High-risk HPV infection-associated hypermethylated genes in oropharyngeal squamous cell carcinomas

Background

HPV-positive oropharyngeal squamous cell carcinomas (OPSCCs) are sensitive to chemo-radiation therapy and have favorable survival outcomes compared with HPV-negative cancers. These tumors are usually not related to tobacco and alcohol exposure. Therefore, diagnosing HPV-positive OPSCCs for the appropriate disease management is crucial, and no suitable markers are available for detecting early malignancies in HPV-infected tissues. In this study, we attempt to find HPV-specific epigenetic biomarkers for OPSCCs.

Methods

A total of 127 surgical samples were analyzed for HPV positivity and promoter methylation of a panel of genes. HPV detection was performed by PCR detection of HPV E6 and E7 viral oncoproteins. In addition, promoter methylation of a total of 8 genes (DAPK, FHIT, RASSF1A, TIMP3, AGTR1, CSGALNACT2, GULP1 and VGF) was analyzed by quantitative-methylation specific PCR (QMSP), and their associations with HPV positivity or RB/p16 expressions were evaluated.

Results

AGTR1 and FHIT were frequently methylated in HPV-positive OPSCC samples with a good area under the curve (AUC over 0.70). In addition, these genes' promoter methylation was significantly associated with p16 positive and RB negative cases, which were the characteristics of OPSCC cases with favorable survival outcomes. Either AGTR1 or FHIT methylated cases were significantly associated with HPV-positive cancers with 92.0% sensitivity (P < 0.001). Also, they had significantly better overall survival (P = 0.047) than both unmethylated cases.

Conclusions

A combination of AGTR1 and FHIT methylation demonstrated a suitable detection marker of OPSCCs derived from the HPV-infected field, familiar with p16-positive and RB-negative phenotypes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-10227-w.

Abstract P094: Targeted sequencing revealed clonal genetic changes in spatially different foci in urothelial carcinoma of bladder

Urothelial Carcinoma of Bladder (UCB) is a disease of multiple origins of the same bladder with varying in morphology and genetic changes. The origin of spatially different tumors in the same bladder has been proposed to occur through clonal changes with intraluminal migration or field effect with synchronous transformation of multiple cells by carcinogens. A clear molecular understanding of the origin of multifocal UCB will have important implications for the proper tailoring of personalized targeted treatment and diagnostics. Despite efforts to identify intertumoral heterogeneity, the clonal origin of UCB is still debated. To further understand the genetic mechanism behind the multifocality of UCB, we performed targeted next-generation sequencing (tNGS) on 39 UCB lesions obtained from 15 cystectomized bladders. Germline distant muscle DNA was used as a control. We technically validated selected mutational events by using ultra-sensitive droplet digital PCR (ddPCR). Our data showed that multifocal UCB is of clonal origin, with lesions from individual patients displaying nearly identical mutational landscapes, with few heterogeneous events that may have been acquired at a later point. tNGS demonstrated similar genetic drivers within the same patient and reveal that clonal expansion is an early event of tumorigenesis. In addition, we found distinct gene mutations in different UCB patients suggesting prominent interpatient heterogeneity of clonal events in the UCB. Among others, our result showed that TP53, FGFR3, and NOTCH4 are the most frequently mutated genes in UCB samples. ddPCR assay of mutational events on TP53, FGFR3, AKT, PIK3CA genes confirmed TNGS data and solidified that mutation in TP53, FGFR3, AKT, PIK3CA genes are associated with tumorigenesis of uroepithelium. In summary, this study conveys insight into the clonal origin of multifocal UCB and demonstrates that TNGS is a sensitive and reliable method for interrogating the molecular landscape of UCB. These findings also may inform clinical practice as sequencing of a single focus from a patient presenting with the multifocal disease may be sufficient to understand the mutational profile and guide personalized treatment and risk stratification.

Citation Format: M. Talha Ugurlu, Rachel Goldberg, Pritam Sadhukhan, Mohammad O. Hoque. Targeted sequencing revealed clonal genetic changes in spatially different foci in urothelial carcinoma of bladder [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P094.

Urothelial Carcinoma In Situ of the Bladder: Correlation of CK20 Expression With Adaptive Immune Resistance, Response to BCG Therapy, and Clinical Outcome

Immunohistochemical stains have been suggested to aid in diagnostically challenging cases of urothelial carcinoma in-situ (CIS). Although full thickness immunostaining for CK20 is supportive of CIS, a subset of CIS cases is CK20(-), the clinical significance of which was unknown. This study included 43 patients with primary diagnosis of bladder CIS including 32 with only CIS, 5 with CIS and separate noninvasive high-grade papillary urothelial carcinoma, and 6 with CIS and separate high-grade urothelial carcinoma with lamina propria invasion. Digital morphometric image analysis showed that the average nuclear areas of enlarged nuclei were similar in CK20(+) and CK20(-) CIS (26.9 vs. 24.5 µM2; P=0.31). Average Ki67 index for CK20(+) CIS was higher than CK20(-) CIS (31.1% vs. 18.3%; P=0.03). Patients with CK20(+) CIS [28 (65%)] and patients with CK20(-) CIS [15 (35%)] had the same rates of Bacillus Calmete-Guerin (BCG) failure but patients with CK20(-) CIS had higher stage progression [3 CK20(+) (11%) vs. 6 CK20(-) (40%); P=0.02]. Given recent approval of immune checkpoint inhibitors in patients with CIS refractory to BCG, programmed death ligand-1 expression and colocalization with CD8(+) lymphocytes was investigated as signature of adaptive immune response and was seen in 8 patients regardless of CK20 status and exclusively among patients who failed BCG. Our results confirm that negative CK20 IHC does not exclude CIS and that those patients have similar clinical outcomes as patients with CK20(+) CIS. Programmed death ligand-1 and CD8 colocalization seen among patients who failed BCG therapy is an easy assay to perform to identify patients who could potentially benefit from combined BCG therapy and immune checkpoint inhibition.

Effect of COVID-19 on Lungs: Focusing on Prospective Malignant Phenotypes

Simple Summary

According to the coronavirus virus resource center of Johns Hopkins Medicine, more than 75 million people are presently affected worldwide, including 1.7 million deaths due to severe acute respiratory syndrome since December 2019. Apart from the common symptoms similar to the common flu, a characteristic computed tomography (CT) feature i.e., Ground Glass Opacity (GGO) is highlighted in this article. GGOs have been observed in COVID-19 patients with severe symptoms including pneumonia in both lungs. It is important to reflect that GGO may indicate the onset of lung fibrosis and may be an indicative feature of high-risk subjects for developing lung cancer. In this article, the causes of the appearance of GGOs and their effects are mainly discussed, along with the brief immunopathogenesis of COVID-19 in comparison with other oncogenic viruses. In this pandemic situation, it is also important to consider the long-term effects of coronavirus infection and the ways to follow-up the patients who recovered from this disease.

Abstract

Currently, the healthcare management systems are shattered throughout the world, even in the developed nations due to the COVID-19 viral outbreak. A substantial number of patients infected with SARS-CoV2 develop acute respiratory distress syndrome (ARDS) and need advanced healthcare facilities, including invasive mechanical ventilation. Intracellular infiltration of the SARS-CoV2 virus particles into the epithelial cells in lungs are facilitated by the spike glycoprotein (S Protein) on the outer side of the virus envelope, a membrane protein ACE2 (angiotensin-converting enzyme 2) and two proteases (TMPRSS2 and Furin) in the host cell. This virus has unprecedented effects on the immune system and induces a sudden upregulation of the levels of different pro-inflammatory cytokines. This can be a cause for the onset of pulmonary fibrosis in the lungs. Existence of a high concentration of inflammatory cytokines and viral load can also lead to numerous pathophysiological conditions. Although it is well established that cancer patients are among the high-risk population due to COVID-19-associated mortality, it is still unknown whether survivors of COVID-19-infected subjects are at high-risk population for developing cancer and whether any biologic and clinical features exist in post-COVID-19 individuals that might be related to carcinogenesis.

