Oncogenic Biomarker Research Articles

Abstract 3388: Analytical validation and clinical verification of phosphoprotein biomarker modulation using a novel preservation system-based flow cytometry assay in multiple myeloma clinical trials

Abstract Propelled by the advent of novel oncogenic pathway-targeting drugs and increasing regulatory expectations to fulfil proof of mechanism endpoints in clinical trials, there is a critical need to reliably evaluate target inhibition by investigational drugs in biologically relevant compartments. However, the ability to monitor modulation of labile oncogenic pathway biomarkers in global hematomalignancy clinical trials is complicated by varying technical expertise at clinical sites, when specimen stability considerations do not permit analysis at a central specialty laboratory. To address this critical gap, we developed a novel preservation system, designated NovaPerm3 (NP3), that enables stabilization of phosphoprotein based biomarker specimens in a single step, requires less than 20 minutes, and can be implemented in routine clinical trial settings. Stabilized specimens can be frozen and analyzed even after 90 days in a specialized laboratory. Using the NP3 preservation system, we systematically developed and validated a flow cytometry assay that not only enables reliable identification of neoplastic plasma cells but also allows for quantitation of phosphoprotein biomarkers in the tumor cells of interest present in both the peripheral blood (PB) and bone marrow (BM). We will describe a) modulation of phosphorylation levels of the S6 ribosomal protein (pS6RP) by a novel anticancer agent in multiple myeloma patients b) qualitative concordance between NP3-flow cytometry and western blot results from multiple drug treated leukemia cell lines c) sensitive detection of neoplastic plasma cells up to 1% of the total white cells and d) specimen (pS6RP) stabilization over a 90 day period. In conclusion, our novel preservation method and clinical trial laboratory validated flow assay enables reliable quantification of signaling biomarkers in hematomalignancy trials with ease in a specialized central laboratory while reducing the procedural burden for collecting biomarker specimens in global clinical trials. Citation Format: Anil Pahuja, Shyam Sarikonda, Benjamin Lee, Armin Graber, Shabnam Tangri, Naveen Dakappagari. Analytical validation and clinical verification of phosphoprotein biomarker modulation using a novel preservation system-based flow cytometry assay in multiple myeloma clinical trials. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3388. doi:10.1158/1538-7445.AM2015-3388

Abstract 3383: Correlation of mutations detected in liquid and tissue biopsies

Abstract Circulating cell-free DNA (ccfDNA) in plasma can be used to detect biomarkers that show great promise for diagnosis and monitoring of cancer, giving rise to the possibility of liquid biopsies that obviate the need for invasive tissue collection. The low concentration and highly fragmented nature of ccfDNA, coupled with the low frequency of potential oncogenic biomarkers, presents challenges and will require a purification method that is efficient and highly reproducible. Here we describe a method for purifying nucleic acids based on novel surface and binding chemistries. The combination of these two approaches allows for increased binding of fragmented DNA. The method can be partially automated to ensure highly reproducible results. Up to 4mls of plasma can be processed and eluted in as little as 15ul, giving DNA concentrations of 1-10ul. This greatly facilitates use in Next Generation Sequencing. Using the automated method, ccfDNA was purified from the plasma of 7 patients who had previously undergone surgical resection for malignancy. DNA was also purified from the FFPE malignant tissue off of slides, following macrodissection, from the same patients. NGS was used to interrogate both sample types for potentially oncogenic variants. Several laboratory developed tests, all including COLD-PCR, were also employed to verify the presence or absence of variants. The two types of samples showed excellent correlation on mutations, suggesting that use of a less invasive liquid biopsy has the potential to enable actionable mutation detection without using more invasive solid tumor biopsy means. Citation Format: Douglas H. White, Douglas Horejsh, Molly Accola, William Rehrauer, Marjeta Urh. Correlation of mutations detected in liquid and tissue biopsies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3383. doi:10.1158/1538-7445.AM2015-3383

Isorhamnetin augments the anti-tumor effect of capeciatbine through the negative regulation of NF-κB signaling cascade in gastric cancer

