliogenesis, which regulates left-right patterning were investigated with zebrafish knockdown and mouse knockout models, mouse airway cell cultures, and liver transcriptome analysis.

Results

Single nucleotide polymorphisms in Mannosidase-1-α-2 (MAN1A2) were significantly associated with BA and with other polymorphisms known to affect MAN1A2 expression but were not differentially enriched in either BA subtype. In zebrafish embryos, man1a2 knockdown caused poor biliary network formation, ciliary dysgenesis in Kupffer’s vesicle, cardiac and liver heterotaxy, and dysregulated egfra and other developmental genes. Suboptimal man1a2 knockdown synergized with suboptimal EGFR signaling or suboptimal knockdown of the EGFR pathway gene, adenosine-ribosylation-factor-6, which had minimal effects individually, to reproduce biliary defects but not heterotaxy. In cultured mouse airway epithelium, Man1a2 knockdown arrested ciliary development and motility. Man1a2^–/– mice, which experience respiratory failure, also demonstrated portal and bile ductular inflammation. Human BA liver and Man1a2^–/– liver exhibited reduced Man1a2 expression and dysregulated ciliary genes, known to cause multisystem human laterality defects.

Conclusion

BA requiring transplantation associates with sequence variants in MAN1A2. man1a2 regulates laterality, in addition to hepatobiliary morphogenesis, by regulating ciliogenesis in zebrafish and mice, providing a novel developmental basis for multisystem defects in BA.

CD154-expressing CMV-specific T cells associate with freedom from DNAemia and may be protective in seronegative recipients after liver or intestine transplantation

Cell-mediated immunity to CMV, if known, could improve antiviral drug therapy in at-risk children and young adults with LT and IT. Host immunity has been measured with CMV-specific T cells, which express IFNγ, but not those which express CD154, a possible substitute for IFNγ. CMV-specific CD154+ T cells and their subsets were measured with flow cytometry after stimulating PBL from recipient blood samples with an overlapping peptide mix of CMV-pp65 antigen for up to 6 hours. CMV-specific CD154+ T cells co-expressed IFNγ in PBL from three healthy adults and averaged 3.8% (95% CI 3.2%-4.4%) in 40 healthy adults. CMV-specific T cells were significantly lower in 19 CMV DNAemic LT or IT recipients, compared with 126 non-DNAemic recipients, 1.3% (95% CI 0.8-1.7) vs 4.1 (95% CI 3.6-4.6, P < .001). All T-cell subsets demonstrated similar between-group differences. In logistic regression analysis of 46 training set samples, 12 with DNAemia, all obtained between days 0 and 60 from transplant, CMV-specific T-cell frequencies ≥1.7% predicted freedom from DNAemia with NPV of 93%. Sensitivity, specificity, and PPV were 83%, 74%, and 53%, respectively. Test performance was replicated in 99 validation samples. In 32 of 46 training set samples, all from seronegative recipients, one of 19 recipients with CMV-specific T-cell frequencies ≥1.7% experienced DNAemia, compared with 8 of 13 recipients with frequencies <1.7% (P = .001). CMV-specific CD154+ T cells are associated with freedom from DNAemia after LT and IT. Among seronegative recipients, CMV-specific T cells may protect against the development of CMV DNAemia.

Type I interferon gene signature test–low and –high patients with systemic lupus erythematosus have distinct gene expression signatures

Objectives

Type I interferon (IFN) is implicated in systemic lupus erythematosus (SLE) pathogenesis. We aimed to identify type I IFN signaling-dependent and -independent molecular pathways in a large population of patients with SLE.

Methods

Baseline blood samples from adult patients with moderate to severe SLE from two Phase IIb studies (NCT01438489, n = 265; NCT01283139, n = 416) were profiled using whole transcriptome array analyses. Type I IFN gene signature (IFNGS) test status (high or low) was determined using a validated qualitative polymerase chain reaction–based test. IFN-type-specific signatures were developed by stimulating healthy blood with IFN-β, IFN-γ, IFN-λ, IFN-ω, or pooled IFN-α. These, and multiple literature-derived cell type and cytokine pathway signatures, were evaluated in individual and pooled study populations. A Fisher’s exact test was used for associations, adjusted for false discovery rate.

Results

Whole blood samples from IFNGS test–high patients were enriched versus IFNGS test–low patients for CD40L signaling ( Q < 0.001), CXC cytokine ( Q < 0.001), TLR8-mediated monocyte activation ( Q < 0.001), IgG ( Q < 0.001), major histocompatibility complex class I ( Q < 0.001), and plasma cell ( Q < 0.001) gene expression signatures. IFNGS test–low patients had significant enrichment of eosinophil ( Q < 0.001), IFN-γ-specific ( Q = 0.005), and T-cell or B-cell ( Q < 0.001) signatures. Similar enrichment profiles were demonstrated in patients with primary Sjögren’s syndrome, systemic sclerosis, and dermatomyositis.

Conclusions

IFNGS test–high patients overexpressed many gene signatures associated with SLE pathogenesis compared with IFNGS test–low patients, reflecting broad immune activation. These results provide new insights into the molecular heterogeneity underlying SLE pathogenesis, highlighting shared mechanisms beyond type I IFN, across several autoimmune diseases.

Trial registration

Clinicaltrials.gov: NCT01438489 and NCT01283139.

Abstract 2795: Dissemination score of CD8+ TILs by automated image analysis is a potential marker of immune activity in human cancers

The overall density of CD8+ tumor-infiltrating lymphocytes (TILs) is important for characterizing the level of immune activity in the tumor microenvironment (TME). Beyond the densities of CD8+ TILs, both their location and distributional patterns may also have relevance to immune activity. We evaluated 645 resected tumors encompassing seven cancer types, and correlate location and spatial patterns of CD8+ TILs to immune pathway activity.

We integrated image analysis results from digitized immunohistochemistry (IHC) slides with gene expression data from a targeted Ion Torrent Panel. Overall density of CD8+ TILs and the exact position of individual CD8+ lymphocytes were determined from IHC slides. A dissemination score was defined as ratio of global density and average local density of CD8+ TILs. This score is the inverse of the Ripley’s K statistic and becomes high for disseminated spatial patterns. We used this quotient as a continuous metric to identify tumors with a disseminated TIL pattern and to distinguish them from tumors with focal distribution of CD8+ TILs. Within a subset of tumors, the continuous dissemination metric was correlated with biological pathways using targeted mRNA sequencing and gene set enrichment analysis. In addition, association of the dissemination score with overall survival was tested on a subset of cases.

CD8+ TIL distributional patterns differed significantly between tumor types. Breast and pancreatic cancers more frequently showed a focal distribution of CD8+ TILs, while lung tumors comparatively exhibited a disseminated pattern. Transcriptional profiling data revealed differences between both image analysis phenotypes. On average, cases with more disseminated patterns of CD8+ T cells were associated with mRNA expression of genes that fall in pathways related to motility, migration and activation status of tumor infiltrating T cells. We also found a trend to better overall survival in patients whose tumors had a disseminated TIL score compared to those with a focal pattern. This trend was significant in non-small cell adenocarcinoma of the lung (log rank p = 0.018).