Abstract PO-016: Modulating cancer stem cell pathways to enhance systemic therapeutic efficacy

Chemoresistance and poor immune sensitivity are one of the major challenges to treat different cancer types including lung, bladder and head & neck. Different epigenetic regulators and cancer stem cells (CSCs) regulatory pathways play a critical role in the development of therapeutic resistance. Prolonged chemotherapy treatment enriches CSCs in the tumor microenvironment and in a previous study we have shown that inhibition of the CSCs regulatory pathway/s combined with chemotherapy decreased CSC properties and efficiently inhibit tumor growth in patient-derived xenografts (PDXs) models. The purpose of this study is to determine the chemo and immunotherapeutic efficacy in combination with several CSC pathway/s modulatory agent/agents to treat different solid tumors. To identify relevant CSC regulating pathways, we tested the therapeutic efficacy of different agents such as 5-Azacytidine (DNA methyltransferase 1 inhibitor), Vismodegib (SMO inhibitor), Romidepsin (HDAC1 inhibitor), Olaparib (PARP1 inhibitor), and GSK343 (EZH2 inhibitor) using different bladder and head & neck cancer cell lines and also determined the numerous CSCs properties. Our data indicate that in vitro treatment with these potential therapeutic agents decreases cell viability, sphere formation and wound healing that suggest that, these drugs may be effective in reducing CSCs population when combined with chemo and/or immunotherapy. Our immunoblotting experiments indicate reduced expression of some CSCs markers and factors such as such as NANOG, OCT4, CD133 and CD24. Interestingly, after treating the cells with some of these agents and array analysis, we have found differential expression of some of the key genes regulating the immunogenic response. Further, to confirm the array-based data, selected candidate immune-associated genes were analyzed by qRT-PCR. Moreover, our preliminary data suggest that combination treatment with epigenetic drugs and an immune agent may effectively reduce tumor growth in vivo compared to either of these drugs. In conclusion, although comprehensive mechanistic studies are ongoing, our initial results highlight the importance of considering combination of epigenetic and immune therapy for patients with diverse cancer types that respond poorly to immune and chemotherapy.

Citation Format: Pritam Sadhukhan, Masahiro Shibata, M. Talha Ugurlu, Rachel Goldberg, Mohammad O. Hoque. Modulating cancer stem cell pathways to enhance systemic therapeutic efficacy [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-016.

Concurrent Targeting of Potential Cancer Stem Cells Regulating Pathways Sensitizes Lung Adenocarcinoma to Standard Chemotherapy

Cancer stem cells (CSC) are highly resistant to conventional chemotherapeutic drugs. YAP1 and STAT3 are the two transcription factors that facilitate the therapeutic resistance and expansion of CSCs. The objective of this study was to understand the cross-talk between YAP1 and STAT3 activities and to determine the therapeutic efficacy of targeting dual CSC-regulating pathways (YAP1 and STAT3) combined with chemotherapy in lung adenocarcinoma. Here, we showed that YAP1 contributes to CSC regulation and enhances tumor formation while suppressing apoptosis. Mechanistically, YAP1 promotes phosphorylation of STAT3 by upregulating IL6. In lung adenocarcinoma clinical specimens, YAP1 expression correlated with that of IL6 (P < 0.01). More importantly, YAP1 and phosphorylated STAT3 (pSTAT3) protein expressions were significantly correlated (P < 0.0001) in primary lung adenocarcinoma as determined by IHC. Immunoblotting of 13 lung adenocarcinoma patient-derived xenografts (PDX) showed that all YAP1-expressing PDXs also exhibited pSTAT3. Additional investigations revealed that chemotherapy resistance and malignant stemness were influenced by upregulating NANOG, OCT4, and SOX2, and the expression of these targets significantly attenuated by genetically and pharmacologically hindering the activities of YAP1 and STAT3 in vivo and in vitro Therapeutically, the dual inhibition of YAP1 and STAT3 elicits a long-lasting therapeutic response by limiting CSC expansion following chemotherapy in cell line xenograft and PDX models of lung adenocarcinoma. Collectively, these findings provide a conceptual framework to target the YAP1 and STAT3 pathways concurrently with systemic chemotherapy to improve the clinical management of lung adenocarcinoma, based on evidence that these two pathways expand CSC populations that mediate resistance to chemotherapy.

GULP1 regulates the NRF2-KEAP1 signaling axis in urothelial carcinoma

Disruption of the KEAP1-NRF2 pathway results in the transactivation of NRF2 target genes, consequently inducing cell proliferation and other phenotypic changes in cancer cells. Here, we demonstrated that GULP1 was a KEAP1-binding protein that maintained actin cytoskeleton architecture and helped KEAP1 to sequester NRF2 in the cytoplasm. In urothelial carcinoma of the bladder (UCB), silencing of GULP1 facilitated the nuclear accumulation of NRF2, led to constitutive activation of NRF2 signaling, and conferred resistance to the platinum drug cisplatin. Knockdown of GULP1 in UCB cells promoted tumor cell proliferation in vitro and enhanced tumor growth in vivo. In primary UCB, GULP1 silencing was more prevalent in muscle-invasive UCB compared to nonmuscle-invasive UCB. GULP1 knockdown cells showed resistance to cisplatin treatment. In parallel with decreased GULP1 expression, we observed increased expression of NRF2, HMOX1, and other candidate antioxidant genes in cisplatin-resistant cells. Furthermore, low or no expression of GULP1 was observed in most cisplatin nonresponder cases. Silencing of GULP1 was associated with GULP1 promoter hypermethylation in cell lines and primary tumors, and a high frequency of GULP1 promoter methylation was observed in multiple sets of primary clinical UCB samples. Together, our findings demonstrate that GULP1 is a KEAP1-binding protein that regulates KEAP1-NRF2 signaling in UCB and that promoter hypermethylation of GULP1 is a potential mechanism of GULP1 silencing.

Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma

Mutations in mitochondrial DNA (mtDNA) have been linked to risk, progression, and treatment response of head and neck squamous cell carcinoma (HNSCC). Due to their clonal nature and high copy number, mitochondrial mutations could serve as powerful molecular markers for detection of cancer cells in bodily fluids, surgical margins, biopsies and lymph node (LN) metastasis, especially at sites where tumor involvement is not histologically apparent. Despite a pressing need for high-throughput, cost-effective mtDNA mutation profiling system, current methods for library preparation are still imperfect for detection of low prevalence heteroplasmic mutations. To this end, we have designed an ultra-deep amplicon-based sequencing library preparation approach that covers the entire mitochondrial genome. We sequenced mtDNA in 28 HNSCCs, matched LNs, surgical margins and bodily fluids, and applied multiregional sequencing approach on 14 primary tumors. Our results demonstrate that this quick, sensitive and cost-efficient method allows obtaining a snapshot on the mitochondrial heterogeneity, and can be used for detection of low frequency tumor-associated mtDNA mutations in LNs, sputum and serum specimens. These findings provide the foundation for using mitochondrial sequencing for risk assessment, early detection, and tumor surveillance.

Expression of programmed cell death ligand 1 in non-small cell lung cancer: Comparison between cytologic smears, core biopsies, and whole sections using the SP263 assay

BACKGROUND

Evaluation of programmed cell death ligand 1 (PD-L1) expression can be made on both resection specimens and diagnostic biopsies; however, more than 30% of patients with advanced non-small cell lung cancer (NSCLC) do not have adequate histologic material to perform PD-L1 assays and require additional biopsies. In addition, in our practice, more than 16% of cases have cytological smears as the only available material. Our aim was to validate the PD-L1 immunocytochemistry assay on cytological smears and compare its accuracy with the results obtained from tissue cores and whole tumor sections using the clinically relevant cutoff of 50%.

