Fresh Tumor Tissue Research Articles

Effect of bavituximab in combination with nivolumab on tumor immune response in a 3D ex vivo system of lung cancer patients.

e23091 Background: Bavituximab is a chimeric monoclonal antibody that targets the membrane phospholipid phosphatidylserine (PS) exposed on endothelial cells and cancer cells in solid tumors. Our previous studies showed that bavituximab enhances the activation of CD8+ TILs that correlates with increased cytokine production by lymphoid and myeloid cells in lung cancer with low PD-L1 expression suggesting that the interruption of the PD-1/PD-L1 axis by nivolumab may enhance the bavituximab effect in tumors. Methods: Fresh tumor tissues obtained from consented patients with NSCLC at the time of surgical resection were utilized in a 3D ex vivo tumor miscrosphere assay, where 3D tumor microspheres were treated with bavituximab or nivolumab alone or in combination at 10 mg/ml for 36 hours. At the end of the treatment, a multiplex human cytokine assay was used to simultaneously analyze the differential secretion of cytokines, including human IFNg, in culture media as a surrogate of TIL activation. In addition, a gene expression analysis using a NanoString platform containing probes to quantitate 770 immune function genes. Results: Preliminary results indicate the combination treatment with bavituximab and nivolumab led to increased expression of genes involved in M1 polarization of tumor associated macrophages in a subpopulation of lung tumors that closely correlated with release of cytokines such as MIP1b (CCL4) which is a chemoattractant for natural killer cells, monocytes and a variety of other cells involved in tumor immune response. Conclusions: This lung patient derived ex-vivo approach indicates that bavituximab in combination with nivolumab may enhance immune response. This response likely involves M1 polarization of tumor associated macrophages and suggests potential clinical implications in the treatment of lung cancer.

Clinical Significance and Tumor-Suppressive Function of miR-516b in Nonsmall Cell Lung Cancer.

MicroRNA-516b (miR-516b) has been recently reported to be downregulated in nonsmall cell lung cancer (NSCLC). However, its clinical significance and biological function in NSCLC remain to be clarified. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of miR-516b in 82 paired fresh primary tumor tissues and NSCLC cell lines. The association of miR-516b expression with clinicopathological factors and prognosis was statistically analyzed by SPSS 21.0 software, Kaplan-Meier method, and Cox regression analyses. Cell Counting Kit-8, colony formation, flow cytometric, Transwell migration, and invasion assays were used to evaluate the proliferation, cell cycle, apoptosis, migration, and invasion of NSCLC cells after miR-516b mimics or negative control of mimics transfection. The expression level of miR-516b was found to be significantly lower in NSCLC tissues and cell lines than in corresponding normal tissues and cells. Decreased miR-516b expression was significantly associated with tumor size (p = 0.004), Tumor Node Metastasis (TNM) stage (p = 0.016), and shorter overall survival (p = 0.0039). Multivariate analysis suggested that miR-516b was an independent risk factor for NSCLC (hazard ratio = 2.435, 95% confidence interval: 1.423-2.457; p = 0.003). Furthermore, overexpression of miR-516b could inhibit NSCLC cell proliferation, cell cycle progression, migration and invasion, and promoted cell apoptosis. The qRT-PCR results indicated that overexpressing miR-516b reduced the mRNA expression of CDK2, MMP-2, and MMP-9, whereas increased BAX mRNA expression in NSCLC cells. Their protein expression levels presented similar trends, as confirmed by Western blotting. Findings in this study demonstrated for the first time that miR-516b expression might be a novel diagnostic and prognostic factor, as well as a promising target for NSCLC.

Prognostic Correlation Between MFG-E8 Expression Level and Colorectal Cancer

Colorectal cancer (CRC) is one of the leading causes of cancer-related death all over the world. Milk fat globule-epidermal growth factor (EGF)-factor VIII (MFG-E8) was found to be highly expressed in a variety of cancers. However its role in CRC is unclear. This study investigates the expression of MFG-E8 in CRC tissues and the correlation with clinicopathological features and prognosis in CRC patients. The expression of MFG-E8 proteins was detected by immunohistochemical staining in 90 samples of CRC. The localization of MFG-E8 in colorectal tumor was examined by immunofluorescence staining. The correlation between MFG-E8 protein expression and the clinical pathological features of CRC were evaluated by χ2 test and Fisher's exact test. The survival rates were analyzed by the Kaplan-Meier method, and the relationship between prognostic factors and patient survival was analyzed by the Cox proportional hazard models. Our results showed that MFG-E8 expression increased significantly in colorectal cancer compared with normal mucosa tissues (p <0.001). We further validated MFG-E8 overexpression in 6 pairs of fresh tumor and adjacent normal mucosa tissues from colorectal cancer patients by Western blot (p <0.05). Immunofluorescence staining showed that MFG-E8 accumulated in close proximity to endothelial cells in human colorectal tumor tissue. In addition, high MFG-E8 protein expression was correlated with lymph node metastasis and some pathological classifications (p <0.05). Furthermore, patients with high protein level of MFG-E8 showed shortened overall survivals (p <0.05). Our results showed that MFG-E8 could be a potential novel prognostic marker for CRC and overexpression of MFG-E8 might be involved in lymph node metastasis and angiogenesis of CRC.

