Tumor Biopsy Samples Research Articles

Targeted Inhibition of Fibroblast Growth Factor Receptor 1-GLI Through AZD4547 and GANT61 Modulates Breast Cancer Progression.

The underlying mechanism of fibroblast growth factor receptor 1 (FGFR1) mediated carcinogenesis is still not fully understood. For instance, FGFR1 upregulation leads to endocrine therapy resistance in breast cancer patients. The current study aimed to identify FGFR1-linked genes to devise improved therapeutic strategies. RNA-seq and microarray expression data of 1,425 breast cancer patients from two independent cohorts were downloaded for the analysis. Gene Set Enrichment Analysis (GSEA) was performed to identify differentially expressed pathways associated with FGFR1 expression. Validation was done using 150 fresh tumor biopsy samples of breast cancer patients. The clinical relevance of mRNA and protein expression of FGFR1 and its associated genes were also evaluated in mouse embryonic fibroblasts (MEFs) and breast cancer cell line (MDA-MB-231). Furthermore, MDA-MB-231 cell line was treated with AZD4547 and GANT61 to identify the probable role of FGFR1 and its associated genes on cells motility and invasion. According to GSEA results, SHH pathway genes were significantly upregulated in FGFR1 patients in both discovery cohorts of breast cancer. Statistical analyses using both discovery cohorts and 150 fresh biopsy samples revealed strong association of FGFR1 and GLI1, a member of SHH pathway. The increase in the expression of these molecules was associated with poor prognosis, lymph node involvement, late stage, and metastasis. Combined exposures to AZD4547 (FGFR1 inhibitor) and GANT61 (GLI1 inhibitor) significantly reduced cell proliferation, cell motility, and invasion, suggesting molecular crosstalk in breast cancer progression and metastasis. A strong positive feedback mechanism between FGFR1–GLI1 axis was observed, which significantly increased cell proliferation and metastasis. Targeting FGFR1–GLI1 simultaneously will significantly improve the prognosis of breast cancer in patients.

Exploring microsatellite instability in patients with advanced hepatocellular carcinoma and its tumor microenvironment.

Background and AimImmune checkpoint inhibitors and their combination with other agents have recently been available in advanced hepatocellular carcinoma (HCC). Hence, a thorough understanding of the tumor microenvironment based on tumor samples is yet to be achieved. This study aimed to explore the tumor microenvironment in advanced HCC in terms of microsatellite instability‐high (MSI‐H) by using tumor samples from advanced HCC patients eligible for systemic therapy.MethodsMSI‐H was assessed by polymerase chain reaction, and the expression of mismatch repair proteins, PD‐L1, CD8, VEGF, and HLA‐class1 was evaluated by immunohistochemistry. Whole‐exome sequencing was performed for MSI‐H tumor samples.ResultsOf 50 patients, one (2.0%) was confirmed with MSI‐H. In the MSI‐H advanced HCC tumor, a high tumor mutation burden, infiltration of CD8+ lymphocytes, and low expression of VEGF were identified. Although PD‐L1 expression was negative, there was shrinkage of tumor following pembrolizumab. However, another tumor nonresponsive to pembrolizumab was present simultaneously. Checking the Cancer Genome Atlas (TCGA) database, we found a similar case to this patient. The TCGA case had unique gene features of miR‐21 and miR‐155 overexpression and hypermethylation of the MSH2 gene.ConclusionWe identified a very small number of MSI‐H cases in HCC using one tumor biopsy sample for each patient with advanced HCC. In addition, epigenetic aberrations possibly lead to MSI‐H in HCC patients. Since different HCC clones might coexist in the liver, sampling from multiple tumors should be considered to clarify the true proportion of MSI‐H in HCC and to analyze tumor microenvironments.

Symposium Title: Do Mental Disorders Surf on EEG Waves? Pathophysiological Mechanisms Revisited

Implementing cancer precision medicine in the clinic requires assessing the therapeutic relevance of genomic alterations. A main challenge is the systematic interpretation of whole-exome sequencing (WES) data for clinical care.One hundred sixty-five adults with metastatic colorectal and lung adenocarcinomas were prospectively enrolled in the CanSeq study. WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples. Somatic and germ-line alterations were ranked according to therapeutic or clinical relevance. Results were interpreted using an integrated somatic and germ-line framework and returned in accordance with patient preferences.At the time of this analysis, WES had been performed and results returned to the clinical team for 165 participants. Of 768 curated somatic alterations, only 31% were associated with clinical evidence and 69% with preclinical or inferential evidence. Of 806 curated germ-line variants, 5% were clinically relevant and 56% were classified as variants of unknown significance. The variant review and decision-making processes were effective when the process was changed from that of a Molecular Tumor Board to a protocol-based approach.The development of novel interpretive and decision-support tools that draw from scientific and clinical evidence will be crucial for the success of cancer precision medicine in WES studies.Genet Med advance online publication 26 January 2017

ABCL-261: STR Profiling Reveals Tumor Genome Instability in Primary Mediastinal B-Cell Lymphoma