METHOD

We compared the PD-L1 staining results of cytological smears to those from tissue cores or whole sections in 50 and 53 NSCLC cases, respectively, using the SP263 assay after scanning hematoxylin and eosin slides.

RESULTS

We found an overall agreement of 90.6% between cytological smears and whole sections; specifically, we found absolute concordance between smears with PD-L1 expressed in <10% and ≥50% of cells and whole sections with PD-L1 expressed in <50% and ≥50% of cells, respectively. In addition, slightly lower diagnostic accuracy was found for the cytological smears in comparison with the tissue cores, but the difference was not statistically significant. We found excellent intraobserver and good interobserver agreement in the evaluation of PD-L1 on smears.

CONCLUSION

Immunocytochemistry on cytological smears is a reliable method for determination of PD-L1 at the 50% cutoff when positive cells are <10% or ≥50%; for cases showing PD-L1 expression in 10% to 49% of cells, additional tissue sampling may be necessary.

PD-L1 expression comparison between primary and relapsed non-small cell lung carcinoma using whole sections and clone SP263

We assessed the concordance, in terms of PD-L1 expression, between primary and metastatic non-small cell lung carcinoma (NSCLC) of different histotypes using validated SP263 clone. A few samples of local recurrences have also been analyzed.

Whole sections of consecutive cases of primary NSCLC and paired relapses undergone surgical resection have been stained with PD-L1 clone SP263; for scoring purposes, a three-tiered system was applied using the following thresholds: <1%, 1–49% and ≥50%.

Eighty-four cases of paired primary and relapsed tumors from 83 patients were analyzed, including 75 metastases and 9 local recurrences. Regarding metastases, when considering a cutoff of 1%, discrepancy in PD-L1 expression occurred in 9/75 (12%) paired samples (kappa value = 0.75); at 50% cutoff, discrepancy in PD-L1 expression was detected in 7/75 (9.3%) of paired samples (kappa value = 0.61). Regarding recurrences, at 1% cutoff, the discrepancy in PD-L1 expression was seen in 3/9 (33%) paired samples and in all cases there was a gained PD-L1 expression; at 50% cutoff, 1/9 (11%) paired samples showed gained PD-L1 expression.

Our data provide important information regarding the concordance between primary and relapsed NSCLC and the degree of reliability of metastatic sites in terms of PD-L1 expression evaluation.

Abstract 1132: PAX6 drives cancer cells toward a stem like state via GLI-SOX2 signaling axis in lung adenocarcinoma

PAX6 is an essential transcription factor for embryonic stem cell maintenance, but its contribution to lung cancer stem cells (CSCs) remains unexplored. We demonstrate that PAX6 acts as an oncogene responsible for induction of cancer stemness properties and plays a biological role in tumor initiation and CSC expansion in lung adenocarcinoma (LUAD). Mechanistically, PAX6 activates Hedgehog-GLI signaling in a SMO-independent noncanonical manner, resulting in SOX2 upregulation directly by the binding of GLI to the proximal promoter region of the SOX2 gene. The overexpressed SOX2 enhances the expression of key pluripotent factors (OCT4 and NANOG) and suppresses differentiation lineage factors (HOPX and NKX2-1). Thus, PAX6 drives cancer cells toward a stem-like state via the GLI-SOX2 signaling axis in LUAD. In contrast, in the differentiated non-CSCs that represent most of the tumor cell population, PAX6 is transcriptionally silenced by its promoter methylation. In human lung cancer tissues, the positive linear correlations of PAX6 expression with GLI and SOX2 expression and its negative correlations with HOPX and NKX2-1 expression were observed. Therapeutically, the blockade of the PAX6-GLI-SOX2 signaling axis elicits a long-lasting therapeutic efficacy by limiting CSC expansion following chemotherapy. Our findings provide a rationale for targeting the PAX6-GLI-SOX2 signaling axis with chemotherapy as an effective therapeutic strategy.

Citation Format: Akira Oki, Mohammad O. Hoque. PAX6 drives cancer cells toward a stem like state via GLI-SOX2 signaling axis in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1132.

Abstract 2750: An epigenetic and immunologic approach to optimize therapy for HNSCC

Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, and despite advances in treatment options, the five-year survival rate for patients with HNSCC is dismal. Monotherapy (such as surgery or radiation) can be effective if detected early, however more advanced cases require treatment with various combinations of surgery, radiation and chemotherapy. Recently, interest in the utilization of immunotherapy for advanced HNSCC has increased, including the FDA approval of pembrolizumb and nivolumab (checkpoint inhibitors) for patients with recurrent or metastatic HNSCC. However, about 80% of patients remain unresponsive to checkpoint inhibitors. Numerous pre-clinical and clinical attempts aim to increase the sensitivity of immuno-agents. One such attempt is combination of immune-agents with epigenetic therapy. Epigenetic alterations in tumor cells modulate gene expression patterns that may facilitate evasion of immune recognition. The efficacy of epigenetic modulating agents to reverse these alterations is documented in various cancer types including HNSCC. Here, we sought to explore whether the utilization of combination therapy of epigenetic drugs (DNA methyltransferase inhibitor, 5azacytidine and the histone deacetylase inhibitor, romidepsin) with checkpoint inhibitors to increase the efficacy of immune-agents in a pre-clinical model of HNSCC.

To explore the gene expression alterations induced by epigenetic drugs in HNSCC, we treated six HNSCC cell lines in vitro with 5azacytidine and romidepsin, and analyzed gene expression patterns by microarray and quantitative RT-PCR (QRT-PCR). We found significant differences in immune-related gene expression patterns in epigenetic drug-treated cell lines compared to untreated controls. Further, to explore the immune-associated gene expression changes, we performed QRT-PCR using a Taqman low density (TLDA) human immune array. By this analysis, we found changes in expression patterns of several immune related genes including HMOX1, NFKB2, HLA-DRA, STAT3, IL12a, CSF1, CSF2, FAS, and IL-18 in epigenetic drug-treated cells. Additionally, by QRT-PCR analysis of several candidates of the viral defense pathway, we found significant upregulation of Interferon type 1 (IFN 1) related genes STAT1, OASL, IFI6 and IRF7 in epigenetic drug-treated cell lines. These results indicate that HNSCC cell lines acquire a new immune signature following treatment with epigenetic agents. Next, we used an in vivo syngeneic model of HNSCC, to compare tumor growth following treatment with mono or combination therapy. Our preliminary data suggests that combination treatment with epigenetic drugs and an immune-agent more effectively reduces tumor growth than either of these drugs alone. In conclusion, our results highlight the importance of considering combination of epigenetic and immune therapy for HNSCC patients that respond poorly to immune therapy alone.

Citation Format: Rachel Goldberg, Masahiro Shibata, Evgeny Izumchenko, Luigi Marchionni, David Sidransky, Mohammad O. Hoque. An epigenetic and immunologic approach to optimize therapy for HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2750.

Patient-derived xenografts effectively capture responses to oncology therapy in a heterogeneous cohort of patients with solid tumors

Background

While patient-derived xenografts (PDXs) offer a powerful modality for translational cancer research, a precise evaluation of how accurately patient responses correlate with matching PDXs in a large, heterogeneous population is needed for assessing the utility of this platform for preclinical drug-testing and personalized patient cancer treatment.