Towards the Development of Personalized Medicine: A Novel Tissue Preservation System for the Automation and Standardization of Brain Tumor Harvesting in a Surgical Setting

IntroductionCollection of quality brain tumor bio‐specimens is paramount to subsequent molecular research and clinical decision‐making. Current manual brain tumor procurement, stabilization, preservation and transport methodologies may jeopardize the quality of harvested tissue, thereby compromising the accuracy of subsequent molecular results and disease management. The Tissue Preservation System™, TPS, (NICO Inc. Indianapolis, IN.) is a novel device that automates and standardizes the brain tumor tissue collection process in the operating room. Here the TPS methodology as implemented in United States hospitals is reported.MethodsThe TPS (NICO Inc.) consists of a NICO Myriad™ console; specimen collector and filter element. These three elements exist within a portable, closed, interconnected sterile system that measures 12 × 24 × 8 inches, residing on a 39‐inch (height) cart. The methodology includes: Automated Harvesting; Automated Collection; Chilling/Temperature Monitoring; Tissue Perfusion/Preservation and Transport. Briefly, brain tumors are surgically harvested by a neurosurgeon using the NICO Myriad™, an FDA cleared suction/microscissor device that transects tissues and suctions the bio‐specimen into a sterile collection chamber. The closed, sterile, specimen collection chamber is affixed with a 300Aμm filter and housed within a Styrofoam chiller. Harvested tissue is held within the collection chamber and perfused with preservation media of choice. The chilling apparatus keeps bio‐specimens on ice at 4–8 °C or dry ice. Bio‐specimen collection chambers are labeled with institution‐specific identifiers (e.g.: name, birthdate etc.) according to each institution's standard operating procedures. Labeled samples are then transported in a closed, controlled temperature environment from the operating room to the pathology laboratory for analysis.ResultsThe TPS system: 1. Automates the inter‐operating room collection, preservation and storage of all resected brain tumor bio‐specimens in a closed, sterile environment; and 2. Provides stable temperature control of tissue samples within the operating room and during transport from the operating room to the laboratory. A dozen United States hospitals currently utilize TPS methodology. Preliminary observations suggest greater tumor specimen volume/yield and cellular viability as compared with manual tumor harvesting techniques. Further, the TPS methodology is tailored to individual institutional standard operating procedures for tissue acquisition and transport and allows automated tumor harvesting from distinct anatomical locations.ConclusionsThe TPS represents a novel methodology that automates and standardizes the collection of brain tumor tissue within the operative theater. Here the step‐wise process of procurement, stabilization, preservation and transport of fresh tumor tissue is described. The TPS limits bio‐sample exposure to environmental factors, thereby likely enhancing tissue quality for subsequent molecular analysis and tissue banking—key components in the development of personalized medicine strategies. Further studies are required to confirm these hypotheses. The current TPS methodology demonstrates that the TPS is a compact, portable, automated and efficient device that addresses methodological limitations of current fresh tumor harvesting, collection and transport methods.Support or Funding InformationDr. Cartwright is a scientific consultant to NICO Inc.

Overexpression of placenta specific 8 is associated with malignant progression and poor prognosis of clear cell renal cell carcinoma.

Placenta specific 8 (PLAC8) plays an important role in many different cellular processes and human diseases, including multiple types of cancer. However, the functional role of PLAC8 in clear cell renal cell carcinoma (ccRCC) has never been elucidated. PLAC8 mRNA expression was investigated in 31 pairs of fresh ccRCC tumor tissues and matched adjacent non-tumor tissues by RT-qPCR and confirmed by analyzing the TCGA KRCC dataset which contains RNA-seq data of 534 ccRCC and 72 solid normal tissues. Protein level of PLAC8 expression was also investigated using immunohistochemistry in 129 ccRCC samples. Correlations with clinicopathological factors and overall survival were analyzed. To examine its effect on the biological activity, PLAC8 siRNAs were transfected into ccRCC cells. Cell proliferation was assessed by CCK8 cell viability assays, clone formation assays, and EdU incorporation assays. Cell invasion was examined using transwell assays. RNA sequencing was then performed to further elucidate the mechanisms by which PLAC8 regulates the cancer. PLAC8 expression was positively correlated with tumor size, metastasis, and clinical stage of ccRCC. Additionally, high PLAC8 expression was closely associated with a shorter overall survival time. Knockdown of PLAC8 with siRNAs significantly reduced the proliferation and invasion of RCC cells and increased the sensitivity of RCC cells to cisplatin. RNA-seq analysis revealed that knockdown of PLAC8 down-regulated the expression of a panel of inflammatory mediators, which suggested that PLAC8 is associated with the ccRCC inflammatory microenvironment. Patients with high expression of PLAC8 had a significantly higher number of infiltrative lymphocytes than patients with low expression of PLAC8. Our findings suggest that PLAC8 may be a potential prognostic indicator and therapeutic target for ccRCC.

Antioxidant enzymes in canine mammary tumors

Abstract Spontaneous mammary tumors are very common in bitches. The involvement of oxidative stress and the function of antioxidant enzymes in cancerogenesis have been studied in depth in human medicine, while data in veterinary medicine are still fragmentary. The main aim of this study was to evaluate the activity and the expression of superoxide dismutases (Cu-ZnSOD and MnSOD) and the activity of catalase (CAT) in canine mammary tumors in comparison with the adjacent healthy tissue. Six female dogs (mean age 10.4 years) were included in this study. After surgery, fresh tumor and healthy tissue samples were immediately frozen in dry ice and stored at −80°C for biochemical analyses, while the remaining parts were used for histopathological analysis. Enzyme activity was measured by spectrophotometric assays and protein expression by western blotting. In canine mammary tumors, Cu-ZnSOD activity and expression increased significantly compared with healthy control tissues (p=0.03). MnSOD showed a significantly lower activity in tumoral tissues at stage 2 (p&lt;0.05), while a significant increase of expression was measured in tumors. CAT activity was significantly higher in healthy tissues respect to tumors (p=0.015). These variations of antioxidant enzymes activities and expression could be related to an increase of oxidative stress in breast cancer tissues and could be considered as biomarker candidates for neoplastic transformation.