Development of drug resistance to standard chemotherapy is a common phenomenon that leads to poor prognosis in patients. Thus, novel agents that can attenuate chemoresistance are urgently needed. Therefore, we analyzed whether isorhamnetin (IH), a 3′-O-methylated metabolite of quercetin, can enhance the potential efficacy of capecitabine in gastric cancer. The potential effect of IH on viability was analyzed by MTT assay, apoptosis by flow cytometric analysis, and NF-κB activation by DNA binding as well as Western blot assays. The in vivo effect of IH was also examined on the growth of subcutaneously implanted tumors in nude mice. IH inhibited the viability, potentiated the apoptotic effects of capecitabine, abrogated NF-κB activation, and suppressed the expression of various NF-κB regulated gene products in tumor cells. In a gastric cancer xenograft model, administration of IH alone (1 mg/kg body weight, i.p.) significantly suppressed the tumor growth alone as well as in combination with capecitabine. IH further reduced NF-κB activation and the expression of various proliferative and oncogenic biomarkers in tumor tissues. Overall, our results demonstrate that IH can significantly enhance the anti-tumor effects of capecitabine through the negative regulation of NF-κB regulated oncogenic genes.

Clinical significance of upregulation of mir-196a-5p in gastric cancer and enriched KEGG pathway analysis of target genes.

miRNAs are relatively recently discovered cancer biomarkers which have important implications for cancer early diagnosis, treatment and estimation of prognosis. Here we focussed on expression of mir-196a-5p in gastric cancer tissues and cell lines so as to analyse its significance for clinicopathologic characteristics and generate enriched KEGG pathways clustered by target genes for exploring its potential roles as a biomarker in gastric cancer. The expression of mir-196a-5p in poorly, moderate and well differentiated gastric cancer cell lines compared with GES-1 was detected by RT-qPCR, and the expression of mir-196a-5p in gastric cancer tissues comparing with adjacent non cancer tissues of 58 cases were also assessed by RT- qPCR. Subsequently, an analysis of clinical significance of mir-196a-5p in gastric cancer and enriched KEGG pathways was executed based on the miRWalk prediction database combined with bioinformatics tools DAVID 6.7 and Mirfocus 3.0. RT-qPCR showed that mir-196a-5p was up-regulated in 6 poorly and moderate differentiated gastric cancer cell lines SGC-7901, MKN-45, MKN-28, MGC-803, BGC-823, HGC-27 compared with GES-1, but down-regulated in the highly differentiated gastric cancer cell line AGS. Clinical data indicated mir-196a-5p to beup-regulated in gastric cancer tissues (47/58). Overexpression of mir-196a-5p was associated with more extensive degree of lymph node metastasis and clinical stage (P <0.05; x2 test). Enriched KEGG pathway analyses of predicted and validated targets in miRWalk combined with DAVID 6.7 and Mirfocus 3.0 showed that the targeted genes regulated by mir-196a-5p were involved in malignancy associated biology. Overexpression of mir-196a-5p is associated with lymph node metastasis and clinical stage, and enriched KEGG pathway analyses showed that targeted genes regulated by mir-196a-5p may contribute to tumorgenesis, suggesting roles as an oncogenic miRNA biomarker in gastric cancer.

Preface: Oncogenic Biomarkers and Signal Transduction

Preface: Oncogenic Biomarkers and Signal Transduction

Abstract LB-96: A novel blood preservation system to study oncogenic signaling pathway biomarkers by flow cytometry in leukemia/lymphoma clinical trials