We demonstrate the value of spatial image analysis to automatically score CD8+ TIL dissemination as a marker of immune activity in the TME. Jointly analyzing transcriptional profiles appears to identify a biologically meaningful activation phenotype in tumors with high dissemination scores. Our data further suggests that this phenotype is associated with improved overall survival in some cancer patients.

Citation Format: Stefan Bentink, Andreas Spitzmueller, Tze Heng Tan, Hadassah Sade, Song Wu, Brandon W. Higgs, Keith E. Steele. Dissemination score of CD8+ TILs by automated image analysis is a potential marker of immune activity in human cancers [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 2795.

Prognostic Significance of Liver Metastasis in Durvalumab-Treated Lung Cancer Patients

INTRODUCTION

Two clinical studies (Study 1108 and ATLANTIC) were analyzed to evaluate the prognostic value of baseline liver metastases (LMs) in advanced/metastatic non-small-cell lung cancer patients treated with durvalumab 10 mg/kg every 2 weeks.

PATIENTS AND METHODS

A multivariate Cox proportional hazards analysis was conducted; covariates included performance status, tumor stage, histology, sex, age, smoking status, and programmed cell death ligand 1 (PD-L1) status.

RESULTS

In all, 569 patients were included. LMs were present in 31.6% (96/304) of Study 1108 patients and 17.9% (47/263) of ATLANTIC patients. Median overall survival (OS) was shorter in patients with LMs than in those without in both studies. In both studies, LMs were an independent negative prognostic factor for OS and progression-free survival. Objective response rates were also significantly lower. PD-L1 independently predicted benefit across all patients.

CONCLUSION

Liver metastases were associated with worse outcomes irrespective of PD-L1 status, but PD-L1 status predicted benefit from durvalumab irrespective of LMs.

Correlation of angiogenic and immunomodulatory proteins with clinical outcomes of durvalumab (anti-PDL1) in recurrent/metastatic head and neck squamous cell carcinoma

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Background: The potential for durvalumab, a PD-L1 blocking monoclonal antibody, to treat head and neck squamous cell carcinoma (HNSCC) is being evaluated in multiple clinical trials. We assessed circulating protein biomarkers in HNSCC patients prior to treatment to better understand pathways related to clinical outcomes and potentially relevant for targeting in combination with durvalumab. Methods: Sixty-six selected serum proteins were measured by multiplex immunoassay at baseline in HNSCC patients receiving durvalumab treatment: 106 patients with high PD-L1 (≥25% tumor cells; SP263 assay) in phase II HAWK trial and 52 patients with low/no PD-L1 in phase II CONDOR trial. Results: Multivariate Cox modeling demonstrated that higher baseline concentrations of angiogenic, pro-inflammatory, and myeloid-associated proteins (ANGPT2, CRP, IL6, S100A12) were associated with shorter overall survival (OS), while higher concentration of a bone formation marker and immunostimulatory hormone (BGLAP) correlated with longer OS in 158 durvalumab-treated HNSCC patients ( P< 0.05). These 4 proteins also showed higher baseline levels in patients with progressive disease (PD) compared to stable disease (SD) and partial or complete responses (PR/CR), while BGLAP had lower levels in PD compared to SD or PR/CR (Mann-Whitney P< 0.05). The 5 proteins remained significantly associated with OS in a multivariate model including PD-L1, ECOG, tumor size, and neutrophil count. Bone metastasis status had no impact on the association of BGLAP with OS, which has not been reported before in HNSCC. Interestingly, ANGPT2 level above median showed the highest hazard ratio (HR = 2.2, P <0.001) among all evaluated variables. Furthermore, higher levels of VWF, an angiogenesis-related protein, correlated with shorter OS by univariate survival analysis ( P < 0.001). Conclusions: Our results suggested an important role of angiogenesis in the resistance of HNSCC patients to durvalumab treatment, and ANGPT2 may have predictive utility for durvalumab combination with an anti-angiogenic agent. The predictive value of BGLAP remains to be evaluated in a randomized clinical study. Clinical trial information: NCT02207530; NCT02319044.

Early incidence of immune-related adverse events (irAEs) predicts efficacy in patients (pts) with solid tumors treated with immune-checkpoint inhibitors (ICIs)

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Background: Treatment with ICIs can manifest immune-related adverse events (irAEs), which have correlated with clinical outcomes in certain tumors. However, timing of these events and how early irAEs correlate with outcomes is unclear. We assessed whether early occurring irAEs could predict survival in pts treated with durvalumab (D), an anti-PDL1 and combined with tremelimumab (D+T), an anti-CTLA4 in two clinical studies. Methods: Two phase 2 non-randomized clinical trials evaluating D (D4190C00001 (1108), N=756; available data per internal data re-use policy) or D+T (D4190C00010 (C10), N=327; expansion and ICI naïve cohorts) in multiple solid tumor types were analyzed. Prevalence of pts experiencing irAEs, regardless of grade was 30% and 59% in studies 1108 and C10, respectively, with most frequent including dermatitis/rash (25%), thyroid (15%), diarrhea/colitis (14%), and pancreatic enzyme elevation (5%). Overall survival (OS) was correlated with irAE timing prior to 6, 8, 12, 16, 20 and 24 weeks following D or D+T treatment. Kaplan Meier and log-rank analyses were used. Results: In both studies, pts who experienced at least one irAE by study completion had improved median OS (mOS, 1108: 23.1 mos [18.2, 26.9]; C10: 16.3 mos [12.5, 31.4]) relative to those who experienced none (1108: 6.3 mos [5.4, 7.3]; C10 4.6 mos [3.3, 6.1]). Median time (weeks) to first and second irAE occurred earlier in C10 compared to 1108, 3.9 vs. 5.6 and 6.9 vs. 10.1, respectively. When associating timing of irAEs with survival, there was a significant differential in mOS at each time interval evaluated between pts with at least one irAE and those with none, with differentiation at 6 weeks and maximal survival benefit at 24 weeks following treatment with D or D+T (Table). Conclusions: Early occurrence of irAEs may be predictive of survival benefit in pts treated with D or D+T. OS by 1+ or no irAE(s) occurring up to 6 or 24 weeks post treatment. [Table: see text]

Exome analysis of oncogenic pathways and tumor mutational burden (TMB) in triple-negative breast cancer (TNBC): Results of the translational biomarker program of the neoadjuvant double-blind placebo controlled GeparNuevo trial