Generation and characterization of antitumor infiltrating lymphocytes from patients with breast cancer for adoptive cell transfer therapy.

145 Background: Clinical trials have shown that adoptive cell transfer therapy is a promising method for cancer treatment. In the current study, we aim to generate and characterize anti-tumor tumor-infiltrating lymphocytes from patients with breast cancer for adoptive cell transfer therapy. Methods: In vitro culture method was used to generate anti-tumor, tumor-infiltrating lymphocytes from patients with breast cancer. FACS analysis, ELISA, and Elispot assay were used to characterize tumor-infiltrating lymphocytes. Autologous anti-tumor tumor-infiltrating lymphocytes from patients with breast cancer were used in adoptive cell transfer therapy. Results: FACS analysis indicated that tumor-infiltrating lymphocytes were present in the tumor tissues, but not detectable in the normal breast tissues from patients with breast cancer. Tumor-infiltrating lymphocytes could be generated in vitro from fresh tumor specimens of patients with breast cancer. Both CD4 T cells and CD8 T cells were detected in tumor-infiltrating lymphocytes. Autologous tumor cells could also generate in vitro from fresh tumor tissue samples of patients with breast cancer. Among 22 samples screened, 6 samples (25%) of tumor-infiltrating lymphocytes are tumor-reactive. Anti-tumor, tumor-infiltrating lymphocytes could recognize autologous tumor cells and allogenic tumor cells. After a large scale T cell expansion, anti-tumor reactivity was maintained in tumor-infiltrating lymphocytes. All of tumor-infiltrating lymphocytes were NK cells in some samples from patients with breast cancer, and these NK cells could recognize autologous tumor cells and a panel of allogenic tumor cells. T cell cloning assay demonstrated that some of the tumor-reactive, tumor-infiltrating lymphocytes were CD4 T cells. Conclusions: The results suggest that anti-tumor, tumor-infiltrating lymphocytes may be generated from patients with breast cancer, which may be used in clinical applications of adoptive cell transfer therapy for patients with breast cancer. The clinical trial of adoptive cell transfer therapy using autologous anti-tumor tumor-infiltrating lymphocytes for patients with breast is under way.

Abstract A62: Investigating the role of follicular helper T cells, B cells and CXCL13 in breast cancer-associated tertiary lymphoid structures

Abstract Patient outcomes have been linked to the presence of tumor infiltrating lymphocytes (TIL) in solid tumors. In human breast cancer (BC), higher TIL infiltration is associated with a better prognosis and also predicts relevant responses to pre-operative chemotherapy. TIL are primarily composed of T cells, albeit around 20% of BC patients show significant B cell infiltration, and can organize in tertiary lymphoid structures (TLS) located in the peritumoral stroma 1, which are associated with survival in HER2+ and triple negative BC patients. Further, these studies revealed that CD4+ follicular helper T (Tfh) cells producing CXCL13 were specifically associated with peritumoral TLS. CXCL13 is an important B cell chemoattractant whose function is to recruit B cells to the germinal center (GC) in secondary lymphoid organs and TLS, where they can mature and differentiate into memory or antibody-producing B cells. Our recent efforts have focused on exploring the role of Tfh, B cells and CXCL13 play in the development and/or maintenance of GC-like structures in BC-associated TLS. We first derived a GC-B cell gene signature for integration in our published Tfh cell gene signature 1. The combined gene signature was tested for its ability to sensitively detect BC-associated TLS using a qRT-PCR-based assay and a retrospective series (n=54) of formalin-fixed paraffin-embedded (FFPE) BC tissues. These data revealed a correlation between gene signature expression and the extent of TIL and TLS scored by trained pathologists on dual-immunohistochemistry stained (CD3+CD20 for T and B cells, respectively) FFPE tissue sections. The detection of TLS using our combined GC-B cell/Tfh cell gene signature was subsequently confirmed using tissues from our prospective BC cohort (n=83). In addition, CXCL13 gene expression was well correlated with genes associated with GC-B cells and Tfh, indicating these parameters are closely related, as confirmed by immunofluorescence staining on FFPE tissues. Further understanding the factors that promote TLS formation in vivo could provide important insight for treatment decisions in BC. CXCL13 expression was originally identified as an important signal associated with TLS that was predictive for patient outcomes 1. Factors capable of inducing CXCL13 expression in CD4+ T cells isolated from peripheral blood were investigated using flow cytometry. TGFβ1 alone or together with several cytokines (IL4, IL12, IL21, IL23 and in particular IL2 blockade) increased CXCL13 expression in activated CD4+ T cells. Similar to our characterization of Tfh TIL in fresh tumor tissues, these CXCL13-producing CD4+ T cells were CXCR5 negative and expressed the Tfh marker ICOS; however, they only had low levels of PD-1 expression compared to PD-1hi Tfh cells. CD8+ T cells were also found to produce CXCL13 albeit at low levels. The currently ongoing identification of critical genes involved in regulating CXCL13 production in treated CD4+T cells will help to elucidate the mechanism(s) underlying chemokine induction. The increased accuracy in TIL and TLS detection in BC together with a better understanding of the role Tfh and CXCL13 play in these structures (and GC) development should help to identify the critical immune components involved in BC TLS formation. 1Gu-Trantien et al. J Clin Invest. 2013 Citation Format: Edoardo Migliori, Chunyan Gu-Trantien, Soizic Garaud, Gert Van den Eynden, Alexandre De Wind, Pushpamali De Silva, Cinzia Solinas, Anais Boisson, Celine Naveaux, Denis Larsimont, Martine Piccart-Gebhart, Karen Willard-Gallo. Investigating the role of follicular helper T cells, B cells and CXCL13 in breast cancer-associated tertiary lymphoid structures. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A62.