<h3>Context</h3> Molecular factors to determine the prognosis for primary mediastinal B-cell lymphoma (PMBCL) are not described yet. In this regard, the loss of heterozygosity (LOH) in STR loci and elevated microsatellite alteration at selected tetranucleotides (EMAST) in the tumor genome are of interest. <h3>Objective</h3> To analyze the frequency of LOH and EMAST in tumor cells of PMBCL patients at diagnosis and to check possible association with disease features. <h3>Design</h3> STR profiles of the DNA of tumor cells were analyzed in a cohort of 72 PMBCL patients undergoing EPOCH regimen treatment at the National Research Center for Hematology (Moscow, Russia). <h3>Setting</h3> DNA was isolated from tumor biopsy samples taken at diagnosis. Control DNA samples were taken from the blood of patients in complete remission or from the buccal epithelium. STR profiles for LOH and EMAST analysis were assessed by PCR with the COrDIS Plus multiplex kit for amplification of 19 STR markers and amelogenin loci (Gordiz Ltd, Russia). The fragment analysis was performed on an ABI3130 Genetic Analyzer. <h3>Patients</h3> Inclusion criterion: <i>de novo</i>-diagnosed PMBCL patients. Exclusion criterion: pre-treatment. <h3>Main Outcomes Measures</h3> Progression-free survival (PFS) and overall survival (OS) at 24 months from diagnosis were used to assess the independent impact of genetic instability as a risk factor. <h3>Results</h3> LOH was detected in 37 of 72 patients (51.4%). EMAST was found in 40 patients (55.5%); 24 had a combination of EMAST with LOH. For all EMAST-positive patients, the number of involved loci was no more than 4 out of 19 (EMAST-low, less than one-third of the panel of microsatellite markers). It was shown that OS and PFS were the highest in patients with a stable STR tumor profile. <h3>Conclusions</h3> STR profiling of PMBCL tumor genome revealed LOHs associated with deletions or uniparental disomy and detected EMAST attributed to failure of DNA mismatch repair. The high incidence of LOH and EMAST in PMBCL can be associated with standard therapy failure in a significant number of patients. <h3>Funding</h3> This study was supported by Rakfond grant 2/2020.

A wake-up call for cancer DNA damage: the role of Schlafen 11 (SLFN11) across multiple cancers.

DNA-damaging agents exploit increased genomic instability, a hallmark of cancer. Recently, inhibitors targeting the DNA damage response (DDR) pathways, such as PARP inhibitors, have also shown promising therapeutic potential. However, not all tumors respond well to these treatments, suggesting additional determinants of response are required. Schlafen 11 (SLFN11), a putative DNA/RNA helicase that induces irreversible replication block, is emerging as an important regulator of cellular response to DNA damage. Preclinical and emerging clinical trial data suggest that SLFN11 is a predictive biomarker of response to a wide range of therapeutics that cause DNA damage including platinum salts and topoisomerase I/II inhibitors, as well as PARP inhibitors, which has raised exciting possibilities for its clinical application. In this article, we review the function, prevalence, and clinical testing of SLFN11 in tumor biopsy samples and circulating tumor cells. We discuss mounting evidence of SLFN11 as a key predictive biomarker for a wide range of cancer therapeutics and as a prognostic marker across several cancer types. Furthermore, we discuss emerging areas of investigation such as epigenetic reactivation of SLFN11 and its role in activating immune response. We then provide perspectives on open questions and future directions in studying this important biomarker.

Programmed Cell Death Ligand 1 Expression in Circulating Tumor Cells as a Predictor of Treatment Response in Patients with Urothelial Carcinoma

Simple SummaryProgrammed cell death ligand 1 (PD-L1) inhibitors are commonly used in treating advanced-stage urothelial carcinoma. Contrary to evaluating PD-L1 expression in tumor biopsy samples, this study assessed whether PD-L1 expression in circulating tumor cells (CTCs) can be a predictor of treatment response to PD-L1 inhibitors. The current study proved that there was no statistically significant correlation between the presence of PD-L1-positive CTCs and PD-L1 expression in tumor tissues. Moreover, PD-L1-positive CTCs at baseline could be used as a biomarker to identify patients suitable for PD-L1 blockade therapy. Dynamic changes in PD-L1-positive CTCs during the course of treatment are predictive factors of immunotherapy response and prognostic factors of disease control.Programmed cell death ligand 1 (PD-L1) inhibitors are commonly used in treating advanced-stage urothelial carcinoma (UC). Therefore, this study evaluated the relationship between PD-L1 expression in circulating tumor cells (CTCs) and treatment response to PD-L1 inhibitors using blood samples collected from patients with UC (n = 23). Subsequently, PD-L1 expression and its clinical correlation were analyzed. All patients had CTCs before PD-L1 inhibitory treatment, of which 15 had PD-L1-positive CTCs. However, PD-L1-positive expression in CTCs was not correlated with PD-L1 expression in tumor biopsy samples. Patients with PD-L1-positive CTCs had better disease control (DC) rates than those without PD-L1-positive CTCs. Moreover, changes in the proportion of PD-L1-positive CTCs were associated with disease outcomes. Furthermore, the PD-L1-positive CTC count in 9 of 11 patients who achieved DC had significantly decreased (p = 0.01). In four patients with progressive disease, this was higher or did not change. PD-L1-positive CTCs at baseline could be used as a biomarker to identify patients suitable for PD-L1 blockade therapy. Dynamic changes in PD-L1-positive CTCs during the course of treatment are predictive factors of immunotherapy response and prognostic factors of disease control. Hence, PD-L1-positive CTCs could be employed as a real-time molecular biomarker for individualized immunotherapy.

NGS Analysis of Liquid Biopsy (LB) and Formalin-Fixed Paraffin-Embedded (FFPE) Melanoma Samples Using Oncomine™ Pan-Cancer Cell-Free Assay.