Patients and methods

Tumors obtained from surgical or biopsy procedures from 237 cancer patients with a variety of solid tumors were implanted into immunodeficient mice and whole-exome sequencing was carried out. For 92 patients, responses to anticancer therapies were compared with that of their corresponding PDX models.

Results

We compared whole-exome sequencing of 237 PDX models with equivalent information in The Cancer Genome Atlas database, demonstrating that tumorgrafts faithfully conserve genetic patterns of the primary tumors. We next screened PDXs established for 92 patients with various solid cancers against the same 129 treatments that were administered clinically and correlated patient outcomes with the responses in corresponding models. Our analysis demonstrates that PDXs accurately replicate patients' clinical outcomes, even as patients undergo several additional cycles of therapy over time, indicating the capacity of these models to correctly guide an oncologist to treatments that are most likely to be of clinical benefit.

Conclusions

Integration of PDX models as a preclinical platform for assessment of drug efficacy may allow a higher success-rate in critical end points of clinical benefit.

PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections

INTRODUCTION

Determination of programmed death ligand 1 (PD-L1) expression defines eligibility for treatment with pembrolizumab in patients with advanced NSCLC. This study was designed to better define which value across core biopsy specimens from the same case more closely reflects the PD-L1 expression status on whole sections and how many core biopsy specimens are needed for confident classification of tumors in terms of PD-L1 expression.

METHODS

We built tissue microarrays as surrogates of biopsies collecting five cores per case from 268 cases and compared PD-L1 staining results obtained by using the validated clone SP263 with the results obtained by using whole tumor sections.

RESULTS

We found an overall positivity in 39% of cases at a cutoff of 1% and in 10% of cases at a cutoff of 50%. The maximum value across cores was associated with high concordance between cores and whole sections and the lowest number of false-negative cases overall. To reach high concordance with whole sections, four and three cores are necessary at cutoffs of 1% and 50%, respectively. Importantly, with 20% as the cutoff for core biopsy specimens, fewer than three cores showed high sensitivity and specificity in identifying cases with 50% or more of tumor cells positive for PD-L1 on whole sections. Specifically, for PD-L1 expression values of 20% to 49% on cores, the probabilities of a tumor specimen expressing PD-L1 in at least 50% of cells on a whole section were 46% and 24% with one and two biopsy specimens, respectively.

CONCLUSIONS

An accurate definition of the criteria to determine the PD-L1 status of a given tumor may greatly help in selecting those patients who could benefit from anti-programmed cell death 1/PD-L1 treatment.

YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells

Overcoming acquired drug resistance remains a core challenge in the clinical management of human cancer, including in urothelial carcinoma of the bladder (UCB). Cancer stem-like cells (CSC) have been implicated in the emergence of drug resistance but mechanisms and intervention points are not completely understood. Here, we report that the proinflammatory COX2/PGE2 pathway and the YAP1 growth-regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSCs. Mechanistically, COX2/PGE2 signaling induced promoter methylation of let-7, resulting in its downregulation and subsequent SOX2 upregulation. YAP1 induced SOX2 expression more directly by binding its enhancer region. In UCB clinical specimens, positive correlations in the expression of SOX2, COX2, and YAP1 were observed, with coexpression of COX2 and YAP1 particularly commonly observed. Additional investigations suggested that activation of the COX2/PGE2 and YAP1 pathways also promoted acquired resistance to EGFR inhibitors in basal-type UCB. In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. Our findings provide a preclinical rationale to target these pathways concurrently with systemic chemotherapy as a strategy to improve the clinical management of UCB.Significance: These findings offer a preclinical rationale to target the COX2 and YAP1 pathways concurrently with systemic chemotherapy to improve the clinical management of UCB, based on evidence that these two pathways expand cancer stem-like cell populations that mediate resistance to chemotherapy. Cancer Res; 78(1); 168-81. ©2017 AACR.

Abstract 1551: GULP1 is an epigenetically altered and functional tumor suppressor in urothelial carcinoma through regulation of Nrf2-Keap1 signaling axis

We identified GULP1 as a novel tumor suppressor gene (TSG) selectively silenced during urothelial cancer (UC) progression through promoter hypermethylation (PH) analyzed by quantitative methylation specific PCR (QMSP) and novel methylation specific digital droplet PCR (ddPCR) assay. Numerous cell based assays revealed that GULP1 silencing confers growth advantage to tumor cells. Correspondently, in vivo tumorigenicity after xenotransplantation of GULP1 knockdown T24 cells was significantly higher than control cells. Further mechanistic analysis revealed that GULP1 has a crucial role in the regulation of Nrf2-Keap1 axis, maintaining actin cytoskeleton architecture and helping Keap1 to scaffold Nrf2 in the cytoplasm. Moreover, GULP1 silencing induces constitutive activation of Nrf2 target signature, responsible for chemoresistance of UCs. Additionally, we analyzed GULP1 PH and expression in cisplatin-based therapy responsive and resistant primary UC samples, and in isogenic cisplatin sensitive and resistant T24 cell lines. Interestingly, GULP1 expression at transcription level was lower in both resistant primary UC samples and resistant T24 cell line. Cell lines with lower expressions of GULP1 (SW780 and UM-UC-3) also showed higher resistance to cisplatin than those with higher expression (T24 and BFTC905). Altogether, our findings determined that GULP1 is an epigenetically silenced potential TSG in UC and GULP1 expression and/or PH may guide in selecting candidate patients for cisplatin based neo-adjuvant therapy.

Citation Format: Masamichi Hayashi, Elisa Guida, Rachel Goldberg, Yoshikuni Inokawa, Leonardo Reis, Akira Oki, Evgeny Izumchenko, Leonel Maldonado, Luigi Marchionni, Mariana Brait, Trinity Bivalacqua, Alexander Baras, George J. Netto, Wayne Koch, David Sidransky, Mohammad O. Hoque. GULP1 is an epigenetically altered and functional tumor suppressor in urothelial carcinoma through regulation of Nrf2-Keap1 signaling axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1551. doi:10.1158/1538-7445.AM2017-1551

Abstract 4667: mtDNA sequencing in HNSCC as a measurer of intratumoral heterogeneity and lymph node metastasis

Head and neck squamous cell carcinoma (HNSCC), accounts for 650,000 new cases worldwide. It is notorious for poor prognosis, which reflects its propensity to present as metastatic disease upon diagnosis. The prognosis and treatment regiments vary dramatically upon the manifestation of lymph node (LN) metastasis. Detection of regional LN metastasis is usually based on the clinical examination and imaging, followed by post-operational histological analysis. Unfortunately, current tools for detection of tumor cells in surgically resected LN may, in some cases, miss the presence of micrometastasis. Novel strategies for detection of micrometastasis based on the analysis of tumor-derived genetic aberrations by next generation sequencing (NGS) offer new hope for improved risk assessment and better selection of the treatment regimen. However, detection of mutations in minuscule metastatic lesions comprised of only few neoplastic cells may still fall below the detection threshold of these highly sensitive techniques. By virtue of their clonal nature, higher mutation rate and copy number, assessing tumor-specific mitochondrial DNA (mtDNA) mutations in histologically clean LN may provide a more sensitive diagnostic tool and eventually reduce the false negative rate in patients. Additionally, due to its circular configuration, mtDNA thought to be more stable than genomic DNA, and may also be suitable for sequencing formalin-fixed paraffin-embedded (FFPE) -derived genomic material, an invaluable resource for clinical research. However, current methods for library preparation are still imperfect for detection of low prevalence variants and heteroplasmy with high depth of coverage, especially in highly degraded samples. To this end, we aimed to set up a novel NGS assay for mtDNA analysis in primary and metastatic samples. Amplicon-based NGS library preparation approach, consisting of 148 primers pairs that cover the entire mitochondrial genome (with a dual coverage of 86.18%) was designed in collaboration with Fluidigm to be used on Access Array™ platform. To enhance the coverage of degraded material the amplicon size was limited to ~170 base pairs. Primers for three nuclear housekeeping genes were added to the panel to allow quantitative copy number analysis. To address mitochondrial mutational patterns, heteroplasmy and heterogeneity, we have used this novel high-throughput enrichment technology to sequence mtDNA from different areas of 16 primary HNSCC tumors (fresh frozen and FFPE), and multiple matched metastatic or histologically clean lymph-nodes. We obtained over 99% coverage with a median average depth of 3000X and no difference between fresh frozen and FFPE samples. This method allows obtaining a snapshot on the extent of mitochondrial heterogeneity of these lesions and may be used for detection of low frequency tumor-associated mtDNA mutations as a measurer of possible metastatic processes in histologically clean LN.