Actin-like protein 6A is a novel prognostic indicator promoting invasion and metastasis in osteosarcoma

Osteosarcoma harbors highly metastatic properties, accounting for postoperative recurrence and metastasis. Actin-like protein 6A(ACTL6A) regulates cell proliferation, migration and differentiation. However, the biologic role of ACTL6A in osteosarcoma remains unknown. In this study, the results showed that, by analysis of frozen fresh primary tumor tissues, matched non-cancerous bone tissues(NCBTs) and biopsy lung metastatic nodule tissues from 30osteosarcoma patients after radical surgical resection, ACTL6A was overexpressed in osteosarcoma tissues compared with matched NCBTs, and its expression level was associated with osteosarcoma metastasis. Immunohistochemical analyses of osteosarcoma tissue samples from two independent cohorts of formaldehyde-fixed, paraffin-embedded osteosarcoma tissue samples from total of 186osteosarcoma patients showed that high ACTL6A expression correlated with malignant clinicopathological features such as larger tumor size, high Ennecking grade, high histologic grade, and advanced tumor node metastasis stage. High ACTL6A expression was associated with poor prognosis for patients with osteosarcoma, and an independent and significant risk factor for disease-free survival and overall survival after radical tumor resection. Both invitro and invivo assays showed that ACTL6A overexpression promoted osteosarcoma cell invasion and metastasis, whereas knockdown of ACTL6A expression reduced osteosarcoma cell malignant behavior such as invasion and metastasis. Furthermore, we proved that ACTL6A promoted osteosarcoma cells of metastasis through facilitating epithelial-mesenchymal transition(EMT). Inconclusion, data from the present study demonstrated that ACTL6A was associated with poor survival and promoted osteosarcoma cell metastasis through EMT, suggesting that ACTL6A may be a novel prognostic biomarker and therapeutic target for osteosarcoma.

Assessment of blood and tissue myeloid derived suppressor cells (MDSC), clinicopathologic factors, and treatment response in urothelial carcinoma (UC) patients (pts) undergoing surgery.

362 Background: MDSC are heterogeneous immunosuppressive cells with potential predictive/prognostic role in cancer. The association between MDSC, clinicopathologic factors and pathologic response in pts with UC merits evaluation. Methods: Peripheral blood and/or tissue was collected from 120 pts. MDSC were measured in fresh unfractionated whole blood (WB), in peripheral blood mononuclear cells (PBMC) and fresh tumor tissue. MDSCs were identified by flow cytometry in WB and defined as LinloCD33+/HLADR- ((T)otal MDSC). MDSC subsets were defined as LinloCD33+/HLADR- and (G)ranulocytic (CD15+CD14-), (M)onocytic (CD15-CD14+), (I)mmature (CD15-CD14-, CD11b+ ). MDSC populations were presented as % of live nucleated blood cells and as absolute numbers from WB. Spearman correlations (r) and Wilcoxon rank sum test were used to assess correlations between MDSC populations, clinicopathologic factors and pT0N0%. Results: Of 120 pts, 82 were non-metastatic: 58 had only blood, 23 had blood &amp; tissue, 1 had only tissue available for analysis. Of these 82 non-metastatic pts, 70 were men, median age 68; 81 pts had primary UC histology, 1 small cell cancer, 24 had mixed UC histology; 24 had prior intravesical therapy, 34 had neoadjuvant therapy (79% cisplatin-based, 21% unknown), 4 pts had post-op recurrence. At cystectomy: 15/82 pT0, 22/82 pT3/4; 37/82 CIS; 8/78 pN+. Significant associations were seen between MDSC blood levels and mixed histology, CIS, pN+, and lower pT0N0% (Table). Tumor M-MDSCs were associated with pN+ (p=0.05). There was significant correlation between tumor and WB % M-MDSC (r=0.55, p=0.007), and tumor and WB % G-MDSC (r=0.46, p=0.03). Conclusions: Blood MDSC levels correlate with several clinicopathologic factors and may predict pathological complete response (pT0N0). Assessment of association between MDSC levels, outcome and immunotherapy response is ongoing including in metastatic pts. [Table: see text]

Abstract PD2-08: Neratinib + fulvestrant in ERBB2-mutant, HER2–non-amplified, estrogen receptor (ER)-positive, metastatic breast cancer (MBC): Preliminary analysis from the phase II SUMMIT trial