509

Background: GeparNuevo (G9) showed a numerical increase in pCR rate of 53% vs 44%; p = 0.287 compared to placebo in TNBC with the addition of the anti-PD-L1 antibody durvalumab (D) to a neoadjuvant anthracycline-taxane containing chemotherapy (Loibl S et al. ASCO 2018). Somatic mutations in malignant cells manifest over the evolutionary history of a tumor. Reports in selected tumor types suggest that TMB may predict clinical outcomes on immune-checkpoint inhibitors (ICI). The clinical relevance of TMB in breast cancer has not been studied widely. Here, we investigated the hypothesis that TMB predicts response to ICI. Methods: Whole exome sequencing was conducted on patient-matched fresh-frozen core biopsies and blood samples with Illumina (n = 149/174). SNVs and indels were called with Mutect and pureCN was used for copy number calls. Mutational signatures were identified as described by Alexandrov et al. (Cell Rep. 3, 2013). Data from G9 were compared to The Cancer Genome Atlas (TCGA) TNBC cohort. Results: A similar genomic landscape was observed between G9 and TCGA with primary mutations in TP53 (69%), c-MYC (26%), BRCA1 (13%), BRCA2 (6%), PIK3CA (11%) and PTEN (11%). Median TMB was 1.52 mut/MB. TMB in G9 was slightly lower than TCGA TNBC. TMB correlated with older age, higher mutation rates in BRCA2, ARID1A, and TP53, and higher burden in variant signatures such as DDR, HRD, GFRs, APOBEC and Alexandrov’s signatures 3 and 6. Continuous TMB predicted pCR in univariate (OR = 1.62, 95%-CI: 1.20 - 2.20, p = 0.0018) and multivariate (OR = 2.06, 95%-CI: 1.33 - 3.20, p = 0.0012) logistic regression models, but did not predict a D effect. After dichotomisation of TMB at the top tertile, 50 patients had high TMB and 29 of these (58%) achieved a pCR, while 99 had low TMB and only 38 of these (38%) had a pCR (p = 0.0242). Conclusions: Results show that TMB may predict pCR in primary TNBC. The trial was financially supported by Astra Zeneca and Celgene. Clinical trial information: NCT02685059.

Molecular circulating tumor DNA response to identify long-term survival in patients receiving immunotherapy with initial radiologic stable disease

2546

Background: Early on-treatment changes in ctDNA may identify responders to immunotherapy and complement radiologic assessment of benefit. Here we investigate how early changes in ctDNA associate with long-term survival following treatment with immunotherapy, and if differential patterns in molecular ctDNA response (MCR) among patients with radiologic stable disease (SD) at first on-treatment scan could identify patients deriving benefit from treatment. Methods: Paired pre- and on-treatment (week 6-8) plasma samples from 3 cohorts of patients treated with durvalumab (D) +/- tremelimumab (D+T) were evaluated (NCT01693562, NCT02087423, NCT02261220). CtDNA was profiled with the 73-gene Guardant 360 assay. Nonsynonymous variants were summarized per patient to calculate variant allelic frequency changes (dVAF) and on-treatment variant allele frequency (pVAF). A combination of dVAF and pVAF was used to define MCR. Results: The reduction of ctDNA (dVAF<0) and undetectable on-treatment ctDNA (pVAF=0) were each associated with improved OS and PFS. An optimal threshold for MCR was determined from one cohort, then applied to the other cohorts. MCR associated with significantly improved PFS and OS across all three cohorts (Table). MCR was then applied to a pooled subgroup of patients with initial radiologic SD from all three cohorts (n=78). Patients with radiologic SD and MCR were significantly more likely than those without MCR to achieve radiologic CR or PR (pooled Odds ratio 12.7, p<0.001), had improved PFS (stratified pooled HR 0.36, p<0.001), and improved OS (stratified pooled HR 0.38, p=0.005). Conclusions: MCR is an early on-treatment tool that may identify patients with improved long-term survival and patients with radiologic SD who derive clinical benefit from immunotherapy. MCR may be a supportive endpoint in prospective clinical trials. MCR and survival benefit. [Table: see text]

Automated image analysis of NSCLC biopsies to predict response to anti-PD-L1 therapy

Background

Immune checkpoint therapies (ICTs) targeting the programmed cell death-1 (PD1)/programmed cell death ligand-1 (PD-L1) pathway have improved outcomes for patients with non-small cell lung cancer (NSCLC), particularly those with high PD-L1 expression. However, the predictive value of manual PD-L1 scoring is imperfect and alternative measures are needed. We report an automated image analysis solution to determine the predictive and prognostic values of the product of PD-L1+ cell and CD8+ tumor infiltrating lymphocyte (TIL) densities (CD8xPD-L1 signature) in baseline tumor biopsies.

Methods

Archival or fresh tumor biopsies were analyzed for PD-L1 and CD8 expression by immunohistochemistry. Samples were collected from 163 patients in Study 1108/NCT01693562, a Phase 1/2 trial to evaluate durvalumab across multiple tumor types, including NSCLC, and a separate cohort of 199 non-ICT- patients. Digital images were automatically scored for PD-L1+ and CD8+ cell densities using customized algorithms applied with Developer XD™ 2.7 software.

Results

For patients who received durvalumab, median overall survival (OS) was 21.0 months for CD8xPD-L1 signature-positive patients and 7.8 months for signature-negative patients (p = 0.00002). The CD8xPD-L1 signature provided greater stratification of OS than high densities of CD8+ cells, high densities of PD-L1+ cells, or manually assessed tumor cell PD-L1 expression ≥25%. The CD8xPD-L1 signature did not stratify OS in non-ICT patients, although a high density of CD8+ cells was associated with higher median OS (high: 67 months; low: 39.5 months, p = 0.0009) in this group.

Conclusions

An automated CD8xPD-L1 signature may help to identify NSCLC patients with improved response to durvalumab therapy. Our data also support the prognostic value of CD8+ TILS in NSCLC patients who do not receive ICT.

Trial registration

ClinicalTrials.gov identifier: NCT01693562.

Study code: CD-ON-MEDI4736-1108.

Interventional study (ongoing but not currently recruiting).

Actual study start date: August 29, 2012.

Primary completion date: June 23, 2017 (final data collection date for primary outcome measure).

Electronic supplementary material

The online version of this article (10.1186/s40425-019-0589-x) contains supplementary material, which is available to authorized users.

The transcription factor c-Myb regulates CD8+ T cell stemness and antitumor immunity

Stem cells are maintained by transcriptional programs that promote self-renewal and repress differentiation. Here, we found that the transcription factor c-Myb was essential for generating and maintaining stem cells in the CD8+ T cell memory compartment. Following viral infection, CD8+ T cells lacking Myb underwent terminal differentiation and generated fewer stem cell-like central memory cells than did Myb-sufficient T cells. c-Myb acted both as a transcriptional activator of Tcf7 (which encodes the transcription factor Tcf1) to enhance memory development and as a repressor of Zeb2 (which encodes the transcription factor Zeb2) to hinder effector differentiation. Domain-mutagenesis experiments revealed that the transactivation domain of c-Myb was necessary for restraining differentiation, whereas its negative regulatory domain was critical for cell survival. Myb overexpression enhanced CD8+ T cell memory formation, polyfunctionality and recall responses that promoted curative antitumor immunity after adoptive transfer. These findings identify c-Myb as a pivotal regulator of CD8+ T cell stemness and highlight its therapeutic potential.