Citation Format: Adrian D. Schubert, Evgeny Izumchenko, William H. Westra, Aditi Chatterjee, Wayne M. Koch, Mohammad O. Hoque, David Sidransky. mtDNA sequencing in HNSCC as a measurer of intratumoral heterogeneity and lymph node metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4667. doi:10.1158/1538-7445.AM2017-4667

Abstract 2458: Spatial genomic heterogeneity of multifocal bladder cancer

Urothelial cancer (UC) is a well-known multifocal disease with frequent recurrences. The clonal origin of spatially separated UC foci is controversial. Here we propose to elucidate the multifocal UC genome by next generation sequencing (NGS) and thereby identify novel clonal heterogeneity among the lesions of a single bladder. Until now, all experiments aimed at understanding the molecular heterogeneity were generated mostly by candidate gene approach and older technologies. There is a lack of comprehensive molecular information in these multifocal lesions partly due to inadequate sample size for comprehensive molecular studies. Identification of mutational status at the gene level in different multifocal lesions will allow us to identify markers for prognostic classification, and predictive classification of response to UC therapies, as well as identify potential therapeutic targets.

To understand the molecular heterogeneity among the lesions of a single bladder, we used The Ion AmpliSeq™ Comprehensive Cancer Panel (CCP) (ThermoFisher). The Ion AmpliSeq™ CCP was designed to target all exons of 409 key tumor suppressor genes (TSGs) and oncogenes most frequently cited and mutated in cancer. We tested 41 lesions from 16 cystectomized bladders. Among these lesions, we performed an initial analysis of a total of 21 lesions and 8 germ line controls from 8 patients. We further technically validated selected mutational events found by NGS by a complementary approach, namely droplet digital PCR (ddPCR). We then compared the intra- and inter-tumoral mutation profiles. Two separate lesions were used for analysis in 3 patients and 3 lesions were taken from each of the remaining 5 patients. Our initial analysis showed mutational heterogeneity among the lesions of most of the samples. Briefly, two of the patients had one clone found at all sites, while the rest of the patients showed more variation amongst their lesions. For instance, ARID2, TRRAP, PDGFB, and FBXW7 were mutated in two out of three lesions in one of the patients, indicating hotspot for heterogeneous mutational events. Three mutational events were confirmed by ddPCR, denoting the accuracy of our NGS data analysis.

Our analysis demonstrates that targeted next generation sequencing is a sensitive and reliable method for interrogating the molecular landscape of bladder cancer, and indicates that both clonal and spontaneous events can account for multifocal bladder cancer.

Our data suggests that sequencing of multiple lesions from an individual patient is necessary to accurately elucidate the mutation profile and tailor appropriate targeted treatment. Further analysis in an extended number of samples is necessary to fully understand the molecular heterogeneity at the mutational level in urothelial cancer.

Citation Format: Rachel Goldberg, Maria Del Carmen Rodriguez, Leslie Cope, Aline C. Tregnago, Evgeny Izumchenko, George J. Netto, David Sidransky, Mohammad O. Hoque. Spatial genomic heterogeneity of multifocal bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2458. doi:10.1158/1538-7445.AM2017-2458

Mitochondria in chronic obstructive pulmonary disease and lung cancer: where are we now?

Recent advances in mitochondrial biogenesis have provided the emerging recognition that mitochondria do much more than 'simply providing energy for cellular function'. Currently, a constantly improving understanding of the mitochondrial structure and function has been providing valuable insights into the contribution of defects in mitochondrial metabolism to various human diseases, including chronic obstructive pulmonary disease and lung cancer. The growing interest in mitochondria research led to development of new biomedical fields in the two main smoking-related lung diseases. However, there is considerable paucity in our understanding of mechanisms by which mitochondrial dynamics regulate lung diseases. In this review, we will discuss our current knowledge on the role of mitochondrial dysfunction in the pathogenesis of chronic obstructive pulmonary disease and non-small-cell lung cancer.

In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia

A subset of patients with oral squamous cell carcinoma (OSCC), the most common subtype of head and neck squamous cell carcinoma (HNSCC), harbor dysplastic lesions (often visually identified as leukoplakia) prior to cancer diagnosis. Although evidence suggest that leukoplakia represents an initial step in the progression to cancer, signaling networks driving this progression are poorly understood. Here, we applied in silico Pathway Activation Network Decomposition Analysis (iPANDA), a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in OSCC and pre-neoplastic oral lesions. In tumor samples, our analysis detected major conserved mitogenic and survival signaling pathways strongly associated with HNSCC, suggesting that some of the pathways identified by our algorithm, but not yet validated as HNSCC related, may be attractive targets for future research. While pathways activation landscape in the majority of leukoplakias was different from that seen in OSCC, a subset of pre-neoplastic lesions has demonstrated some degree of similarity to the signaling profile seen in tumors, including dysregulation of the cancer-driving pathways related to survival and apoptosis. These results suggest that dysregulation of these signaling networks may be the driving force behind the early stages of OSCC tumorigenesis. While future studies with larger leukoplakia data sets are warranted to further estimate the values of this approach for capturing signaling features that characterize relevant lesions that actually progress to cancers, our platform proposes a promising new approach for detecting cancer-promoting pathways and tailoring the right therapy to prevent tumorigenesis.

MicroRNA expression profiling of Xp11 renal cell carcinoma

Renal cell carcinomas (RCCs) with Xp11 translocation (Xp11 RCC) constitute a distinctive molecular subtype characterized by chromosomal translocations involving the Xp11.2 locus, resulting in gene fusions between the TFE3 transcription factor with a second gene (usually ASPSCR1, PRCC, NONO, or SFPQ). RCCs with Xp11 translocations comprise up to 1% to 4% of adult cases, frequently displaying papillary architecture with epithelioid clear cells. To better understand the biology of this molecularly distinct tumor subtype, we analyze the microRNA (miRNA) expression profiles of Xp11 RCC compared with normal renal parenchyma using microarray and quantitative reverse-transcription polymerase chain reaction. We further compare Xp11 RCC with other RCC histologic subtypes using publically available data sets, identifying common and distinctive miRNA signatures along with the associated signaling pathways and biological processes. Overall, Xp11 RCC more closely resembles clear cell rather than papillary RCC. Furthermore, among the most differentially expressed miRNAs specific for Xp11 RCC, we identify miR-148a-3p, miR-221-3p, miR-185-5p, miR-196b-5p, and miR-642a-5p to be up-regulated, whereas miR-133b and miR-658 were down-regulated. Finally, Xp11 RCC is most strongly associated with miRNA expression profiles modulating DNA damage responses, cell cycle progression and apoptosis, and the Hedgehog signaling pathway. In summary, we describe here for the first time the miRNA expression profiles of a molecularly distinct type of renal cancer associated with Xp11.2 translocations involving the TFE3 gene. Our results might help understanding the molecular underpinning of Xp11 RCC, assisting in developing targeted treatments for this disease.