Next-generation sequencing (NGS) in liquid biopsies may contribute to the diagnosis, monitoring, and personalized therapy of cancer through the real-time detection of a tumor’s genetic profile. There are a few NGS platforms offering high-sensitivity sequencing of cell-free DNA (cfDNA) samples. The aim of this study was to evaluate the Ion AmpliSeq HD Technology for targeted sequencing of tumor and liquid biopsy samples from patients with fourth-stage melanoma. Sequencing of 30 samples (FFPE tumor and liquid biopsy) derived from 14 patients using the Oncomine™ Pan-Cancer Cell-Free Assay was performed. The analysis revealed high concordance between the qPCR and NGS results of the BRAF mutation in FFPE samples (91%), as well as between the FFPE and liquid biopsy samples (91%). The plasma-tumor concordance of the non-BRAF mutations was 28%. A total of 17 pathogenic variants in 14 genes (from 52-gene panel), including TP53, CTNNB1, CCND1, MET, MAP2K1, and GNAS, were identified, with the CTNNB1S45F variant being the most frequent. A positive correlation between the LDH level and cfDNA concentration as well as negative correlation between the LDH level and time to progression was confirmed in a 22-patient cohort. The analysis showed both the potential and limitations of liquid biopsy genetic profiling using HD technology and the Ion Torrent platform.

Abstract 2725: Immune-cell profiling in breast cancer patients by race and triple negative breast cancer status

Abstract Breast cancer is the most frequently diagnosed cancer and the second leading cause of cancer-related death among American women. Underserved minorities suffer from higher mortality rates and a higher prevalence of triple-negative breast cancer (TNBC). Previous studies showed that African Americans (AA) have a higher risk for TNBC, advanced tumor, pro-inflammatory tumor microenvironment, and worse survival. Immune responses and inflammatory processes play critical roles in cancer initiation, progression, and suppression. Therefore, this study was designed to investigate the complex interplay among the tumor, microenvironment, and immune response by race and TNBC status. Tumor biopsy samples from 96 breast cancer cases were used for the NanoString PanCancer IO 360 Gene Expression Panel analysis. The panel is a 770 gene Code Set that is designed for profiling tumor biopsies and characterizing gene expression patterns associated with the tumor, the immune response, and the microenvironment that shape tumor-immune interactions. After quality control for 20 reference genes, gene expression data from 93 samples were used for subsequent data analysis with nSolver 4.0 to calculate expression changes, pathway mapping based on annotations, sample clustering (heat maps), and 14 immune cell type abundance signatures. Then we conducted a Student's t-test and ANOVA for comparison of immune cell types by patient demographics and clinical characteristics using SAS University Edition 2019. In 10 TNBC and 83 non-TNBC, the expression of 12 genes was significantly different, 4 were higher and 8 were lower in TNBC (False Discovery Rate adjusted p&amp;lt;0.05). AA patients had significantly higher B cells (p=0.02), T cells (p=0.03), macrophages (p=0.02), CD45 (p=0.02), and Treg cells (p=0.04) than white patients. Patients diagnosed at a young age had significantly lower neutrophil counts (p=0.02). Nonsmokers had significantly higher mast cell scores than smokers (p=0.03). Mast cells were significantly lower in ER-negative (p&amp;lt;0.01), PR-negative (p&amp;lt;0.01), and TNBC (p&amp;lt;0.01) patients than ER-positive, PR-positive, and non-TNBC patients. Our study results suggest that gene expression and immune cell types are different by race and TNBC status. Future data analysis will focus on 18-gene tumor inflammation signature, 15+ proprietary gene expression signatures, and 14 immune cell type abundance signatures with a single sample and dataset analysis report, and automatic predictive algorithm training. With the recent FDA accelerated approval of PD-L1 inhibitor atezolizumab as a treatment for PD-L1-positive metastatic TNBC, the NanoString PanCancer IO 360 panel may provide the capability to both discover new biomarkers and create potentially predictive signatures for immunotherapies, which in turn may help improve minority health and reduce survival disparities. Citation Format: Xiaozhuang Hu, Fernando Collado-Mesa, George R. Yang, Isildinha M. Reis, Jennifer J. Hu. Immune-cell profiling in breast cancer patients by race and triple negative breast cancer status [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2725.

Abstract 385: Identification of NF-kappaB phospho-p50 as a predictive biomarker for IRAK4 inhibitor CA-4948 in patients with non-Hodgkin's lymphoma

Abstract Background: IRAK4, a serine/threonine kinase, was identified as a therapeutic target in hematological malignancies. IRAK4-mediated activation of NF-kappaB could play an important role in NF-kappaB-regulated survival and chemoresistance of cancer cells. CA-4948, a first-in-class small molecule inhibitor of IRAK4, has been tested in Phase 1 clinical trial with evidence of clinical activity in Non-Hodgkin's Lymphoma (NHL) patients. To support the development of companion diagnostic for CA-4948, we developed an immunohistochemical (IHC) assay and explored expression of potential biomarkers of response to CA-4948 in tumor biopsy samples obtained from NHL patients. Materials and Methods: IHC assay was developed and used for analysis of NF-kappaB p-p50 and p-IRAK1 expression in tumor biopsy samples obtained from 14 patients with NHL. Patients were defined according to their clinical response to CA-4948 treatment: stable disease (SD), 6 cases and progressive disease (PD), 8 cases. Results: We found nuclear and/or cytoplasmic expression of NF-kappaB p-p50 in all 6 SD cases treated with 50 mg QD (2 cases, tumor regression), 50 mg BID (1 case), 200 mg BID (1 case, tumor regression) and 400 mg BID (2 cases). Expression of NF-kappaB p-p50 was not detected in 7 of 8 cases with PD including patients treated with 50 mg QD (1 case), 100 mg QD (1 case), 100 mg BID (3 cases), 200 mg BID (1 case) and 400 mg BID (1 case). We found statistically significant correlation between expression of NF-kappaB p-p50 in tumor biopsy and SD in NHL patients treated with CA-4948 (p&amp;lt;0.05). Analysis of NF-kappaB p-p50 expression in paired tumor biopsy samples (3 cases) collected before and after the treatment with CA-4948 revealed a significant downregulation of NF-kappaB p-p50 expression in tumors obtained from CA-4948-treated NHL patients. In support of our in vivo findings, our in vitro experiments demonstrated that expression of NF-kappaB p-p50 was depleted in 3D lymphoma organoids treated with a clinically relevant concentration of CA-4948. Our results support further development of NF-kappaB p-p50 as a potential predictive and pharmacodynamic biomarker of IRAK4 inhibitor CA-4948. We found that expression of p-IRAK1 in tumor biopsies was not correlated with clinical response. Conclusions: Although the cohort size is small, our findings suggest that expression of NF-kappaB p-p50 can serve as biomarker to predict SD in response to the treatment with IRAK4 inhibitor CA-4948 in NHL patients. NF-kappaB p-p50 selection strategy might be used in future clinical trials to identify NHL patients which are most likely to respond to CA-4948 in combination with chemotherapy or targeted therapeutics. Citation Format: Andrey Ugolkov, Maria Samson, Rosanna Hok, Reinhard von Roemeling, Robert Martell. Identification of NF-kappaB phospho-p50 as a predictive biomarker for IRAK4 inhibitor CA-4948 in patients with non-Hodgkin's lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 385.