Baseline Plasma Cell Gene Signature Predicts Improvement in Systemic Sclerosis Skin Scores Following Treatment With Inebilizumab (MEDI-551) and Correlates With Disease Activity in Systemic Lupus Erythematosus and Chronic Obstructive Pulmonary Disease

OBJECTIVE

B cells impact the progression of systemic sclerosis (SSc; scleroderma) through multiple pathogenic mechanisms. CD19 inhibition in mice reduced skin thickness, collagen production, and autoantibody levels, consistent with CD19 expression on plasma cells (PCs), the source of antibody production. PC depletion could effectively reduce collagen deposition and inflammation in SSc; therefore, we investigated the effects of PC depletion on SSc disease activity.

METHODS

A PC gene signature was evaluated in SSc skin biopsy samples in 2 phase I clinical trials. We assessed microarray data from tissue from public studies of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), dermatomyositis (DM), systemic lupus erythematosus (SLE), and atopic dermatitis, as well as blood from a phase IIb clinical trial in SLE.

RESULTS

The PC signature was elevated in SSc skin specimens compared to healthy donor skin (P = 2.28 × 10^-6 ) and correlated with the baseline modified Rodnan skin thickness score (MRSS) (r = 0.64, P = 0.0004). Patients with a high PC signature at baseline showed greater improvement in the MRSS (mean ± SD change 35 ± 16%; P = 6.30 × 10^-4 ) following anti-CD19 treatment with inebilizumab (MEDI-551) than did patients with a low PC signature at baseline (mean ± SD change 8 ± 12%; P = 0.104). The PC signature was overexpressed in tissue from patients with SLE, DM, COPD, interstitial lung disease, and IPF relative to controls (all fold change >2; P < 0.001). The PC signature also differed significantly between SLE patients with mild-to-moderate disease and those with severe disease (SLE Disease Activity Index cutoff at 10) (fold change 1.44; P = 3.90 × 10^-3 ) and correlated significantly with the degree of emphysema in COPD (r = 0.53, P = 7.55 × 10^-8 ).

CONCLUSION

Our results support the notion that PCs have a role in the pathogenesis of SSc and other autoimmune or pulmonary indications. An elevated pretreatment PC signature was associated with increased benefit from MEDI-551 in SSc.

Abstract 1007: Durvalumab + tremelimumab increase T cells and decrease expression of genes involved in angiogenesis, EMT, and the Th2 pathway in the NSCLC tumor microenvironment

Background

Cancer cells utilize multiple mechanisms to suppress the development of an effective anti-tumor immune response. Overcoming these suppressive mechanisms to restore effector function to exhausted tumor infiltrating lymphocytes (TILs) is critical for response to checkpoint blockade; however, the specific changes associated with different IO treatments has yet to be fully characterized. We treated NSCLC tumor fragments or digests ex vivo with the anti-PD-L1 antibody durvalumab (D) alone or in combination with the anti-CTLA-4 antibody tremelimumab (T) to explore changes in gene and protein expression associated with checkpoint blockade.

Methods

10 NSCLC tumors (5 fresh and 5 frozen) were analyzed. Minced fresh tumor fragments or frozen tumor digests were seeded in media containing low dose interleukin-2 (IL-2) plus D and/or T or the appropriate isotype controls. After 1-2 weeks of treatment, TILs were evaluated for changes in cytokine production, as well as the expression of inhibitory receptors and other immune-related markers. Microarray gene expression analysis was performed on a subset (n = 2) of the NSCLC tumors evaluated.

Results

Of 10 NSCLC tumors tested, 4 showed a robust increase in IFNg production (&gt; 2-fold) relative to isotype controls in both D and D + T treated conditions, with an additional 3 tumors showing smaller, but consistent 30-40% increases in IFNg production. 4 NSCLC tumors showed at least a 30% increase in CD4+ and CD8+ T cell proliferation following D and D+T, with a maximum increase of 120% in CD4+ T cells due to D+T. D and D+T reduced expression of the Th2 pathway genes IL-4, IL-5, and IL-9 (2-8 fold compared to isotype control) and &gt; 2-fold increased expression of THEMIS and CXCL13, genes important for TCR signaling and T follicular helper cell mediated B cell recruitment, respectively. D + T treatment resulted in greater reduction compared to D in expression of genes involved in regulating angiogenesis (VHL, FGD5; &gt; 2-fold), as well as metastasis (PFTK1; 2.2-fold), epithelial to mesenchymal transition (EMT) (CD133; 2-fold), and T reg function (TGFB2 and IL17RB; 1.8-2-fold).

Conclusions

Our results demonstrate that D + T augmented the effects of D in the microenvironment of this set of NSCLC tumors. The specific impact of D + T on the regulation of angiogenesis and TGFb-mediated immunosuppression warrants further evaluation in a larger set of tumors.

Citation Format: Li Cheng, Lydia M. Greenlees, Nicholas M. Durham, Fernanda Pilataxi, Todd Creasy, Brandon W. Higgs, Koustubh Ranade, Katie Streicher. Durvalumab + tremelimumab increase T cells and decrease expression of genes involved in angiogenesis, EMT, and the Th2 pathway in the NSCLC tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1007.

Abstract 4677: A new pipeline to predict and confirm tumor neo-antigens

Identification of tumor-specific neo-antigens is crucial to developing new immunotherapeutic approaches, e.g. personalized vaccines. While computer algorithms can predict Class I or II HLA specific neoantigens, experimental confirmation of these potentially immunogenic neoantigens remains challenging, primarily due to the complexity associated with understanding the MHC-antigen and T cell receptor interaction. Here, we developed a systematic pipeline to efficiently identify immunogenic neoantigens and evaluate their immunogenicity in healthy donors.

Whole-exome sequencing(WES) of a melanoma was used to identify non-synonymous mutations. MHC presentation was predicted with digital HLA typing and MHC class I allele-restricted binding affinity/stability algorithms (netMHCpan/netMHCstab). The tumor clonal architecture was identified for each peptide to prioritize clonal over subclonal neoantigens using BubbleTree (https://bioconductor.org/packages/release/bioc/html/BubbleTree.html). Immunogenicity testing was done using a novel in-vitro assay with blood from healthy HLA-A201 donors. Naïve CD8 T cells were stimulated with autologous dendritic cells pulsed initially with peptide pools followed by individual peptides. The presence of antigen-specific T cells was determined via MHC-multimer staining and function was assessed by intracellular staining and IFNy EliSpot.