Patient-derived xenografts as tools in pharmaceutical development

Successful drug development in oncology is grossly suboptimal, manifested by the very low percentage of new agents being developed that ultimately succeed in clinical approval. This poor success is in part due to the inability of standard cell-line xenograft models to accurately predict clinical success and to tailor chemotherapy specifically to a group of patients more likely to benefit from the therapy. Patient-derived xenografts (PDXs) maintain the histopathological architecture and molecular features of human tumors, and offer a potential solution to maximize drug development success and ultimately generate better outcomes for patients. Although imperfect in mimicking all aspects of human cancer, PDXs are a more predictable platform for preclinical evaluation of treatment effect and in selected cases can guide therapeutic decision making in the clinic. This article summarizes the current status of PDX models, challenges associated with modeling human cancer, and various approaches that have been applied to overcome these challenges and improve the clinical relevance of PDX cancer models.

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA

Lungs resected for adenocarcinomas often harbour minute discrete foci of cytologically atypical pneumocyte proliferations designated as atypical adenomatous hyperplasia (AAH). Evidence suggests that AAH represents an initial step in the progression to adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA) and fully invasive adenocarcinoma. Despite efforts to identify predictive markers of malignant transformation, alterations driving this progression are poorly understood. Here we perform targeted next-generation sequencing on multifocal AAHs and different zones of histologic progression within AISs and MIAs. Multiregion sequencing demonstrated different genetic drivers within the same tumour and reveal that clonal expansion is an early event of tumorigenesis. We find that KRAS, TP53 and EGFR mutations are indicators of malignant transition. Utilizing droplet digital PCR, we find alterations associated with early neoplasms in paired circulating DNA. This study provides insight into the heterogeneity of clonal events in the progression of early lung neoplasia and demonstrates that these events can be detected even before neoplasms have invaded and acquired malignant potential.

Atypical adenomatous hyperplasia is thought to be a precursor lesion for lung adenocarcinoma. Here, using targeted deep sequencing, the authors demonstrate that hyperplastic lesions contain somatic mutations associated with malignant disease and that these can be detected in circulating tumour cells.

An integrated genome-wide approach to discover deregulated microRNAs in non-small cell lung cancer: Clinical significance of miR-23b-3p deregulation

In spite of significant technical advances, genesis and progression of non-small cell lung cancer (NSCLC) remain poorly understood. We undertook an integrated genetic approach to discover novel microRNAs that were deregulated in NSCLCs. A total 119 primary NSCLCs with matched normal were analyzed for genome-wide copy number changes. We also tested a subset of matched samples by microRNA expression array, and integrated them to identify microRNAs positioned in allelic imbalance area. Our findings support that most of the identified deregulated microRNAs (miR-21, miR-23b, miR-31, miR-126, miR-150, and miR-205) were positioned in allelic imbalance areas. Among microRNAs tested in independent 114 NSCLCs, overexpression of miR-23b was revealed to be a significantly poor prognostic factor of recurrence free survival (HR = 2.40, P = 0.005, 95%CI: 1.32–4.29) and overall survival (HR = 2.35, P = 0.005, 95%CI: 1.30–4.19) in multivariable analysis. In addition, overexpression of miR-23b in H1838 cell line significantly increased cell proliferation, while inhibition of miR-23b in H1437 and H1944 cell lines significantly decreased cell doubling time. In summary, integration of genomic analysis and microRNA expression profiling could identify novel cancer-related microRNAs, and miR-23b could be a potential prognostic marker for early stage NSCLCs. Further biological studies of miR-23b are warranted for the potential development of targeted therapy.

Epigenetic inactivation of VGF associated with Urothelial Cell Carcinoma and its potential as a non-invasive biomarker using urine

BACKGROUND

To identify new epigenetic markers and further characterize Urothelial Cell Carcinoma (UCC), we tested the promoter methylation (PM) status of 19 genes previously identified as cancer specific methylated genes in other solid tumors.

METHODS

We used bisulfite sequencing, methylation specific PCR and quantitative methylation specific PCR (QMSP) to test the PM status of 19 genes in urothelial cancer cell lines.

RESULTS

Among the 19 genes tested, VGF was found to be completely methylated in several UCC cell lines. VGF QMSP analysis showed that methylation values of almost all the primary 19 UCC tissues were higher than the paired normal tissues (P=0.009). In another cohort, 12/35 (34.3%) of low grade UCC cases displayed VGF methylation. As a biomarker for non-invasive detection of UCC, VGF showed a significantly higher frequency of methylation in urine from UCC cases (8/20) compared to controls (1/20) (P=0.020). After treatment of cell lines with 5-Aza-2'-deoxycytidine, VGF was robustly re-expressed. Forced expression of VGF in bladder cancer cell lines inhibited cell growth.

CONCLUSION

Selection of candidates from genome-wide screening approach in other solid tumors successfully identified UCC specific methylated genes.

Cyclin A1 expression predicts progression in pT1 urothelial carcinoma of bladder: a tissue microarray study of 149 patients treated by transurethral resection

AIMS

To evaluate the immunoexpression of cyclin A1 in pT1 urothelial carcinomas of the bladder (UC) from a cohort of patients treated by transurethral resection of the bladder (TURB), to determine its value in predicting tumour recurrence, tumour progression, or systemic metastases.

METHODS AND RESULTS

Five tissue microarrays (TMAS) were constructed from representative paraffin blocks of high-grade pT1 UC from 149 consecutive patients. Cyclin A1 immunoexpression was evaluated as the percentage of tumour cells with positive nuclear staining estimated at each TMA spot. The cutoff for cyclin A1 positivity was set at 10% of cells. Outcome variables included tumour recurrence and tumour progression as the primary endpoints. Cyclin A1 positivity was associated with tumour progression but not with tumour recurrence or the presence of adjacent carcinoma in situ in the biopsy. Also, patients with pT1b at biopsy and cyclin A1 expression showed higher progression rates than patients with pT1a at biopsy and without cyclin A1 expression, respectively. Combining pT1 stage at biopsy and cyclin A1 expression more accurately predicted tumour progression than pT1 stage at biopsy alone and cyclin A1 expression alone.

CONCLUSIONS

Cyclin A1 immunoexpression is of potential utility in predicting disease progression in patients with pT1 UC.

Abstract 1363: Epigenetic inactivation of VGF in urothelial cell carcinoma and its potential as a non-invasive biomarker using urine

Background: Urothelial Cell Carcinoma (UCC) presents as a very heterogeneous disease which cannot sufficiently be characterized with the currently known genetic and epigenetic markers. To identify new epigenetic markers for UCC we scrutinized the methylation status of 19 genes that has been shown to be cancer specific methylated genes in other solid tumors in our comprehensive genome-wide discovery approach.

Methods: We performed promoter methylation of 19 genes (CAMK4, CKMT1b, FKBP4, GALE, HOXB5, HPN, KRT14, LPAR2, MAL, NBR1, NDP, NF1, PDLIM3, PHKA2, PVRL1, RGS4, SGK1, VGF and ZMYM2) that are related to key molecular pathways involved in urothelial carcinogenesis including MAPK pathway or PI3K/AKT pathway. The methods we used includes bisulfite sequencing, methylation specific PCR and quantitative methylation specific PCR(QMSP). All the 19 genes and/or a particular gene were evaluated in urothelial cancer cell lines, primary tumor tissues and urine sediments.