Abstract Background: Somatic mutations in ERBB2 are a new class of oncogenic drivers in HER2–non amplified MBC. Neratinib is an irreversible pan-HER tyrosine kinase inhibitor that inhibits the growth of ERBB2-mutant breast tumors in preclinical models and has encouraging single-agent clinical activity in patients (pts) with ERBB2-mutant, HER2–non amplified MBC. Bi-directional signaling between HER2 and ER may limit the effectiveness of endocrine and HER2 directed therapy, if each is given alone, in ER+ MBC with ERBB2 amplifications/mutations. Preclinical data suggest that dual blockade of ER and HER2 signaling results in enhanced anti-tumor activity in ER+ HER2+ MBC. SUMMIT, a multicenter multi-histology phase II 'basket' trial, is investigating the efficacy of neratinib monotherapy (in ER+ and ER– pts) and neratinib + fulvestrant (ER+ pts only) in ERBB2-mutant MBC. Methods: MBC pts with ERBB2 mutations documented by local testing were eligible and received oral neratinib 240 mg qd. Pts with ER+ MBC received fulvestrant 500 mg, a selective ER degrader, in addition to neratinib on d1 &amp; 15 of month 1 then on d1 q4w. Patients received high dose loperamide prophylaxis during cycle 1. Primary endpoint is objective response rate (ORR) at 8w, defined using RECIST 1.1 and/or modified PERCIST assessments. Secondary endpoints include ORR, clinical benefit rate (CBR), progression free survival (PFS), and safety. Mutation profiling and central confirmation of ERBB2 mutation(s) from available fresh or archival tumor tissues and plasma DNA were performed retrospectively by next-generation sequencing (MSK-IMPACT). Clinicaltrials.gov: NCT01953926. Results: As of 23 Sep 2016, 35 efficacy-evaluable ERBB2-mutant MBC pts received neratinib, either as monotherapy (n=24) or in combination with fulvestrant (n=11). Efficacy findings are shown in the table. The overall safety profile of neratinib + fulvestrant was similar to that previously reported with neratinib monotherapy. Grade 3 diarrhea rate was 24% with neratinib monotherapy and 18% with neratinib + fulvestrant. Neratinib monotherapyNeratinib + fulvestrant(n=24)(n=11)Best Overall Response (confirmed and unconfirmed), n (%)8 (33.3)6 (54.5)[95% CI][15.6–55.3][23.4–83.3]CR3 (12.5)2 (18.2)PR5 (20.8)4 (36.4)aORR at 8 weeks, n (%)8 (33.3)5 (45.5)[95% CI][15.6–55.3][16.7–76.6]CR2 (8.3)2 (18.2)PR6 (25.0)3 (27.3)ORR confirmed, n (%)5 (20.8)2 (18.2)b[95% CI][7.1–42.2][2.3–51.8]CR3 (12.5)1 (9.1)PR2 (8.3)1 (9.1)CBR, n (%)10 (41.7)6 (54.5)[95% CI][22.1–63.4][23.4–83.3]CR, complete response; PR, partial response.aThere was 1 pt with PR at week 16; bAt time of data cut-off 4 pts are still on treatment. Conclusions: Encouraging clinical activity has been observed with neratinib + fulvestrant in heavily pretreated pts with ERBB2-mutant, ER+ MBC. Clinical efficacy in the ER+ MBC cohort met pre-specified efficacy requirements; a confirmatory trial of neratinib + fulvestrant for targeting ERBB2 mutations in ER+ MBC is warranted. The safety profile of neratinib was acceptable and diarrhea was manageable with loperamide prophylaxis. Citation Format: Hyman D, Piha-Paul S, Saura C, Arteaga C, Mayer I, Shapiro G, Loi S, Lalani A, Xu F, Cutler R, Butturini A, Bryce R, Meric-Bernstam F, Baselga J, Solit D. Neratinib + fulvestrant in ERBB2-mutant, HER2–non-amplified, estrogen receptor (ER)-positive, metastatic breast cancer (MBC): Preliminary analysis from the phase II SUMMIT trial [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD2-08.

Evaluation of genome-wide genotyping concordance between tumor tissues and peripheral blood

Tumor tissues were potential resources in cancer susceptibility studies. To assess the genotyping concordance between tumor tissues and peripheral blood, we conducted this study in a large sample size and genome-wide scale. Genome-wide genotypes of human colon adenocarcinoma (COAD) retrieved from The Cancer Genome Atlas (TCGA) was analyzed. A total of 387 pairs of matched fresh frozen tumor tissues and peripheral blood samples passed the quality control processes. High concordant rate (94.85% with no-calls and 97.89% without no-calls) was found between tumor tissues and peripheral blood. The discordant rate raised with the increase of heterozygote rate, and the tendency was statistically significant. The total missing rate was 3.10%. We also verified 14 susceptibility SNPs and the average genotyping concordant rate was 97.42%. These findings suggest that majority of SNPs could be accurately genotyped using DNA isolated from tumor tissues.

Association of DOCK6 with cancer stem cell development and as an independent prognostic factor of gastric cancer.

68 Background: The prognosis of advanced gastric cancer (GC) remains poor, and the key players in molecular pathogenesis are predominantly unknown at present. Methods: In order to identify novel prognostic factor of GC, we compared the data of iTRAQ proteomics from 6 GC samples with that of Oncomine database from 86 GC samples to intersect 122 high-expression proteins in gastric cancer tissue. The candidate biomarkers were further characterized in fresh GC tumor tissues compared with adjacent non-tumor tissue by using Q-RT-PCR, immunohistochemical staining and western blot. GC cells with depletion of DOCK6 were examined to identify downstream molecules and establish their effects on cell motility, invasion and gastric cancer stem cell (CSC) markers. The possible signaling pathway of DOCK6 were also investigated. Results: DOCK6 is identified as one of the potential GC biomarkers in iTRAQ proteomics. Our data confirm the overexpression of DOCK6 in GC tumor tissue compared with adjacent non-tumor tissue. In addition, the clinical data shows higher DOCK6 expression was positive correlated to depth of invasion, lymph node metastasis, vascular invasion and pathological stage. Furthermore, higher DOCK6 expression represented significantly shorter cumulative survival both in univariate and multivariate analysis for survival outcome. Depletion of DOCK6 repressed the cell migration, proliferation, sphere formation, anchorage-independent growth and tumorigenicity as well as gastric cancer stem cell (CSC) markers. In order to explore the downstream effector of DOCK6, we correlated thousands of gene with DOCK6 in three GC dataset published in the literature. The DOCK6 positive-correlated genes were subsequently analyzed by Metacore. They were significantly involved in WNT/β-catenin signaling pathway. Our result demonstrates nuclear b-catenin, as well as CD44, was decreased accompanied by depleting DOCK6. Moreover, the interaction between DOCK6 and β-catenin was observed in GC cells. Conclusions: Our studies unveil the role of DOCK6 in the self-renewal of CSC and propose DOCK6 as an independent marker of tumor progression.