Nonsynonymous somatic mutations (N = 205) were identified by WES from the melanoma tumor biopsy. From a library of mutated tumor-specific peptides (N = 7512), 18 candidates predicted to be Class I neo-antigens were selected for immunogenicity testing. A new in-vitro assay using blood from healthy HLA-A201 donors identified one peptide that expanded antigen-specific T cells. Analysis of this mutation showed a VAF of 29.3% and TCGA revealed that the mutation identified was unique. IFNy secretion indicated that these antigen-specific T cells produced 6-fold higher IFNy to the mutant peptide vs the wildtype peptide. Direct binding of peptide to HLA was confirmed in vitro. Interrogation of the peptide expanded T cells by TCRseq showed clonal T cell expansion in response to the peptide. Unique TCR sequences identified in these T cells were present in the original melanoma tumor biopsy but not in adjacent tissue, confirming that naïve T cell donors can be used to validate neoantigens identified in cancer patients. The same TCR sequences were also identified in the peptide pool stimulated cells, suggesting that deconvolution may not be necessary to monitor neoantigen responses.

Using a newly developed pipeline combining next generation sequencing, epitope and clonal prediction algorithms, as well as an in-vitro assay to screen and evaluate putative neoantigens as targets of antitumor immunity, we confirmed one predicted neo-antigen from a melanoma patient. This pipeline could allow for the efficient and rapid identification of personalized neoantigens.

Citation Format: Nicholas M. Durham, Yelena Lazdun, Han Si, Todd Creasy, Brandon W. Higgs, Katie Streicher. A new pipeline to predict and confirm tumor neo-antigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4677.

Abstract 5390: microRNA signature of T cell exhaustion

Background: T cell exhaustion is driven by persistence of antigen and inflammation, common features of cancer. The success of a checkpoint inhibitor blockade may depend upon reactivation of pre-existing tumor-specific CD8+ T cells in the tumor microenvironment. Using an in vitro model and tumor infiltrating lymphocytes (TILs) isolated from multiple tumors, we explored microRNAs (miRNA, miR) involved in T cell dysfunction in order to identify pathways that may be important for altering this phenotype following immunotherapy.

Methods: We used an established in vitro model of T cell exhaustion: healthy donor CD8+ T cells were stimulated with anti-CD3/CD28 for six days. We used RNASeq and quantitative PCR to evaluate genomic (mRNA and microRNA (miR)) changes associated with T cell function and paired differentially expressed microRNAs with predicted target genes. Exhaustion of CD8+ TILs isolated from melanoma (n = 2), NSCLC (n = 3), renal (n = 3), bladder (n = 10), and colorectal tumors (n = 2) was measured by flow cytometry analysis of PD-1/TIM-3. miRNA and mRNA relationships identified by the in vitro model were evaluated in a subset of TILs from NSCLC, renal, and bladder tumors (n = 6).

Results: Results showed expected phenotypic and functional changes across 6 donors stimulated chronically with anti-CD3/CD28: 2-4-fold increased PD-1 and TIM-3 surface expression with a 3-5-fold loss of intracellular IFNg production (p &lt; 0.05). Comparing exhausted T cells with unstimulated T cells revealed ~1300 differentially expressed genes and ~100 differentially expressed miRs (p &lt; 0.05). A set of differentially expressed genes/miRs from the in vitro exhaustion model was then confirmed in TILs from NSCLC, bladder, and renal tumors. Differentially expressed miRs included microRNAs-155 and 181a, previously implicated in regulating IFNg signaling and T cell proliferation, respectively. Focusing on miRs that were altered between activation and exhaustion revealed a novel miR exhaustion signature, which was increased ≥4-fold relative to activated T cells. Evaluating this miR exhaustion signature in TCGA demonstrated a 16-fold range in expression across indications, with melanoma, head and neck, and NSCLC, among the highest median expression, while renal, HCC and rectal cancers were among the lowest. In HCC, GITR and OX40 pathway activation signatures were increased &gt;2-fold in tumors with high miR signature, while in renal cancer, B cell and CD40 pathway signatures were enriched. In melanoma, high miR signature showed a trend toward increased myeloid-derived suppressor cell (MDSC) signature expression (&gt;1.5-fold change), while the opposite trend was observed in head and neck cancer.

Conclusions: We identified a novel miRNA exhaustion signature associated with immune-related pathways in multiple tumor types. This signature may help generate hypotheses to guide prioritization of specific IO combination treatments.

Citation Format: Lydia M. Greenlees, Michael Kuziora, Yinong Sebastian, Todd Creasy, Young S. Lee, Fernanda Pilataxi, Nick Holoweckyj, Li Cheng, Brandon W. Higgs, Koustubh Ranade, Katie Streicher. microRNA signature of T cell exhaustion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5390.

Interferon Gamma Messenger RNA Signature in Tumor Biopsies Predicts Outcomes in Patients with Non-Small Cell Lung Carcinoma or Urothelial Cancer Treated with Durvalumab

Purpose: To identify a predictive biomarker for durvalumab, an anti-programmed death ligand 1 (PD-L1) mAb.Experimental Design: RNA sequencing of 97 advanced-stage non-small cell lung carcinoma (NSCLC) biopsies from a nonrandomized phase Ib/II clinical trial (1108/NCT01693562) were profiled to identify a predictive signature; 62 locally advanced or metastatic urothelial cancer tumors from the same study were profiled to confirm predictive utility of the signature. Thirty NSCLC patients provided pre- and posttreatment tumors for messenger RNA (mRNA) analysis. NSCLC with ≥25% tumor cells and urothelial cancer with ≥25% tumor or immune cells stained for PD-L1 at any intensity were scored PD-L1 positive (PD-L1⁺). Kaplan-Meier and Cox proportional hazards analyses were used to adjust for gender, age, prior therapies, histology, ECOG status, liver metastasis, and smoking. Tumor mutation burden (TMB) was calculated using data from The Cancer Genome Atlas (TCGA).Results: In the NSCLC discovery set, a four-gene IFNγ-positive (IFNγ⁺) signature comprising IFNγ, CD274, LAG3, and CXCL9 was associated with higher overall response rates, longer median progression-free survival, and overall survival compared with signature-low patients. IFNγ⁺-signature NSCLC patients had improved survival regardless of IHC PD-L1 status. These associations were replicated in a urothelial cancer cohort. The IFNγ⁺ signature was induced 2-fold (P = 0.003) by durvalumab after 8 weeks of therapy in patients with NSCLC, and baseline signature was associated with TMB but not survival in TCGA data.Conclusions: The IFNγ⁺ mRNA signature may assist in identifying patients with improved outcomes with durvalumab, independent of PD-L1 assessed by IHC. Clin Cancer Res; 24(16); 3857-66. ©2018 AACR.