Results: By bisulfite sequencing, methylation frequencies for CAMK4, CKMT1b, FKBP4, GALE, HOXB5, HPN, KRT14, LPAR2, MAL, NBR1, NDP, NF1, PDLIM3, PHKA2, PVRL1, RGS4, SGK1, VGF and ZMYM2 were 33.3%, 42.9%, 71.4%, 100.0%, 42.9%, 71.4%, 85.7%, 28.6%, 100.0%, 16.7%, 42.9%, 100.0%, 33.3%, 16.7%, 16.7%, 33.3%, 16.7%, 57.1% and 57.1% respectively in urothelial cancer cell lines. Based on methylation frequencies and known functional evidence, CAMK4, HOXB5, MAL, RGS4, VGF and ZMYM2 were selected for re-expression analysis after 5-Aza-2′-deoxycytidine treatment of UCC cell lines. We also found that promoter methylation of these 6 genes were inversely correlated with gene expression. Since VGF gene was found to be completely methylated in the representative cell lines, we further performed QMSP analysis on 19 primary UCC tissues of different stages and grades with paired normal. Quantitative methylation values were higher in almost all the primary UCC tissues than the paired normal (student's t-test, P=0.005). In an independent cohort of 35 low grade UCC primary tissues, we performed QMSP assay. Twelve out of thirty-five (34.3%) of low grade UCC cases displayed VGF methylation that indicate VGF could be a marker for determining initiation of neoplastic transformation. To explore the potential of methylated VGF as a biomarker for non-invasive detection of UCC, we tested 20 urine samples from UCC cases and 20 urine samples from subjects without any known neoplastic diseases. VGF showed significantly high frequency of QMSP positive status (Fisher's exact test, P=0.020) in urine from UCC cases (8/20) compared to controls (1/20).

Conclusion: Our selected genes from genome-wide screening approach successfully identified UCC specific methylated genes that can be determined in primary tissues and urine. Further studies are needed to understand the role of VGF in urothelial carcinogenesis and its potential for the detection of low grade UCC using urine.

Citation Format: Masamichi Hayashi, Heike Bernert, Luciane Tsukamoto Kagohara, Mariana Brait, Mark Schoenberg, Trinity Bivalacqua, George Netto, Wayne Koch, David Sidransky, Mohammad O. Hoque. Epigenetic inactivation of VGF in urothelial cell carcinoma and its potential as a non-invasive biomarker using urine. [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 1363. doi:10.1158/1538-7445.AM2014-1363

Abstract 558: Mutational heterogeneity related to neoadjuvant therapy response in muscle invasive urothelial cell carcinoma revealed by whole-exome sequencing

Twenty five to thirty-five percent of urothelial cell carcinoma (UCC) patients either present with or develop muscle-invasive disease (MIUCC). Cisplatin-eligible MIUCC patients is treated with neoadjuvant cisplatin-based combination chemotherapy followed by radical cystoprostatectomy and pelvic lymph node dissection. In spite of this approach, the incidence of systemic relapse of MIUCC is high with only 50% of patients remaining alive and disease free at 5 years. Therapies targeted at altered genetic pathways have proven efficacy in different localized solid tumors. However, no such targeted therapies have proven clinical benefit in MIUCC. This may partially due to comparatively few genetic characterizations or no characterization of neoadjuvant therapy sensitive (NAS) and neoadjuvant therapy resistant (NAR) MIUCC patient's samples. So, we attempted to define molecular signatures of NAR and NAS MIUCC samples to identify differential mutational events that could predict therapy response and may eventually use for targeted therapy. To this end, we performed whole exome sequencing of three pairs of urothelial cell carcinomas and matched normal tissues. One patient was neoadjuvant therapy responder (NAS) and the other two were non-responders (NAR). Using these pilot data, candidate tumor-specific mutations in NAS and NAR were extracted. Initially we determined tumor specific mutations in MIUCC. The numbers of identified tumor-specific mutated genes in each of the 3 samples were 127, 57 and 68 respectively. Only two genes (FAM75A3 and GOLGA6L10) were detected as common tumor-specific mutations in all three tissue sets. Eight genes (TP53, CUL1, CENPC1, IGSF10, OR2AG2, ZNF93, LRRFIP1 and CRIPAK) were detected as candidate non responder-specific mutations in both of the NAR samples but not in the NAS samples. In conclusion, genome-wide mutation analysis of coding genes successfully revealed candidate lists of novel tumor-specific gene mutations in MIUCC and neoadjuvant therapy response specific gene mutations that were not reported previously. Further studies in extended set of NAS and NAR samples and technical validation are in progress to well define the molecules that are related to neoadjuvant therapy response. Functional studies of the selected molecules will be undertaken to understand the molecular basis of these genes to modulate neoadjuvant therapy response.

Citation Format: Masamichi Hayashi, Enrico Munari, Christina Michailidi, Mariana Brait, Mark Schoenberg, Trinity Bivalacqua, George Netto, Wayne Koch, David Sidransky, Mohammad O. Hoque. Mutational heterogeneity related to neoadjuvant therapy response in muscle invasive urothelial cell carcinoma revealed by whole-exome sequencing. [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 558. doi:10.1158/1538-7445.AM2014-558

Abstract 5231: Prognostic significance of miR-23b and miR-31 expression in non-small-cell lung cancer

Background: Despite optimal and early surgical treatment of non-small-cell lung cancer (NSCLC), many patients die of recurrent NSCLC. In a recent study, we have undertaken an integrated genetic approach to discover novel loci and miRNA that are deregulated in NSCLC. Here we investigated the association between a panel of miRNA and clinicopathological parameters of the tumor.

Methods: To study association between allelic imbalance/LOH and deregulation of miRNAs, we analyzed a subset (8 pairs) of samples for miRNA expression and correlate the miRNA expression profile with allelic imbalance data generated by SNP analysis. Two types of analysis (The average expression ratio for each miRNA and Mean tumor expression profile) were carried out to identify miRNA probes which show differential expression between tumor and adjacent normal tissues, and the findings were correlated with allelic imbalance area determined by SNP array analysis. A set of 8 miRNA (miR-21, miR-23b, miR-31, miR-126, miR-145, miR-150, miR-205, miR-296) were further analyzed in two independent cohorts of samples to determine their relationship with clinicopathological parameters including outcome. Each of the samples of these cohorts has at least 10 years of follow-up. Statistical analysis were performed the Mann-Whitney U-test, X2 test or Fisher's exact test, where appropriate. Overall survival rates were analyzed by the Kaplan-Meier and log-rank tests. The level of statistical significance was set at P &lt; 0.05. Functional studies were performed for miR-23b.

Results: We initially performed technical validation of 8 miRNAs by quantitative RT-PCR (Q-RT-PCR). In general, miRNA expression pattern determined by microarray and Q-RT-PCR are consistent. To determine cut off values, we further analyzed all the 8 miRNAs in 19 tumor samples with adjacent normal. By an optimal cut point, miR-21, miR-23b and miR 31 were found to be overexpressed in tumor when compared to paired normal, while miR-145 and MiR-150 were down-regulated. Using the same cut off point, we then analyzed an additional independent cohort of 127 early stage NSCLC samples and miR-23b and miR-31 were found to be overexpressed. Kaplan-Meier analysis indicated that patients with high miR-23b and miR 31 expression had a poor overall survival in univariate analysis (P=0.007, 0.012). Most importantly, multivariate analysis showed that miR-23b was an independent significant prognostic factor in patients with NSCLC (p=0.032). Overexpression of miR-23b facilitates NSCLC cell proliferation in vitro while inhibition of miR-23b decreases the cell viability.

Conclusion: miR 23 b and miR-31 overexpression in patients with early stage NSCLC treated with curative intent by means of surgery is associated with poor survival. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of these two miRNA overexpression in early stage NSCLC before clinical application.