Abstract Propelled by the advent of new technologies and an evolving regulatory landscape, the desire to personalize cancer treatments has never been greater. There is a critical need to reliably evaluate target inhibition and pharmacodynamic activity of investigational drugs in biologically relevant compartments. However, the ability to fulfill such a task in global clinical trials is complicated by varying technical expertise available at clinical sites and considerations about specimen stability for centralized laboratory analysis. We developed a novel formalin-based preservation method that enables specimen stabilization in a single step, requiring less than 20 minutes, without the need for specialized training or instrumentation. Stabilized specimens can be frozen for shipping and batched analysis at a later time point, in a specialized laboratory. Using this preservation method, we developed a flow assay enabling identification of multiple cell-types, and quantification of intracellular biomarkers in target cellular compartments, in both the peripheral blood (PB) and bone marrow (BM). We present pharmacodynamic (PD) data for a novel anticancer investigational agent intended for acute myeloid leukemia and multiple myeloma and its effect on multiple target biomarkers of the PI3K signaling pathway, including phosphorylation of the S6 ribosomal protein (S6). Our novel fixation method allowed detection of pS6 modulation in a dose dependent manner in both tumor cells and PB or BM in response to the novel investigational agent. Assay sensitivity and concordance were evaluated by comparing flow assay with western blot analysis, with each assay performed at a different site using the same batched frozen samples; exceptional preservation of phosphorylated proteins for more than 72 hours could be observed, when frozen immediately following fixation. In conclusion, our novel preservation method enables reliable quantification of signaling biomarkers in centralized laboratories at different time points post sample (PB or BM) acquisition requiring minimal processing at collection sites. Citation Format: Anil Pahuja, Abdel Saci, Shyam Sarikonda, Armin Graber, Benjamin Lee, Jelveh Lameh, Shabnam Tangri, Naveen Dakappagari. A novel blood preservation system to study oncogenic signaling pathway biomarkers by flow cytometry in leukemia/lymphoma clinical trials. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-96. doi:10.1158/1538-7445.AM2014-LB-96

PROGNOSTIC FACTORS FOR PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMAS TREATED WITH HIGH-DOSE METHOTREXATE-BASED CHEMO-RADIOTHERAPY

BACKGROUND: Chemotherapy with high-dose methotrexate (HD-MTX) followed by whole brain radiotherapy (WBRT) is a conventional approach to treat primary central nervous system lymphomas (PCNSL), but some tumors relapse early leading to unfavorable outcome. Several biomarkers have been identified as prognostic factors in PCNSL, however, the correlation of both clinical factors including those related to MTX metabolism and B-cell differentiation and oncogenic biomarkers with response to and outcome by therapy is yet unclear. METHODS: We investigated 32 immunocompetent patients (19 males, 13 females) with PCNSL (all diffuse large B-cell type) treated with HD-MTX based therapy with or without WBRT since 2000 in our institution. Paraffin-embedded formalin-fixed tumor tissue sections were stained immunohistochemically with antibodies against following factors: B-cell differentiation markers (CD10, Bcl-6, Mum-1, CD138); MTX metabolism-related (MRP family, LRP, DHFR); cell cycle-related (p27KIP1, MIB-1); drug resistance-related (MGMT, MLH1, MSH2, MSH6, PMS2); and oncogenes (Myc, Bcl-2). Correlation between positivity of these factors and clinical outcomes were evaluated using logrank test and cox regression analysis. RESULTS: Among these factors, complete response to HD-MTX was significantly associated with longer progression-free survival (PFS)(P = 0.0012), while Bcl-6 expression as well as histological subtype (non-germinal center B-cell, non-GCB) was closely correlated with shorter PFS. Age (>60) (P = 0.006) and MSH2 expression (P = 0.017) were found to be better predictor for overall survival (OS), but in multivariate analysis, they were no longer significant. Other factors involved in MTX metabolism, DNA repair enzymes, and oncogenes did not affect outcome. CONCLUSIONS: Non-GCB subtype and Bcl-6 expression may be associated with worse outcome in patients with PCNSL treated with HD-MTX, while MTX-metabolism related factors did not influence prognosis. Further investigation is needed to assess Bcl-6 as a potential prognostic factor in PCNSL. SECONDARY CATEGORY: Clinical Neuro-Oncology.

Abstract C13: Patient derived gastric carcinoma xenograft (PDGCX) models largely maintain the histological and genetic diversities of corresponding patient tumor.