IFNγ mRNA signature (IFNγ sig), circulating tumor DNA (ctDNA), and survival in NSCLC or urothelial cancer (UC) treated with durvalumab (D)

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Background: Associations between early reduction in plasma ctDNA, pretreatment tumoral IFNγ sig, liver metastases and outcomes, and between tumor mutational burden (TMB) and CD274 (PD-L1) mRNA or IFNγ sig in TCGA were evaluated in NSCLC and UC pts treated with D. Methods: Pts received 10 mg/kg Q2W of D in a Phase 1/2 study in advanced solid tumors. RNAseq measured a 4-gene IFNγ sig; top tertile was IFNγ sig+. Pts with PD-L1 expression (Ventana SP263) ≥ 25% tumor cells in NSCLC or ≥ 25% tumor or immune cells in UC were PD-L1+. 70 genes were assayed for DNA variants (Guardant360) in plasma ctDNA pre/posttreatment. TCGA was used to calculate TMB; ≥ median TMB was high. Results: IFNγ sig+ NSCLC or UC pts had higher response and longer median PFS and OS compared with PD-L1+, PD-L1- and IFNγ sig- pts (Table). Responders showed significant decreases in ctDNA mean variant allele frequency (VAF) posttreatment with D; pts with progressive disease showed increased VAF. Pts with decreased VAF at week 6 had longer median PFS and OS compared with those with VAF increases. VAF changes were not associated with IFNγ sig. NSCLC without liver metastases had higher IFNγ sig (P < 0.001) than pts with liver metastases. In TCGA NSCLC and UC, IFNγ sig+ correlated with high TMB; CD274 mRNA did not. Conclusions: IFNγ sig correlated with outcomes and with TMB in NSCLC and UC. CtDNA VAFs were reduced in NSCLC or UC responders after treatment and correlated with longer survival, suggesting utility as an early indicator of clinical benefit. Clinical trial information: NCT01693562. [Table: see text]

Population Modeling of Tumor Kinetics and Overall Survival to Identify Prognostic and Predictive Biomarkers of Efficacy for Durvalumab in Patients With Urothelial Carcinoma

Durvalumab is an anti‐PD‐L1 monoclonal antibody approved for patients with locally advanced or metastatic urothelial carcinoma (UC) that has progressed after platinum‐containing chemotherapy. A population tumor kinetic model, coupled with dropout and survival models, was developed to describe longitudinal tumor size data and predict overall survival in UC patients treated with durvalumab (NCT01693562) and to identify prognostic and predictive biomarkers of clinical outcomes. Model‐based covariate analysis identified liver metastasis as the most influential factor for tumor growth and immune‐cell PD‐L1 expression and baseline tumor burden as predictive factors for tumor killing. Tumor or immune‐cell PD‐L1 expression, liver metastasis, baseline hemoglobin, and albumin levels were identified as significant covariates for overall survival. These model simulations provided further insights into the impact of PD‐L1 cutoff values on treatment outcomes. The modeling framework can be a useful tool to guide patient selection and enrichment strategies for immunotherapies across various cancer indications.

Blockade of GM-CSF pathway induced sustained suppression of myeloid and T cell activities in rheumatoid arthritis

Objectives

Targeting the granulocyte-macrophage colony-stimulating factor (GM-CSF) pathway holds great potential in the treatment of inflammatory diseases. Mavrilimumab, a human monoclonal GM-CSF receptor-α antibody, has demonstrated clinical efficacy in RA. Our current study aimed to elucidate mechanisms of action and identify peripheral biomarkers associated with therapeutic responses of GM-CSF antagonism in RA.

Methods

A 24-week placebo (PBO)-controlled trial was conducted in 305 RA patients who received mavrilimumab (30, 100 or 150 mg) or PBO once every 2 weeks. Serum biomarkers and whole blood gene expression profiles were measured by protein immunoassay and whole genome microarray.

Results

Mavrilimumab treatment induced significant down-regulation of type IV collagen formation marker (P4NP 7S), macrophage-derived chemokine (CCL22), IL-2 receptor α and IL-6 compared with PBO. Both early and sustained reduction of P4NP 7S was associated with clinical response to 150 mg mavrilimumab treatment. Gene expression analyses demonstrated reduced expression of transcripts enriched in macrophage and IL-22/IL-17 signalling pathways after GM-CSF blockade therapy. Myeloid and T cell-associated transcripts were suppressed in mavrilimumab-treated ACR20 responders but not non-responders. While CCL22 and IL-6 down-regulation may reflect a direct effect of GM-CSFR blockade on the production of pro-inflammatory mediators by myeloid cells, the suppression of IL-2 receptor α and IL-17/IL-22 associated transcripts suggests an indirect suppressive effect of mavrilimumab on T cell activation.

Conclusion

Our results demonstrated association of peripheral biomarker changes with therapeutic response to mavrilimumab in RA patients. The sustained efficacy of mavrilimumab in RA may result from both direct effects on myeloid cells and indirect effects on T cell activation after GM-CSFR 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

Increased CD73 and reduced IFNG signature expression in relation to response rates to anti-PD-1(L1) therapies in EGFR-mutant NSCLC

11505

Background: Anti-PD-1(L1) therapies appear to be less efficacious in NSCLC patients whose tumors have EGFR activating mutations, but the underlying mechanism is poorly understood. We investigated the relationship between Methods: Flow cytometry and/or quantitative PCR were used to evaluate genes and proteins in five NSCLC EGFR mt cell lines and 6 wt lines. Anti-EGFR TKIs gefitinib and osimertinib were used at concentrations ranging from 0.001-100uM; EGF was used at 50 ng/mL. CP1108/NCT01693562 was a nonrandomized phase 1/2 trial evaluating durvalumab (10 mg/kg Q2W) in advanced NSCLC. As of 24OCT16, 304 previously treated patients in CP1108 were enrolled. RNA sequencing was conducted on available tumor specimens from 97 patients in CP1108. CP1108 and TCGA were separated by EGFR status for genomic comparisons. Results: Median CD73 expression was increased 10-fold in EGFR mt NSCLC cell lines (n = 5) compared to wt cell lines (n = 6). EGF induced CD73 protein levels 5-40-fold in 3/6 EGFR wt lines. There was dose-dependent inhibition of CD73 expression (45-70 fold maximum) following treatment with gefitinib or osimertinib in 3/5 mt cell lines and 4/6 wt lines, suggesting a causal relationship between the EGFR pathway and CD73 expression. Consistent with these observations, EGFR mutant tumors had ≥2 fold increased expression of CD73 compared to wt (p < 0.05) in TCGA and CP1108 NSCLC adenocarcinoma patients. These EGFR mutants had significantly lower levels of IFNg signature, previously reported to be associated with enhanced benefit from durvalumab. Conclusions: Our findings identify a novel relationship in NSCLC between EGFR pathway activation, expression of the immunosuppressive molecule CD73 and reduced expression of IFNg mRNA signature. These results prompt the hypothesis that over-expression of CD73 in EGFR-mt NSCLC may explain, at least in part, the reduced benefit from anti-PD-1(L1) in this subset of NSCLC, and suggest evaluating anti-CD73 in combination with EGFR TKIs or anti-PD-L1 in EGFR-mt NSCLC.

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.