Microfluidic Biopsy Trapping Device for the Real-Time Monitoring of Tumor Microenvironment.

The tumor microenvironment is composed of cellular and stromal components such as tumor cells, mesenchymal cells, immune cells, cancer associated fibroblasts and the supporting extracellular matrix. The tumor microenvironment provides crucial support for growth and progression of tumor cells and affects tumor response to therapeutic interventions. To better understand tumor biology and to develop effective cancer therapeutic agents it is important to develop preclinical platforms that can faithfully recapitulate the tumor microenvironment and the complex interaction between the tumor and its surrounding stromal elements. Drug studies performed in vitro with conventional two-dimensional cancer cell line models do not optimally represent clinical drug response as they lack true tumor heterogeneity and are often performed in static culture conditions lacking stromal tumor components that significantly influence the metabolic activity and proliferation of cells. Recent microfluidic approaches aim to overcome such obstacles with the use of cell lines derived in artificial three-dimensional supportive gels or micro-chambers. However, absence of a true tumor microenvironment and full interstitial flow, leads to less than optimal evaluation of tumor response to drug treatment. Here we report a continuous perfusion microfluidic device coupled with microscopy and image analysis for the assessment of drug effects on intact fresh tumor tissue. We have demonstrated that fine needle aspirate biopsies obtained from patient-derived xenograft models of adenocarcinoma of the lung can successfully be analyzed for their response to ex vivo drug treatment within this biopsy trapping microfluidic device, wherein a protein kinase C inhibitor, staurosporine, was used to assess tumor cell death as a proof of principle. This approach has the potential to study tumor tissue within its intact microenvironment to better understand tumor response to drug treatments and eventually to choose the most effective drug and drug combination for individual patients in a cost effective and timely manner.

Establishment of patient-derived tumor xenograft (PDTX) models using samples from CT-guided percutaneous biopsy.

This study aimed to investigate the feasibility of the establishment of a human cancer xenograft model using samples from computed tomography (CT)-guided percutaneous biopsy. Fresh tumor tissues obtained from 10 cancer patients by CT-guided percutaneous biopsy were subcutaneously inoculated into NOD-Prkdcem26Il2rgem26Nju (NCG) mice to establish human patient-derived tumor xenograft (PDTX) models. The formation of first and second generation xenografts was observed, and tumor volume was recorded over time. Tumor tissue consistency between the PDTX model and primary tumors in patients was compared using H&E staining and immunohistochemistry. Pharmacodynamic tests of clinically used chemotherapeutic drugs were conducted on second generation xenografts, and their effects on tumor growth and body weight were observed. CT-guided percutaneous biopsy samples were successfully collected from 10 patients with advanced cancers. The PDTX model was established in mice using tumor samples obtained from 4 cancer patients, including one small cell carcinoma sample, two adenocarcinoma samples, and one squamous cell carcinoma sample. The success rate was 40%. The obtained PDTX model maintained a degree of differentiation, and morphological and structural characteristics were similar to primary tumors. The pharmacodynamic test of chemotherapeutic drugs in the PDTX model revealed a therapeutic effect on tumor growth, as expected. CT-guided percutaneous biopsy samples can be effectively used to establish a PDTX model, and test these chemotherapy regimens.

Abstract B57: Effects of MEK inhibition alone or in combination with PI3K-mTOR pathway inhibitors in pancreatic ductal adenocarcinoma in vitro and on an innovative ex vivo fresh tumor tissue culture model