Abstract 1171: Assessing Melanocortin 1 receptor as a target for metastatic melanoma drug delivery

Abstract In as little as six weeks, melanoma can turn life-threatening. Not only is melanoma a fast growing skin cancer, but its annual incidence rate is nearly 100,000 in the United States. Disease identified early can be cured by surgery, but metastatic melanoma is lethal. Despite the striking progress in treating metastatic melanoma using MAPK inhibitors and immune checkpoint inhibitors, improvements in objective response rate (&amp;lt;50%) and 5-yr survival (&amp;lt;30%) are critically needed. Melanocortin 1 receptor (MC1R), a G protein-coupled receptor, has been investigated as a potential target for drug delivery (e.g., peptide receptor radionuclide therapies, peptide-drug conjugates, etc.) to metastatic melanoma cells, as it is overexpressed in melanomas but largely absent in normal tissues. This study aims to further investigate the potential of MC1R as a target for drug delivery, by determining its expression in melanoma cancer cell lines, human melanoma biopsies, as well as normal tissue specimen. Bmax and MC1Rs per cell in five human melanoma cell lines (TXM13, TXM40, Sk-Mel-28, A375, and A2058) were calculated from saturation binding assays using synthetic MC1R ligand [125I]Nle-D-Phe-α-MSH (125I-NDP-α-MSH). An immunohistochemistry (IHC) staining protocol was developed using paraffin-embedded xenografts of TXM13, TXM40, Sk-Mel-28, A375, and A2058 human melanoma cells. IHC staining of MC1R was performed using human melanoma biopsy samples of stage III and IV metastatic melanoma obtained from University of Iowa Tissue Procurement Core Facility. MC1R-IHC was also performed on Caucasian North American normal tissue specimens including skin, muscle, pituitary gland, adrenal gland, cerebellum, and testis obtained from Amsbio. 125I-NDP-α-MSH binding assay results revealed positive staining in all melanoma cell lines, with the density of 2,762 receptors/cell in TXM13, 461 receptors/cell in Sk-Mel-28, 343 receptors/cell in TXM40, 164 receptors/cell in A375, and 93 receptors/cell in A2058. The IHC staining also demonstrated positive immunoreactivity against MC1R in stage III and IV human metastatic melanoma biopsy samples. Heterogenous expression of MC1R was found within the biopsy samples and among tumor biopsy samples, and the staining intensity fell within the range of the melanoma cancer cell line xenografts. Conversely, negative IHC staining of MC1R was found in normal tissue specimen, indicating that the expression of MC1R in normal tissues is largely absent. This study establishes an MC1R-IHC staining protocol optimized for clinical applications, and our data demonstrates high expression of MC1R in human melanoma biopsy samples as well as in melanoma cancer cell lines. The expression of MC1R in normal tissue specimens is largely absent. These results indicate that MC1R-targeted therapies, such as peptide receptor radionuclide therapies, are a promising alternative to current therapies for metastatic melanoma. Citation Format: Brenna Marks, Mengshi Li, Edwin Sagastume, Michael Schultz, Frances Johnson. Assessing Melanocortin 1 receptor as a target for metastatic melanoma drug delivery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1171.

Reproducibility of m7-FLIPI Risk Scores in Follicular Lymphoma Using Tumor Biopsies and Blood Specimens