Association of liver metastases (LM) with survival in NSCLC patients treated with durvalumab (D) in two independent clinical trials

3038

Background: Immunotherapies have improved survival in NSCLC but not all pts benefit. Besides baseline PDL1 expression, routinely measured clinical factors may predict clinical outcomes in immunotherapy trials. LM are associated with poor prognosis in melanoma and bladder cancer pts treated with anti-PD1/L1, respectively. We examined correlation between pretreatment LM and survival in D-treated NSCLC pts. Methods: CP1108/NCT01693562 and ATLANTIC/NCT02087423 were nonrandomized phase 1/2 and 2 trials, respectively, of D 10 mg/kg Q2W in advanced NSCLC. As of Oct 24/Jun 3 2016, 304/265 primarily pretreated pts were enrolled in CP1108/ATLANTIC Cohort 2. Cox proportional hazards analysis was conducted, first among LM+/− pts, then LM+/− and PDL1 high/low pts. Both models accounted for tumor stage, ECOG/WHO PS, histology, sex, age, smoking and PDL1 status. PDL1 high was defined as ≥25% tumor cells immunostained for PDL1 at any intensity. Results: LM absence was a positive independent predictor of OS and PFS in both trials. LM− and PDL1 high or low pts had improved OS and PFS vs PDL1 low/LM+; PDL1 high/LM+ pts had improved PFS vs PDL1 low/LM+. An independent tumor kinetic model indicated LM as a predictive covariate of rapid tumor growth in D-treated pts. Conclusions: LM are associated with shorter survival in D-treated NSCLC pts in 2 trials irrespective of PDL1 status. Clinical trial information: NCT02087423 and NCT01693562. [Table: see text]

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.

Tumor kinetic modeling and identification of predictive factors for tumor response to durvalumab in patients with non-small cell lung cancer (NSCLC)

11555

Background: Durvalumab is a human monoclonal antibody that binds to PD-L1 and blocks its interaction with PD-1 and CD80. The primary objectives of this analysis were to describe the longitudinal tumor size profiles and identify the key factors predicting tumor growth and regression following durvalumab. Methods: Longitudinal tumor size data obtained from NSCLC patients in study 1108 (all lines of therapy) and ATLANTIC (third line and beyond) following durvalumab treatment were modeled using nonlinear mixed effect modeling. Tumor kinetics were described by four key parameters: tumor growth and killing rate constants, fraction of durvalumab-sensitive tumor cells, and delay time for tumor killing. Potential predictive factors for tumor growth and regression were evaluated in a multi-variable covariate analysis. The model was used to simulate response rates at different tumor PD-L1 expression cutoffs. Results: Tumor kinetic modeling accurately described the longitudinal tumor response profiles from NSCLC patients in both studies. The factors associated with more rapid tumor growth were liver metastases, ECOG score > 0, high neutrophil-to-lymphocyte ratio and EGFR/ALK mutation. Tumor cell PD-L1 expression, baseline tumor size and smoking history were identified as significant predictive factors for tumor killing or the fraction of sensitive tumor cells. Simulations using the tumor kinetic model showed increased response rates in patients with higher tumor cell PD-L1 expression (increased by 9-11% and 10-14% with 25% and 50% cutoff, respectively), patients receiving durvalumab as first-line therapy (increased by 12% vs. 2nd line/above), and patients with smoking histories (increased by 4-5% vs. non-smokers). Conclusions: Tumor kinetic modeling identified factors that predict tumor progression and response following durvalumab in NSCLC patients. The multivariate analysis accounts for various predictive factors within predictive biomarker strata, allowing better interpretation of different biomarker cutoffs. The modeling technique can potentially guide patient selection/enrichment, clinical trial design strategies and tumor biology. Clinical trial information: NCT02087423 and NCT01693562.

Mutually exclusive expression of CD73 and PDL1 in tumors from patients (pt) with NSCLC, gastroesophageal (GE) and urothelial bladder carcinoma (UBC)

3079

Background: Tumors use multiple means of immune evasion, notably the programmed death-1 (PD1)/PDL1 pathway. Anti-PD1/PDL1 therapy induces anti-tumor activity and has improved pt outcomes. Activation of the immunosuppressive CD39/CD73/adenosine pathway might play a role in pts who do not benefit from anti-PD1/PDL1 therapies. We evaluated expression of CD73 and PDL1 and explored the association between CD73 and intraepithelial (IE) CD8+ cells (TILs) to begin to understand their potential interplay in cancer. Methods: Immunohistochemistry for PDL1, CD73 and CD8 was conducted on tumors of non-squamous NSCLC (NSq) (n=42), GE (n=50), and UBC (n=50). PDL1 and CD73 were scored by image analysis with Definiens software. IE CD8+ TILs were scored semi-quantitatively by a pathologist (0-2 = low; 3-4 = high). Using the top tertile of PDL1 and CD73 for high expression levels, a Fisher’s meta-analysis was calculated across the three indications. Results: Across all tumors, 25% (35/142) were PDL1 high (+), but CD73 low (-) and another 25% (35/142) were CD73+ but PDL1- (p=0.06, see table). This trend for mutually exclusive high expression of PDL1/CD73 was strongest in GE (p<0.01). In the PDL1+ group 76% (35/46) had high IE CD8+ TILs whereas in the CD73+ group only 35% (16/46) had high TILs (p<0.0001 using a proportions test). In the PDL1+/CD73- pt subset 77% (27/35) were CD8+ high vs only 23% (8/35) in the PDL1-/CD73+ subset. Conclusions: The identification of distinct pt subsets based on high PDL1 and/or CD73 expression suggests that tumors have multiple mechanisms of immune evasion. Increased IE CD8+ TILs were associated with PDL1 expression. The finding that PDL1-/ CD73+ tumors have lower IE CD8+ TILs compared to PDL1+/CD73- tumors suggests a role for CD73 in excluding IE TILs. Larger sample sets are needed to confirm these findings and to further explore any relationship with the tumor microenvironment. Our data suggests potential approaches to identify subsets of pts likely to benefit from immunotherapy targeting PDL1 and CD73. [Table: see text]

Gene expression analysis of tumor biopsies from a trial of durvalumab to identify subsets of NSCLC with shared immune pathways