Abstract Purpose: To assess molecular characteristic of patient derived gastric cancer xenograft (PDGCX) models for evaluating whether these models maintain corresponding patients’ histological and genetic diversities. Experimental procedures: Patient derived gastric carcinoma xenograft models were established by implanting subcutaneously GC patients’ tumor tissue from non-necrotic areas into immune-deficient mice (nude mice or SCID mice). Formalin-fixed paraffin embedded (FFPE) sections of each model and corresponding patient tumor tissue were prepared for characterization studies. Histological features were assessed by pathologist on H&amp;E stained slides. To profile several cancer relevant markers such as ERBB1, ERBB2, ERBB3, FGFR2, MET and PTEN, multilayered biological assays were performed including gene copy number by fluorescent in situ hybridization (FISH) and/or protein expression by immnuohistochemistry (IHC). Results: Twenty patient derived GC xenograft models were established with a take on rate of 17%. These models retained the histological features of their parental tumors. No statistical significance was observed between the successful cases and failed cases in terms of patients’ clinical parameters including age, gender, tumor grade, Lauren type and clinical stage. Gene copy number and/or protein expression of gastric cancer relevant biomarkers such as ERBB1, ERBB2, ERBB3, FGFR2, MET and PTEN were detected by FISH and/or IHC. Among 20 established models, 100% (20/20) were ERBB1 highly expressed, 20%(4/20) were ERBB2 positive, 90% (18/20) were ERBB3 highly expressed, 10% (2/20) harbored FGFR2 amplification, 45% (9/20) lost PTEN expression and 15% (3/20) were defined as MET amplification. This prevalence was comparable with the incidences of these biomarkers in human. High degree of similarity was observed in DNA level for ERBB2, FGFR2 and MET genes between PDGCX model and corresponding primary tumor (k=1). Expression of ERBB2, ERBB3 and PTEN defined by IHC also showed substantial or perfect agreement between PDGCX and their parent tumor (k=0.615∼1), while ERBB1 expression showed slight agreement (k=0). Genetic characteristics between the parent tumor and subsequent passages of the PDGCX were also largely retained. The ERBB2 positive, FGFR2 or MET amplification were recapitulated until passage12. Conclusion: 20 patient derived gastric carcinoma xenograft models were established with 17% engraft rate. The histological assessment and several gastric oncogenic biomarkers’ profiling data demonstrated that these patient derived GC models well represent GC diversity. Furthermore, the stability of the molecular profile across the different passages of individual models showed translational significance that these models could serve for in vivo testing of personalized therapies. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C13. Citation Format: Xinying Su, Tianwei Zhang, Lin Zhang, Yanping Xu, Shuqiong Fan, Yuan Jie Liu, Meizhuo Zhang, Hao Chen, Liang Xie, Jingchuan Zhang, Xiaolu Yin, Yi Gu, Xingzhi Ni. Patient derived gastric carcinoma xenograft (PDGCX) models largely maintain the histological and genetic diversities of corresponding patient tumor. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C13.

English

English

Abstract 3007: Down-regulation of HOXC6 in serous ovarian cancer.

Abstract Objective: The Homeobox (HOX) family of genes consists of 39 genes encoding transcription factors important to morphogenesis and cell differentiation. Usually inactive in normal differentiated tissues, dysregulation of HOX genes has been reported in several malignancies. HOX genes have been linked to genes important in malignant transformation including vascular endothelial growth factor, Ras, interleukin-8, and fibroblast growth factor. We have previously reported up-regulation of HOXA2, HOXA7 and HOXB7 in ovarian cancer. Little is known about HOXC6 gene expression in ovarian cancer. In this study we evaluated HOXC6 expression in normal and malignant human ovarian tissue to characterize expression of HOXC6 in serous ovarian cancer. Methods: Microarray analysis of mRNA from LCM captured cells from human ovarian tissues was performed on 11 samples of normal, and malignant ovarian tissues. These samples were analyzed using the Affymetrix Human EXON 1.0 ST microarray to distinguish the differential pattern of mRNA expression between malignant and normal samples. Real-time reverse transcription PCR was utilized to confirm down-regulation of HOXC6 genes as determined by microarray analysis. HOXC6 protein in tissue was evaluated by immunohistochemistry. Results: Microarray analysis demonstrated significant down-regulation of the HOXC6 gene in malignant serous ovarian tumor samples compared to normal ovarian epithelial cells of control samples. RT-PCR and immunohistochemistry confirmed HOXC6 down-regulation in malignant samples. A 115-fold difference in malignant and normal primary tissue samples and cell lines was seen in the RT-PCR analysis. By immunohistochemistry nuclear staining of HOXC6 protein was seen in the nuclei of normal ovarian surface epithelial tissues but significantly reduced or absent in malignant ovarian samples. Conclusion: HOXC6 is significantly differentially expressed comparing normal ovarian tissue and serous malignant ovarian tissue based on both tissue mRNA and protein analysis. This finding of HOXC6 down-regulation in ovarian cancer is unique and opposite of the up-regulation of other HOX genes previously reported. Down-regulation of HOXC6 in serous ovarian cancer may be an important finding relative to oncogenic pathways and biomarker development. This suggests dysregulation of HOXC6 genes may be an early event in malignant transformation and additional studies to validate the role of the HOXC6 gene in ovarian cancer are warranted. Citation Format: David L. Tait, Zahra Bahrani-Mostafavi, Carol Vestal, Christine Richardson, M. Taghi Mostafavi. Down-regulation of HOXC6 in serous ovarian cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3007. doi:10.1158/1538-7445.AM2013-3007