Background: Follicular lymphoma (FL) is clinically and genetically heterogeneous. While most patients experience an indolent disease course, with median survival of over 15 years, a portion of patients experience early relapse and poor outcomes. The m7-FLIPI risk score has been described as a clinicogenetic method to accurately determine which patients are at highest risk for early relapse and poor outcomes (Pastore et al., Lancet Oncology 2015; Vindi et al., Blood 2015). However, molecular characterization of the m7 genes currently relies on tumor biopsies, which require an invasive procedure and may be unavailable. Furthermore, it is unclear whether the m7-FLIPI score is consistent over the course of disease. Circulating tumor DNA (ctDNA) is an emerging noninvasive biomarker for tumor detection in diverse lymphomas including FL. In this study, we evaluated the stability of m7-FLIPI status over multiple FL relapses as well as the utility of ctDNA for classification of patients with FL into high- and low-risk m7-FLIPI categories.Methods: We applied Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq), a capture-based method for ultra-deep sequencing (Newman et al., Nat Med 2014; Scherer et al., Sci Transl Med 2016 ) to identify risk via m7-FLIPI in pretreatment tumor and plasma samples of 29 FL patients. In addition, we retrospectively analyzed whole exome sequencing (WES) data of 37 patients from two FL cohorts (Green et al., PNAS 2015; Bouska et al., Leukemia 2017). We first validated in silico our capture-based method for identification of m7-FLIPI-relevant somatic alterations in 258 patients from the original publication (Pastore et al., Lancet Oncology 2015). We then identified non-synonymous mutations in CREBBP, EZH2, ARID1A, MEF2B, FOXO1, EP300, and CARD11 presentin each tumor and plasma sample. Using both CAPP-Seq and WES data (n = 66), we compared m7-FLIPI risk group concordance between paired diagnostic tumor biopsies, paired diagnostic and relapse tumor biopsies, paired FL and transformed FL (tFL) tumor biopsies, and paired diagnostic tumor and plasma samples. FLIPI was calculated at first FL time-point available.Results: We observed a 95% agreement in m7-FLIPI risk category between our capture-based method and methods utilizing full exon coverage. A 100% concordance of m7 gene profile and 100% concordance of m7-FLIPI risk category were seen when comparing paired FL tumor biopsy samples from two separate lymph nodes obtained at diagnosis (n = 5). In addition, a 75% agreement in m7 gene profile and 100% agreement of m7-FLIPI risk category were observed when comparing tumor biopsy samples obtained at FL diagnosis and first relapse (n = 36; median time to relapse of 547 days, range 55 - 4200 days). There was a low concordance in m7 genetic profile between tumor biopsy samples from time of initial diagnosis and transformation (48.4%, n = 31). Importantly, concordance of m7 gene profile and m7-FLIPI risk category was 64.3% and 78.6%, respectively, when assessed by paired tumor and plasma samples obtained at FL diagnosis (n = 14; Figure 1). Furthermore, non-concordant mutations could be present in either the tumor or the plasma sample. Across all FL samples, there was no significant difference in concordance based on individual m7 genes. When analyzing pairs in which mutations were observed, concordance between paired samples was lowest for EZH2 (p = 0.028).Conclusions: m7-FLIPI scores appear consistent between multiple FL tumor samples obtained at the time of diagnosis and across FL relapses. However, concordance in m7 gene profile between paired plasma and tumor samples is lower than between paired tumor biopsies, even at ultra-deep sequencing depths. Optimization of blood samples for assessing m7 gene profile should be performed to improve the reliability of ctDNA for determining m7-FLIPI risk status.Figure 1. Concordance of m7-FLIPI risk category. (A) Re-classification of m7-FLIPI risk category when using paired tumor biopsy and plasma samples from 14 patients. (B) Percentage of discordant samples when comparing diagnostic tumor pairs (n = 5), diagnostic versus relapse tumor pairs (n = 37), and diagnostic tumor versus plasma pairs (n = 14). Concordance was lowest for diagnostic tumor and diagnostic plasma pairs (p = 0.013). [Display omitted] DisclosuresDiehn:Varian Medical Systems: Research Funding; Quanticel Pharmaceuticals: Consultancy; Roche: Consultancy; Novartis: Consultancy. Alizadeh:Gilead: Consultancy; Roche: Consultancy; Genentech: Consultancy; Celgene: Consultancy; CiberMed: Consultancy.

EPCT-04. RESULTS OF A PHASE 1 STUDY OF THE ONCOLYTIC ADENOVIRUS DNX-2401 WITH RADIOTHERAPY FOR NEWLY DIAGNOSED DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)

BackgroundA Phase 1, single center study is ongoing to evaluate the conditionally replicative oncolytic adenovirus, DNX-2401 (tasadenoturev), followed by radiotherapy (RT) in pediatric patients with newly diagnosed diffuse intrinsic pontine glioma (DIPG). MethodsPatients 1–18 years with newly diagnosed DIPG with no prior treatment, Lansky/Karnofsky performance score ≥ 70, and adequate organ function were enrolled. A tumor biopsy was performed followed by a single intratumoral injection of 1e10-5e10 virus particles (vp) DNX-2401. Conventional radiotherapy was initiated within 1 month of DNX-2401 administration. ResultsEnrolled subjects (n=12) had a median age of 9 (range 3–18) and performance scores of 90–100 (n=4; 33%) or 70–80 (n=8; 67%). As part of a dose escalation design, subjects were treated with 1e10 vp (n=4) or 5e10 vp DNX-2401 (n=8), which was then followed by standard RT in 11 of 12 subjects (92%). No dose-limiting toxicities were observed and the treatment regimen was well-tolerated. Adverse events (AEs) have been primarily mild to moderate and consistent with underlying disease. The most commonly reported AEs (≥ 5 subjects), regardless of study drug relationship, include headache, asthenia, vomiting, anemia, leukocytosis, and fever. Two SAEs have been reported including grade 3 lymphopenia and grade 3 abdominal pain. Tumor reductions have been observed and efficacy evaluations are ongoing. As of 09Dec2020, 12-month survival (OS-12) was 71% and 4 of 12 patients had survived > 20 months. Four subjects continue to be followed for survival. Correlative analysis of tumor biopsy and peripheral samples is ongoing. ConclusionsDNX-2401 followed by RT can be safely administered to pediatric subjects with newly diagnosed DIPG; clinical activity and preliminary survival are encouraging.

The breast is yet to come: current and future utility of circulating tumour DNA in breast cancer.

Advances in genomic strategies and the development of targeted therapies have enabled precision medicine to revolutionise the field of oncology. Precision medicine uses patient-specific genetic and molecular information, traditionally obtained from tumour biopsy samples, to classify tumours and treat them accordingly. However, biopsy samples often fail to provide complete tumour profiling, and the technique is expensive and, of course, relatively invasive. Advances in genomic techniques have led to improvements in the isolation and detection of circulating tumour DNA (ctDNA), a component of a peripheral blood draw/liquid biopsy. Liquid biopsy offers a minimally invasive method to gather genetic information that is representative of a global snapshot of both primary and metastatic sites and can thereby provide invaluable information for potential targeted therapies and methods for tumour surveillance. However, a lack of prospective clinical trials showing direct patient benefit has limited the implementation of liquid biopsies in standard clinical applications. Here, we review the potential of ctDNA obtained by liquid biopsy to revolutionise personalised medicine and discuss current applications of ctDNA both at the benchtop and bedside.