3041

Background: We previously reported that NSCLC pts with high pretreatment tumoral IFNG mRNA signature (sig) expression have improved outcomes (ORR, PFS, OS) to the anti-PD-L1 therapy durvalumab (D). To explore the relationship of other immunotherapy targets with the IFNG sig, we evaluated expression of CD137, PD1, PDL1, CTLA4, GITR, OX40, TLR7, TLR8, CD73, TIM3, NKG2A, IDO1, CD40, LAG3, A2AR, CXCR4, iNOS, ARG1, and STAT3 in D-treated NSCLC. Methods: CP1108/NCT01693562 was a nonrandomized phase 1/2 trial evaluating D (10 mg/kg Q2W) in advanced NSCLC. As of 24OCT16, 304 primarily previously-treated pts were enrolled. RNA sequencing was conducted on available tumor specimens from 98 pts. ORR was evaluated using RECIST v1.1. 19 genes were z-scored, scaled and clustered across pt tumors. Each gene was coded binary using 0 as a cut point. The proportion of tumors with concordant or discordant over-expression between a gene and the IFNG sig was calculated. Results: In 43% of evaluable NSCLC pts, mRNAs for PD-1, IDO1, PD-L1, CD40, CTLA4, LAG3, TIM3, TLR8, NKG2A, and CD137 were co-expressed with IFNG sig (Spearman’s rho > = 0.7). In 34% of evaluable pts, TLR7, OX40, GITR, A2AR, and CXCR4 mRNAs had moderate concordance with IFNG sig (0.5 < rho < 0.7) and in 23% of evaluable pts iNOS, CD73, ARG1, and STAT3 had low concordance (rho < 0.5). Within the cluster of pts including high IFNG sig, a small subset expressed high iNOS and CD73; however, pts with high STAT3 or ARG1 formed a distinct cluster within the low IFNG sig subset. The subset with high IFNG sig had an ORR of 24% compared to only 10% in all other subsets combined. Conclusions: Our findings enrich understanding of the immune microenvironment of NSCLC by identifying three broad categories of tumors: tumors with pre-existing immunity that have high IFNg sig and select other IO pathways with enhanced responses to D; tumors with moderate expression of IO genes in which the local microenvironment is crucial; finally a distinct “cold” subset of tumors with high expression of STAT3 or ARG1 and characterized by low or no expression of IFNG sig and other IO genes. These results may aid in identifying the right pts for anti-PD-L1 and in prioritizing immunotherapy combinations.

Rational Selection of Syngeneic Preclinical Tumor Models for Immunotherapeutic Drug Discovery

Murine syngeneic tumor models are critical to novel immuno-based therapy development, but the molecular and immunologic features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Across a panel of commonly used murine syngeneic tumor models, we showed variable responsiveness to immunotherapies. We used array comparative genomic hybridization, whole-exome sequencing, exon microarray analysis, and flow cytometry to extensively characterize these models, which revealed striking differences that may underlie these contrasting response profiles. We identified strong differential gene expression in immune-related pathways and changes in immune cell-specific genes that suggested differences in tumor immune infiltrates between models. Further investigation using flow cytometry showed differences in both the composition and magnitude of the tumor immune infiltrates, identifying models that harbor "inflamed" and "non-inflamed" tumor immune infiltrate phenotypes. We also found that immunosuppressive cell types predominated in syngeneic mouse tumor models that did not respond to immune-checkpoint blockade, whereas cytotoxic effector immune cells were enriched in responsive models. A cytotoxic cell-rich tumor immune infiltrate has been correlated with increased efficacy of immunotherapies in the clinic, and these differences could underlie the varying response profiles to immunotherapy between the syngeneic models. This characterization highlighted the importance of extensive profiling and will enable investigators to select appropriate models to interrogate the activity of immunotherapies as well as combinations with targeted therapies in vivo Cancer Immunol Res; 5(1); 29-41. ©2016 AACR.

In Vivo Therapeutic Success of MicroRNA-155 Antagomir in a Mouse Model of Lupus Alveolar Hemorrhage

OBJECTIVE

Diffuse alveolar hemorrhage (DAH) is a rare but life-threatening complication of systemic lupus erythematosus (SLE). Pristane-treated B6 mice develop severe DAH within 2 weeks of treatment. MicroRNA-155 (miR-155) is a pleiotropic microRNA that plays a crucial role in the regulation of immune responses. Recent studies have revealed a pathogenic role of miR-155 in various autoimmune disorders. The purpose of this study was to examine the role of miR-155 in the development of DAH in pristane-induced lupus using miR-155-knockout (miR-155(-/-)) mice and miR-155 antagomir to silence miR-155.

METHODS

DAH was induced by an intraperitoneal injection of 0.5 ml of pristane. MicroRNA-155 antagomir was administered intravenously to silence miR-155 expression. Lung tissues were collected for RNA extraction and were embedded in paraffin for sectioning. Gene expression profiling data were analyzed using Ingenuity Pathway Analysis. Real-time quantitative polymerase chain reaction analysis was used for single-gene validation. Luciferase reporter assay and argonaute 2 immunoprecipitation were performed for target validation.

RESULTS

MicroRNA-155 expression was significantly increased during the development of DAH. Disease progression was reduced in miR-155(-/-) mice as well as by in vivo silencing of miR-155 using a miR-155 antagomir. MicroRNA-155 silencing dampened pristane-induced ectopic activation of multiple inflammatory pathways and reduced the expression of proinflammatory cytokines. Several negative regulators of NF-κB signaling were inhibited by pristane and were reactivated in miR-155(-/-) mice. In particular, the antiinflammatory factor peroxisome proliferator-activated receptor α was identified as a direct target of miR-155.

CONCLUSION

MicroRNA-155 promotes pristane-induced lung inflammation. It contributes to ectopic activation of NF-κB signaling pathways by targeting multiple negative regulators. MicroRNA-155 antagomir may be a promising therapeutic strategy for treating acute lung inflammation in lupus.

Genomic Landscape Survey Identifies SRSF1 as a Key Oncodriver in Small Cell Lung Cancer

Small cell lung cancer (SCLC) is an aggressive disease with poor survival. A few sequencing studies performed on limited number of samples have revealed potential disease-driving genes in SCLC, however, much still remains unknown, particularly in the Asian patient population. Here we conducted whole exome sequencing (WES) and transcriptomic sequencing of primary tumors from 99 Chinese SCLC patients. Dysregulation of tumor suppressor genes TP53 and RB1 was observed in 82% and 62% of SCLC patients, respectively, and more than half of the SCLC patients (62%) harbored TP53 and RB1 mutation and/or copy number loss. Additionally, Serine/Arginine Splicing Factor 1 (SRSF1) DNA copy number gain and mRNA over-expression was strongly associated with poor survival using both discovery and validation patient cohorts. Functional studies in vitro and in vivo demonstrate that SRSF1 is important for tumorigenicity of SCLC and may play a key role in DNA repair and chemo-sensitivity. These results strongly support SRSF1 as a prognostic biomarker in SCLC and provide a rationale for personalized therapy in SCLC.

SCLC patients are initially highly chemo-sensitive with response rates of greater than 80% in both limited and extensive diseases, but suffer uniform disease recurrence or progression in a very short period of time. In the absence of well-defined genomic biomarkers and insights into the resistance mechanism, many targeted treatments have yielded negative results in the last decade Using integrated next generation sequencing (NGS) technology in combination with a high quality surgical sample set with comprehensive clinical annotation, our study not only identified novel recurrent genetic alterations in genes such as CDH10 and DNA repair pathways which may influence outcomes in SCLC patients, but also discovered the expression of SRSF1, an RNA-splicing factor which can both regulate key oncogenic and survival pathways such as BCL2, and play a critical role in patient survival.