Abstract Purpose: Activating KRAS mutations are frequent (&amp;gt;90%) in pancreatic ductal adenocarcinoma (PDAC) and drive downstream deregulation of both MAPK and PI3K-mTOR pathways. MEK inhibitors (MEKi) are under clinical evaluation in PDAC, in combination with other agents including PI3K-mTOR inhibitors. While RAS and BRAF mutations, EMT, PI3K-mTOR activation, and pERK inhibition have been suggested as predictive markers for MEKi efficacy, they are not validated in PDAC. We aimed to explore the cellular and molecular effects of MEKi GSK1120212 (GSK212) alone or in combination with PI3K-mTOR inhibitors, in PDAC cell lines and on an innovative ex vivo system. Methods: GSK212 is an allosteric non-ATP competitive MEKi, everolimus (Ev) a mTORC1 inhibitor, and BKM120 a pan-class PI3K inhibitor. Effects on proliferation were evaluated by MTT assay. Combinations were analyzed by the Chou-Talalay method. Protein expression was assessed by Western blot. Ex vivo drug assays were performed at different drug concentrations on cultures of fresh tumor tissue slices prepared from patient surgical specimens. Apoptosis and proliferation were assessed by cleaved caspase 3 (Cas-3) and MIB-1 (Ki67) immunostainings, respectively; MEKi sensitivity was defined as cleaved Cas-3 expression in 30% or more of cancer cells. Correlations between protein expressions were explored using linear regression and Pearson’s R2 calculation. Samples will be classified into PDAC subtypes according to Collisson’s, Moffit’s and Bailey’s transcriptomic signatures using non-negative matrix factorization and correlation methods. Results: MIAPaCa-2 and PANC-1 are two mesenchymal KRAS mutated/BRAF wild-type PDAC cell lines with very different response to GSK212, MIAPaCa-2 being sensitive (72h-IC50=0.009µM) and PANC-1 resistant (72h-IC50=33µM). MIAPaCa-2 was more sensitive than PANC-1 to Ev (IC50=23.3µM vs 47.0µM) and BKM120 (IC50=4.19µM vs 31.6µM). Combination of GSK212 and Ev or BKM120 for 72h resulted in synergistic effects (CI&amp;lt;1) in MIAPaCa-2 (MEKi sensitive) but not in PANC-1. GSK212 (0.1µM) treatment resulted in pERK extinction in both cell lines but in decreased pS6 expression only in MIAPaCa-2. Combination therapy led to extinction of pERK and pS6 in both cell lines. Apoptosis induction in MIAPaCa-2 was confirmed by PARP cleavage. Eleven tumor specimens were cultured ex vivo. We observed that: (a) GSK212 (0.1µM) treatment for 48h induced significant (≥30%) apoptosis concomitantly with a decrease in pS6 expression in MEKi sensitive tumors; (b) Ev (1µM) or BKM120 (0.1µM) exerted antiproliferative effects but did not induce apoptosis; (c) combinations resulted in higher apoptosis induction associated with a higher decrease in pS6 expression compared to MEKi alone in MEKi sensitive tumors. In sensitive tumors, cleaved Cas-3 induction was inversely correlated with pS6 expression under treatment by MEKi +/- Ev or BKM120. A R2&amp;gt;0.50 discriminated between sensitive and resistant tumors. There was no correlation with RAS/RAF mutation status. Predictive value of transcriptomic signatures for MEKi response will be presented. Conclusion: Response to combined MEK/mTOR pathway inhibition was not correlated with known biomarkers of response to MEKi. Besides the therapeutic potential of MEK/mTOR pathway inhibition in PDAC, this work provides the first evidence of feasibility of pharmacodynamic biomarker monitoring on fresh PDAC tissue slices. Citation Format: Cindy Neuzillet, Annemilaï Tijeras-Raballand, Anguraj Sadanandam, Pierre Bourgoin, Philippe Bourget, Pawan Poudel, Maria Serova, Armand De Gramont, Philippe Ruszniewski, Valérie Paradis, Eric Raymond, Jérôme Cros, Pascal Hammel.{Authors}. Effects of MEK inhibition alone or in combination with PI3K-mTOR pathway inhibitors in pancreatic ductal adenocarcinoma in vitro and on an innovative ex vivo fresh tumor tissue culture model. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr B57.

Clinical Research and Genomic Analysis on Relapsed or Refractory Angioimmunoblastic T Cell Lymphoma with Chidamide Monotherapy

BACKGROUND: This study was to evaluate the efficacy and safety of chidamide monotherapy, which is a new histone deacetylase inhibitor (HDAci) of the benzamide class, in relapsed or refractory Angioimmunoblastic T cell lymphoma (AITL), to investigate its genomic expression signatures as well as the mechanisms of chidamide's anti-lymphoma effect and its resistance.METHODS: Two cases with relapsed or refractory AITL were treated with chidamide. We performed a repeated biopsy on relapsed lymphomas and did whole genome next-generation sequencing (NGS) testing on drug -resistant tumor samples.RESULTS: The first patient is a 54-year-old man presented with stage IV AITL. He underwent autologous stem cell transplantation in his first complete remission (CR) but relapsed 7 months later. In view of resistance to multiple lines of chemotherapy and poor performance status, chidamide was adaministered orally at a standard dose of 30mg twice a week. Pulmonary lesions regressed quickly and a second CR was achieved. Adverse events included grade 2 cytopenias, diarrhea, and reversible QT interval prolongation. The disease free survival was 6 months and AITL relapsed again 4 months ago. He responded to low-dose chidamide combined with lenalidomide and dexamethasone and remains well. Formalin-fixed, paraffin-embeded tumor tissues collected at first relapse were tackled for whole-genome sequencing. The other patient is a 62-year-old woman who had stage III AITL. Disease progressed after two cycles of combined chemotherapy, thereafter a standard dose of chidamide monotherapy was initiated. With well tolerability, an unconfirmed CR was achieved and lasted for nearly 3 months. She is still alive but remains refractory to various salvage therapeutics, including chemotherapies, arsenic trioxide, thalidomide, and pralatrexate. A rebiopsy was perferomed and the histopathological findings confirmed the relapse of AITL, associated with Epstein-barr virus infection. Fresh tumor tissues were sent for whole-genome sequencing. In both cases, NGS testing identified mutations of RHOA gene, epigenetic regulators TET2, IDH1, and DNMT3A, as well as CD28.CONCLUSIONS: Chidamide, a low nanomolar inhibitor of HDAC1, 2, 3, and 10, was approved in China for the management of relapsed and/or refractory peripheral T cell lymphoma. It's reported that patients with AITL tended to have higher response rates and more durable responses to chidamide treatment. Our report showed single-agent chidamide is a reasonable approach to treat the formidable disease but seemed difficult to achieve a sustained remission. Various genetic, epigenetic, and immune alterations involve in the pathogensis of AITL, which provide targets for chidamide therapy. High-throughput sequencing approach is very helpful to clarify the mechanisms. DisclosuresNo relevant conflicts of interest to declare.