Productive Infection of Human Breast Cancer Cell Lines with Human Cytomegalovirus (HCMV).

Breast cancer is the leading cause of cancer deaths among women worldwide. There are many known risk factors for breast cancer, but the role of infectious disease remains unclear. Human cytomegalovirus (HCMV) is a widespread herpesvirus that usually causes little disease. Because HCMV has been detected in breast tumor biopsy samples and is frequently transmitted via human breast milk, we investigated HCMV replication in breast tumor cells. Four human breast cancer cell lines with different expression profiles for the key diagnostic markers of the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), were infected with a bacterial artificial chromosome-derived HCMV clinical strain TB40/E tagged with green fluorescent protein (GFP). Fluorescence microscopy confirmed that all four breast cancer cell lines supported virus entry. RNA was isolated from infected cells and the expression of immediate early (UL123), early (UL54), and late (UL111A) genes was confirmed using PCR. Viral proteins were detected by immunoblotting, and viral progeny were produced during the infection of breast tumor cells, as evidenced by subsequent infection of fibroblasts with culture supernatants. These results demonstrate that breast tumor cells support productive HCMV infection and could indicate that HCMV replication may play a role in breast cancer progression.

Analysis of homologous recombination DNA repair gene mutation status in patients with metastatic small cell lung cancer treated with cediranib and olaparib on NCI 9881 study.

8563 Background: Cediranib, a pan-vascular endothelial growth factor receptor tyrosine kinase inhibitor, suppresses expression of homologous recombination DNA repair (HRR) genes and increases sensitivity of tumors to a poly-(ADP-ribose) polymerase (PARP) inhibitor in vitro and in vivo models of breast and ovarian cancer. Olaparib, a PARP inhibitor, demonstrated clinical efficacy in patients with advanced solid tumor with a deleterious mutation in HRR genes. We hypothesized that cediranib induces HRR deficient phenotype by suppressing expression of HRR genes and cediranib and olaparib combination (C+O) results in an objectives response in patients with HRR proficient (HRP) advanced solid tumors. Herein, we report the biomarker data from analyses of targeted sequencing of 84 DNA repair (DR) genes with BROCA-HR assay in patients with metastatic small cell lung cancer (mSCLC). Methods: This multi-institutional phase 2 trial enrolled patients with mSCLC previously treated with a platinum-based chemotherapy. Patients received cediranib 30mg orally (po) daily plus olaparib 200mg po twice daily until disease progression or unacceptable toxicity. The primary endpoint was objective response rate (ORR) by RECIST v1.1. A tumor biopsy was obtained from the patients with safely accessible metastatic tumor. HRR deficiency (HRD) was defined as presence of a deleterious mutation in any of the 10 key HRR-related genes per BROCA-HR assay including: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12 (somatic mutations only), NBN, PALB2, RAD51C, or RAD51D. Otherwise, the tumors were defined as HRR proficiency (HRP). Results: A total of 25 patients with SCLC received the study treatment. Fourteen patients had available tumor biopsy samples and/or germline available for BROCA-HR. One patient (7%) was determined to have a HRD tumor by a presence of PALB2 mutation. This patient had stable disease as a best overall response but came off study due to unequivocal clinical progression. Thirteen patients (93%) had a HRP tumor. Six of these (46%) patients had PR. Median PFS in patients with HPR tumors was 122 days. The most common gene alterations detected by BROCA-HR assay was TP53 (93%) and RB1 (79%). Other DR gene alterations noted from our study samples were MRE11, CKD12 PALB2, ERCC4, FANCB, and BAP1. Conclusions: HRD was infrequent in our mSCLC samples. C+O resulted in objective responses in 46% of mSCLC patients with HRP tumors. Mutations in TP53 and RB1 were the most common gene alterations. Further investigation in warranted to confirm this observation. Clinical trial information: NCT02498613.

Immune Resistance Interrogation Study (IRIS): A prospective comprehensive multi-omic analysis in patients with intrinsic and acquired resistance to immunotherapy.

TPS2679 Background: Immune checkpoint inhibitors (ICI) have demonstrated efficacy in a wide variety of cancers. Nevertheless, only a small proportion of patients derive a durable benefit. Mechanisms underlying primary and acquired resistance are still incompletely understood. They comprise tumor-intrinsic factors such as genomic and transcriptomic changes; upregulation of immunosuppressive subsets; T cell exhaustion; and promotion of an immune-tolerant tumor microenvironment. The collection of tumor biopsy at disease progression (PD) is challenging both in clinical and research settings as this often occurs at the time of treatment discontinuation. However, the analysis of these samples can lead to novel strategies to prevent or reverse immune resistance. Thus, the current approach to begin a profiling study with patients at the time of PD on ICI enables access and interrogation of such samples. Methods: IRIS is a prospective, investigator-initiated trial at the Princess Margaret Cancer Centre that aims to extensively characterize the genomic, transcriptomic, epigenetic and immunophenotypic profiles of tumors with primary versus acquired resistance to ICI-based therapy. Primary resistance is defined as PD at the first on-treatment imaging, whereas acquired resistance is defined as PD occurring after an initial partial or complete response or following disease stability lasting ≥6 months. Additional objectives include the evaluation of radiomic parameters on standard radiological imaging, investigation of fecal microbiome, generation of patient-derived organoids and facilitation of data and sample sharing with the research community. The planned samples size is 100 patients. A one-time fresh tumor biopsy, blood and stool samples and archival tissue (when available) are collected at the time of PD on ICI (baseline) from all the participants. Longitudinal blood samples are obtained every 2-3 months (around the time of tumor imaging) until PD in patients receiving a subsequent treatment. Subjects who are not amenable for therapy undergo blood collections at the time of further PD. Molecular characterization of tumor samples includes: DNA/RNA sequencing, Assay of Transposase Accessible Chromatin (ATAC)-sequencing, Cellular Indexing of Transcriptomes and Epitopes (CITE)-sequencing, multiplexed immunohistochemistry and flow cytometry. Results of NGS performed on the first biopsy core are returned to patient and physician. Key eligibility criteria include diagnosis of solid tumor, progression to ICI as the most recent line of treatment and disease amenable to core needle biopsy. The IRIS trial, activated in October 2020, is currently open to enrollment. As of January 2021, 21 patients have been enrolled and a total of 92 tissue cores, 42 blood and 20 stool samples have been collected. Clinical trial information: NCT04243720.