Are viruses associated with human breast cancer? Scrutinizing the molecular evidence

The three viruses most studied as possible causes of human breast cancer are mouse mammary tumor virus-like sequences (MMTV-LS), Epstein-Barr virus (EBV), and oncogenic (high risk) types of human papilloma virus (HPV). The first step in fulfilling traditional criteria for inferring that a cancer is caused by a virus is to demonstrate the virus in the affected tissue. Molecular techniques, compared to host antibody assessment and immunohistochemistry, are the most definitive in establishing viral presence. Results of 85 original molecular research investigations to detect one or more of the three viruses have been extremely divergent with no consensus reached. We evaluated the methodology of these studies for the following: type of molecular assay, DNA/RNA quality control, positive and negative assay controls, type of fixation, genome targets, methods for preventing and detecting molecular contamination, pathology of specimens processed, sample size, and proportion of specimens positive for the viral genome region targeted. Only seven of the studies convincingly demonstrated the presence of an oncogenic virus biomarker (EBV: 4/30 studies (13%); HPV 3/29 studies (10%), whereas 25 convincingly demonstrated absence of the virus studied (MMTV-LS: 4/25 (16%); EBV: 15/30 (50%); 6/29 (21%). The remainder of the studies suffered shortcomings, which, in our opinion, prevented a definitive conclusion. Only one of the studies compared frequency of the virus in breast tissue of breast cancer patients versus appropriate normal control subjects with no history of breast cancer. None of the studies were designed as epidemiologic studies to determine if the presence of the virus was significantly associated with breast cancer. Based on our evaluation, the data in the publications reviewed here remain preliminary, and do not justify a conclusion that MMTV-LS, HPV, or EBV are causally associated with breast cancer. However, they form a valuable basis for redirecting future studies.

PIK3CA expression in invasive breast cancer: a biomarker of poor prognosis

The implications of Phosphatidylinositol 3-kinase (PIK3CA) mutations and its aberrant protein expression in breast cancer (BC) different molecular subtypes and patients' outcome remain controversial. The aims of this study were to assess the prevalence and clinical significance of PIK3CA protein expression in BC and to determine its association with its different molecular classes. PIK3CA protein expression was assessed in a well-characterized series of early stage BC (n = 1,394) with long-term follow-up, using tissue microarrays and immunohistochemistry. Associations between PIK3CA expression and clinicopathological variables, molecular classes, and patients' outcome were investigated. Positive PIK3CA expression was associated with poor prognostic variables including higher grade, larger size, nodal involvement, vascular invasion, and higher proliferative fraction (P < 0.001). Increased PIK3CA expression was associated with the basal-like breast cancer (BLBC) and HER2-positive classes as well as triple negative non-basal (TNnon-B) tumors (P < 0.001). The luminal class showed reduced PIK3CA expression relative to other classes. Patients with PIK3CA positive tumors had shorter BC specific and disease free survival, independent of other prognostic factors except grade. Similar associations with outcome were found when the analysis was restricted to the large luminal class of tumors. PIK3CA is an oncogenic biomarker associated with poor prognosis in BC. Although, PIK3CA over-expression was more prevalent in BLBC and HER2-positive tumors it appeared to be a marker of poor differentiation rather than of a particular subtype. Thus, targeting of PIK3CA using specific inhibitors could potentially be beneficial, particularly for patients with more aggressive poorly differentiated tumors, irrespective of their molecular subtype.