Genomic evolution and chemoresistance in germ-cell tumours.

Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types. These tumours also acquire KRAS mutations during the development from precursor to primary disease, and primary testicular GCTs (TGCTs) are uniformly wild type for TP53. In addition, by functional measurement of apoptotic signalling (BH3 profiling) of fresh tumour and adjacent tissue, we find that primary TGCTs have high mitochondrial priming that facilitates chemotherapy-induced apoptosis. Finally, by phylogenetic analysis of serial TGCTs that emerge with chemotherapy resistance, we show how TGCTs gain additional reciprocal loss of heterozygosity and that this is associated with loss of pluripotency markers (NANOG and POU5F1) in chemoresistant teratomas or transformed carcinomas. Our results demonstrate the distinct genomic features underlying the origins of this disease and associated with the chemosensitivity phenotype, as well as the rare progression to chemoresistance. These results identify the convergence of cancer genomics, mitochondrial priming and GCT evolution, and may provide insights into chemosensitivity and resistance in other cancers.

Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors.

Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were in NOD SCID mice. A subset of matched patient and PDX tumors and non-neoplastic lung tissues were profiled by whole exome sequencing, single nucleotide polymorphism (SNP) and methylation arrays, and phosphotyrosine (pY)-proteome by mass spectrometry. The data were compared to published NSCLC datasets of NSCLC primary and cell lines. 127 stable PDXs were established from 441 lung carcinomas representing all major histological subtypes: 52 adenocarcinomas, 62 squamous cell carcinomas, one adeno-squamous carcinoma, five sarcomatoid carcinomas, five large cell neuroendocrine carcinomas, and two small cell lung cancers. Somatic mutations, gene copy number and expression profiles, and pY-proteome landscape of 36 PDXs showed greater similarity with patient tumors than with established cell lines. Novel somatic mutations on cancer associated genes were identified but only in PDXs, likely due to selective clonal growth in the PDXs that allows detection of these low allelic frequency mutations. The results provide the strongest evidence yet that PDXs established from lung cancers closely mimic the characteristics of patient primary tumors.

Abstract PR11: Neo-antigen landscape dynamics during human melanoma-T cell interactions

Abstract Recognition of the neo-antigens that are formed as a consequence of DNA damage is likely to be a major driving force behind the clinical activity of T cell checkpoint blockade and adoptive T cell therapy for treatment of non-virally induced solid cancers. Consequently, strategies to selectively enhance T cell reactivity against genetically defined neo-antigens are currently under development. In mouse models, T cell pressure has been shown to sculpt the antigenicity of tumors through selection of tumor cell variants that do not express the relevant neo-antigens. However, it is unclear whether the T cell-recognized neo-antigen repertoire is constant over time in human cancers. To address this issue, we analyzed the stability of neo-antigen specific T cell responses and the antigens they recognize in stage IV melanoma patients treated by adoptive T cell transfer. Fresh tumor tissue resected before and after treatment was used to establish autologous melanoma cell lines, to culture tumor-infiltrating lymphocytes (TIL) and to generate T-cell infusion products by autologous mixed lymphocyte tumor cell cultures using peripheral blood lymphocytes. Material from 2 patients with objective clinical responses after infusion of autologous tumor-specific CD4+ and CD8+ T cells was analyzed by whole exome and RNA sequencing. Subsequently, 31-mer peptides covering all the non-synonymous somatic mutations were used to test the reactivity of both the T-cell infusion products and TIL isolated from subsequent tumor lesions by ELISA and flow cytometry. The expression of genes encoding T cell-recognized neo-antigens was then analyzed within the tumor cell lines and within the corresponding paraffin-embedded tumor tissue, by real-time PCR analysis, a competitive allele-specific PCR assay, and by analysis of heterozygosity and next generation amplicon sequencing. Analysis of the infusion products showed that 50-80% of T cells reacted to autologous tumor cells, with only a very low percentage of these cells recognizing known shared tumor-associated epitopes. Instead, tumor reactivity was predominantly mediated by CD4+ and CD8+ T cells recognizing clonally expressed neo-antigens formed by private mutations. CD8+ T cells within the infusion products and within TIL populations generated from subsequent tumor lesions of these two patients recognized a total of 6 different neo-antigens, and analysis of these neo-antigens in both the index lesion and subsequent lesions revealed profound alterations in the T cell-recognized neo-antigen landscape. In particular, in 2 cases, the mutant allele was lost from a subsequent tumor, in one case, expression of the mutant gene was substantially reduced in a recurring lesion, and in another case expression of the mutant gene was increased approx. 40-fold in a subsequent tumor. Notably, in 4 out of 4 cases these changes in neo-antigen expression were paralleled by loss or gain of the respective neo-antigen specific T cell response. Collectively, our data demonstrate that under conditions in which a high frequency of tumor-specific T cells is present, tumor cell variants with reduced or lost neo-antigen expression can emerge, similar to what has been observed in mice. This, and the observation of concurrent acquisition of novel T cell reactivity, reveal the dynamics of T cell - neo-antigen interaction in human cancer, and indicate that immunotherapies that maximize the capacity to respond to an altering neo-antigen landscape may offer the highest chance to achieve long-term tumor control. Citation Format: Els M.E. Verdegaal, Noel de Miranda, Marten Visser, Tom Harryvan, Marit van Buuren, Rikke Andersen, Sine Hadrup, Caroline van der Minne, Remko Schotte, Hergen Spits, John Haanen, Ellen Kapiteijn, Ton Schumacher, Sjoerd H. Van Der Burg. Neo-antigen landscape dynamics during human melanoma-T cell interactions [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR11.