The use of cryoablation to overcome resistance to PD-1 blockade in unresectable melanoma.

9538 Background: Percutaneous image-guided cryoablation (cryo) is an established minimally invasive oncologic treatment that modulates the immune microenvironment. We hypothesized that cryo can augment anti-tumor responses in melanoma patients progressing on immune checkpoint inhibitors (ICI). Methods: In this non-randomized phase II single-center study, subjects with unresectable melanoma progressing on ICI underwent cryo of an enlarging lesion and ICI continuation for a minimum of 2 additional cycles. Computed tomography was performed at 6-8 weeks following cryo to determine tumor response in non-ablated lesions per RECIST1.1, with confirmatory scans at 8-12 weeks. The primary endpoint was safety and feasibility. Secondary endpoints were overall response rate (ORR) and disease control rate (DCR) with DCR defined as the percentage of pts who achieve complete response (CR), partial response (PR), and stable disease (SD). Correlative analyses on pre- and post-cryo tumor biopsy and blood samples were performed. Results: From May 2018 through July 2020, 20 pts were screened, 18 enrolled and 17 treated per protocol. All pts received prior PD-1/PD-L1 monotherapy and 12 (67%) experienced primary resistance to ICI. Median follow-up was 8.5 months. Ablated lesions included lymph nodes (n = 4), lung/pleura (n = 4), soft tissue/bone (n = 3), adrenal (n = 3), chest wall (n = 1), and kidney (n = 1). Peri-procedural events occurred in 3 cases (pneumothorax, diaphragm puncture, osteomyelitis). One pt. with underlying ICI-induced hypophysitis experienced an adrenal crisis post-procedure, which rapidly corrected with stress-dose steroid administration; there were no de novo immune-related adverse events post-ablation and there were no grade 4/5 events. In evaluable pts (n = 17), ORR was 18% and DCR was 47% (3 PR, 5 SD). To investigate the inflammatory state of the tumor microenvironment prior to cryo, PD-1, CD8+ TIL IHC, was performed and will be presented at the meeting. Additional exploratory analyses (serial ctDNA analysis, single cell RNA sequencing, HLA-subtyping) are ongoing. Conclusions: Cryoablation in patients with unresectable melanoma following progression on ICI is feasible with an acceptable side effect profile. Efficacy data of this potentially synergistic approach in metastatic melanoma is encouraging. Correlative analyses are underway to identify biomarkers of response to this novel strategy. Clinical trial information: NCT03290677. [Table: see text]

Use of comprehensive next-generation sequencing to identify pathogenic germline variants with therapeutic relevance in metastatic breast cancer.

10527 Background: Among patients with early-stage breast cancer, approximately 6-10% have a pathogenic germline variant (PGV) conferring inherited cancer predisposition. In contrast, few studies have explored the frequency and types of PGVs identified in patients with metastatic breast cancer (MBC); therefore, additional data is needed. Methods: From 2011-2020, 278 patients with MBC underwent fresh tumor biopsy and blood sample collection for paired tumor/normal DNA (targeted exome capture with analysis of 1700 genes) and RNA (tumor transcriptome) sequencing through the Michigan Oncology Sequencing (Mi-ONCOSEQ) program. Somatic and germline alterations were annotated and classified according to degree of clinical actionability with results returned to treating oncologists. Retrospective chart review was performed to determine if: 1) a PGV was identified prior to Mi-ONCOSEQ testing, 2) patients met National Comprehensive Cancer Network (NCCN) guideline criteria for genetic testing on the basis of personal or family cancer history and 3) patients received subsequent therapy informed by a PGV. Results: Forty-eight of the 278 patients (17.3%) had at least one PGV identified, with a total of 50 PGVs identified in this cohort. Only twelve of these PGVs (24%) had been identified prior to Mi-ONCOSEQ testing. The most frequent PGVs identified were in CHEK 2 (n = 9, 18%), MUTYH (n = 6, 12%), BRCA 1 (n = 5, 10%), BRCA2 (n = 5, 10%), ATM (n = 4, 8%) and PALB2 (n = 4, 8%). Somatic loss of heterozygosity events (LOH) occurred in 30 of the 50 cases with PGVs identified (60%). LOH events were observed in 83.3% of BRCA1, BRCA2, ATM and PALB2 PGVs, but were less frequently observed with CHEK2 (33.3%) and MUTYH (66.7%). Two hundred sixteen out of 278 patients (77.7%) in this cohort met NCCN criteria for genetic testing, although six patients with a PGV identified (CHEK2: n = 5; MUTYH: n = 1) did not meet NCCN criteria. Twenty-nine PGVs identified (58%) had potential therapeutic relevance and 11 patients (22.9%) received targeted therapy based on the PGV. Conclusions: The frequency of PGVs identified in this cohort is nearly double the frequency reported for patients with early-stage disease, suggesting that certain PGVs may confer worse prognosis. CHEK2, the most frequently identified PGV, was less likely to have an identifiable LOH event. The direct role of CHEK2 PGVs in tumor pathogenesis is uncertain, but other mechanisms of silencing the wild type allele must be considered. Despite the majority of patients meeting NCCN criteria for genetic testing, those with PGVs in CHEK2 were less reliably identified by this mechanism. The majority of PGVs identified were of potential therapeutic relevance, supporting the recommendation for genetic testing in all patients with MBC.

Using the tumor microenvironment to identify predictors of immunotoxicity to checkpoint inhibitors.

2545 Background: While Immune checkpoint inhibitors (ICI) have revolutionized the field of oncology, the benefits have come at the cost of serious side effects known as immune-related adverse events (irAEs). Approaches that can predict patients’ susceptibility to irAEs are key to their early detection and management. In the present study, we investigate the association between irAEs reported during ICI therapy across multiple cancer types and markers of tumor immune response. Our primary objective is to explore potential biomarkers for assessing patients’ risk of irAEs. Methods: 472 patients were evaluated who had tumor immune profiling performed paraffin embedded formalin fixed archival tumor biopsy samples using Omniseq Immune Report Card (IRC) and subsequently underwent ICI therapy. The IRC consisted of enumeration of tumor infiltrating lymphocytes (TILs) by immunohistochemistry (IHC) and TIL-associated genes by RNA-Seq, PD-L1 expression by IHC, and tumor mutational burden (TMB) by DNA-Seq. irAE type and grade were determined based on retrospective chart review. Fisher’s exact test was used to determined statistically significant associations between immune markers and irAE development. Results: Patients with lung (55%), ovarian (9%), and melanoma (5%) cancers constituted the majority of the cases. The median age of patients was 61, with 56% being female and 44% male. Most patients underwent treatment with (94%). irAEs developed in 36% of patients, with 2% of patients developing high-grade irAEs (Grade 3 or 4). Skin (11%), thyroid (10%), and GI (9%), were the most commonly affected organ systems. Increased TILs were associated with increased risk for any irAE (p = 0.04). A stronger association was noted in patients who underwent anti-PD-1/L1 monotherapy (p = 0.01) and/or in cases of lung cancer (p = 0.01). Interestingly, subanalyses by gender showed a statistically significant correlation between increased TILs and risk for any irAE in males (p = 0.006) but not in females (p = 0.63). High PD-L1 (defined as &gt; 70% by IHC) was also significantly associated with increased risk for any irAE (p = 0.03). Subanalyses by gender and age again showed a similar association in females (p = 0.0002) and/or patients &lt; 65 years (p = 0.04). high TMB and any irAE in female patients (p = 0.01) and in breast cancer cases (p = 0.03). On multivariate analysis, TILs by IHC appeared to be the strongest predictor of irAEs (p = 0.03). Conclusions: The tumor immune microenvironment (TME) has been shown to influence response to ICI, yet its association with irAEs has not been well studied. Our analysis sheds light on potential TME predictors for irAE in patients receiving ICI therapy. Further studies are needed to deepen our understanding of immune toxicity and to develop tools for identifying patients who are at risk.

Features in genomics and tumor immune microenvironment in NSCLC treated with neoadjuvant PD-1 blockade.

9063 Background: Results from several clinical trials have preliminarily demonstrated the safety and effectiveness of single PD-1 inhibitors in neoadjuvant setting for resectable non-small cell lung cancer (NSCLC). However, only around 40% patients could achieve Major Pathological Response. How to select patients who could benefit from single PD-1 blockade remains elusive. Methods: In this study, we aimed to assess the association of PD-L1 expression, tumor mutation burden (TMB), copy number alteration (CNA, including copy number gain and loss) burden with the pathological response to neoadjuvant PD-1 blockade. We also evaluated the dynamic changes of tumor immune microenvironment (TIME) by analyzing pre-immunotherapy treatment tumor biopsy samples from twenty-nine NSCLC patients as well as the matched post-surgery samples after neoadjuvant sintilimab treatment and resection. Targeted DNA sequencing (543 genes), PD-L1 immunochemistry staining (22C3) and multiplex immunofluorescence (CD4, CD8, CD9) were applied. Results: The degree of pathological regression and major pathological response (MPR), were positively correlated with tumor proportion score (TPS) of PD-L1 (R = 0.40, p = 0.04) and negatively correlated with copy number gain (CNgain) burden (R = -0.44, p = 0.04). Of note, the combination of CNgain burden and TPS can better stratify MPR patients compared to CNgain or TPS alone. Whereas, TMB only had a marginal association with pathological response (R = 0.32, p = 0.15). Additionally, PD-1 blockade led to an increase in CD8+PD-1-T cells in the tumor region (p = 0.04, Mann-Whitney U test for paired samples) and a reduction in Tregs and M2 macrophages in the stromal region (p &lt; 0.05, Mann-Whitney U test for paired samples). Further investigation showed that the degree of CD8+PD-1-T cell increase was significantly associated with MPR (p &lt; 0.05, Mann-Whitney U test). Intriguingly, we also observed a substantial reduction in CD19+ cells in the non-MPR group but not in the MPR group, indicating the involvement of B cells in improving neoadjuvant immunotherapy response in NSCLC patients. Conclusions: TPS and CNgain burden were correlated with pathological response to neoadjuvant immunotherapy in NSCLC patients. This may provide potential selective indicators for future clinical trials of neoadjuvant immunotherapy. The dynamic changes of components in the tumor immune microenvironment may provide novel insight into the immune responses induced by neoadjuvant PD-1 blockade therapy.