Citation Format: Begum Shahnaz, Masamichi Hayashi, Takenori Ogawa, Mariana Brait, William H. Westra, Mohammad O. Hoque, David Sidransky. Prognostic significance of miR-23b and miR-31 expression in non-small-cell lung cancer. [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 5231. doi:10.1158/1538-7445.AM2014-5231

The TGFβ-miR200-MIG6 pathway orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors

Although specific mutations in the tyrosine kinase domain of epidermal growth factor receptor (EGFR) identify tumors that are responsive to EGFR tyrosine kinase inhibitors (TKI), these genetic alterations are present in only a minority of patients. Patients with tumors expressing wild-type EGFR lack reliable predictive markers of their clinical response to EGFR TKIs. Although epithelial-mesenchymal transition (EMT) has been inversely correlated with the response of cancers to EGFR-targeted therapy, the precise molecular mechanisms underlying this association have not been defined and no specific EMT-associated biomarker of clinical benefit has been identified. Here, we show that during transforming growth factor β (TGFβ)-mediated EMT, inhibition of the microRNAs 200 (miR200) family results in upregulated expression of the mitogen-inducible gene 6 (MIG6), a negative regulator of EGFR. The MIG6-mediated reduction of EGFR occurs concomitantly with a TGFβ-induced EMT-associated kinase switch of tumor cells to an AKT-activated EGFR-independent state. In a panel of 25 cancer cell lines of different tissue origins, we find that the ratio of the expression levels of MIG6 and miR200c is highly correlated with EMT and resistance to erlotinib. Analyses of primary tumor xenografts of patient-derived lung and pancreatic cancers carrying wild-type EGFR showed that the tumor MIG6(mRNA)/miR200 ratio was inversely correlated with response to erlotinib in vivo. Our data demonstrate that the TGFβ-miR200-MIG6 network orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors, and identify a low ratio of MIG6 to miR200 as a promising predictive biomarker of the response of tumors to EGFR TKIs.

GSTP1 promoter methylation is associated with recurrence in early stage prostate cancer

PURPOSE

Recurrent prostate cancer remains a major problem. Staging, grading and prostate specific antigen level at surgery are helpful but still imperfect predictors of recurrence. For this reason there is an imperative need for additional biomarkers that add to the prediction of currently used prognostic factors.

MATERIALS AND METHODS

We evaluated the extent of promoter methylation of genes previously reported as aberrantly methylated in prostate cancer (AIM1, APC, CCND2, GPX3, GSTP1, MCAM, RARβ2, SSBP2 and TIMP3) by quantitative fluorogenic methylation-specific polymerase chain reaction. We used cancer tissue from a nested case-control study of 452 patients surgically treated for prostate cancer. Recurrence cases and controls were compared and the association between methylation extent and recurrence risk was estimated by logistic regression adjusting for patient age at prostatectomy, prostatectomy year, stage, grade, surgical margins and preprostatectomy prostate specific antigen. All statistical tests were 2-sided with p ≤0.05 considered statistically significant.

RESULTS

The extent of GSTP1 methylation was higher in patients with recurrence than in controls (p = 0.01), especially patients with early disease, ie organ confined or limited extraprostatic extension (p = 0.001). After multivariate adjustment GSTP1 promoter methylation at or above the median was associated with an increased risk of recurrence, including in men with early disease (each p = 0.05).

CONCLUSIONS

Greater GSTP1 promoter methylation in cancer tissue was independently associated with the risk of recurrence in patients with early prostate cancer. This suggests that GSTP1 promoter methylation may be a potential tissue based recurrence marker.

Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression

Purpose

To elucidate the role of biological and clinical impact of aberrant promoter hypermethylation (PH) in ovarian cancer (OC).

Experimental Design

PH of PGP9.5, HIC1, AIM1, APC, PAK3, MGMT, KIF1A, CCNA1, ESR1, SSBP2, GSTP1, FKBP4 and VGF were assessed by quantitative methylation specific PCR (QMSP) in a training set. We selected two genes (VGF and PGP9.5) for further QMSP analysis in a larger independent validation (IV) set with available clinical data. Biologic relevance of VGF gene was also evaluated.

Results

PH frequency for PGP9.5 and VGF were 85% (316/372) and 43% (158/366) respectively in the IV set of samples while no PH was observed in controls. In 372 OC cases with available follow up, PGP9.5 and VGF PH were correlated with better patient survival [Hazard Ratios (HR) for overall survival (OS) were 0.59 (95% Confidence Intervals (CI)  = 0.42–0.84, p = 0.004), and 0.73 (95%CI = 0.55–0.97, p = 0.028) respectively, and for disease specific survival (DSS) were 0.57 (95%CI 0.39–0.82, p = 0.003) and 0.72 (95%CI 0.54–0.96, p = 0.027). In multivariate analysis, VGF PH remained an independent prognostic factor for OS (HR 0.61, 95%CI 0.43–0.86, p<0.005) and DSS (HR 0.58, 95%CI 0.41–0.83, p<0.003). Furthermore, PGP9.5 PH was significantly correlated with lower grade, early stage tumors, and with absence of residual disease. Forced expression of VGF in OC cell lines inhibited cell growth.

Conclusions

Our results indicate that VGF and PGP9.5 PH are potential biomarkers for ovarian carcinoma. Confirmatory cohorts with longitudinal follow-up are required in future studies to define the clinical impact of VGF and PGP9.5 PH before clinical application.

Abstract 4193: Exposure to arsenic and miRNA deregulation: a potential non-invasive screening tool for urothelial cell carcinoma

Background: We hypothesize that gene deregulation caused by aberrant miRNA expression may play a role in arsenic-induced transformation. To confirm this hypothesis and to identify the molecular mechanisms involved, we developed a cell culture model that permit us to study the progressive, transforming effects of arsenic in uro-epithelial cell behavior and to assess the impact of arsenic exposure on bladder tumorigenesis. Identified miRNAs may also have potential for non-invasive screening test using urine.

Materials and Methods: We first aimed to determine which fraction of urine is suitable for miRNA analysis. To this end we extracted RNA from 10 cases of urine samples using a) 600 μL of voided urine directly after collection from patients; b) 600 μL of supernatant after centrifuging for 10 min at 1500 rpm and c) from the urine sediment. Our initial observation suggested that RNA from urine supernatant is suitable for miRNA analysis. Furthermore, we aimed to identify a housekeeping miRNA with consistent non-differential expression levels between controls and urine from UCC patients. Total RNA, including miRNA, was extracted from urine samples obtained from non-neoplastic individuals and UCC patients, using the MirVana miRNA Isolation Kit. For quantitative real-time reverse transcriptase PCR (qRT-PCR) of selected miRNA, cDNA was synthesized from 20 ng of total RNA using TaqMan miRNA specific primers (Applied Biosystems) for each candidate and a TaqMan MicroRNA Reverse Transcription Kit (Applied Biosystems). PCR reactions were carried out in 384-well plates in a 7900 sequence detector (Perkin-Elmer Applied Biosystems) and were analyzed by a sequence detector system (SDS 2.2.1; Applied Biosystems).

Results: RNU6b, RNU48, miR-222, miR-191 and miR-16 were tested as potential housekeeping genes in urine samples from controls and cases. Among the above listed candidates, miR-222 was found to be the optimal miRNA for normalization across the samples. As such, we normalized expression of miR-200a, -200b, -200c, and -205 to miR-222 in 51 urine samples from UCC cases and 5 urine samples from controls. Expression of miR-200a, -200b, -200c, and -205 was observed in 15/51(29%), 22/51(43%), 29/51(57%) and 38/49(78%) respectively, in urine of UCC cases. No expression of any of the miRNAs tested was observed in any of the 5 controls by an optimal cut point. When we consider expression of any of the four miRNAs tested, UCC cases were detected with 100% sensitivity and 100% specificity.

Conclusions: Our initial findings support the assumption that miRNAs may be used as potential biomarkers for non-invasive detection of UCC. Further work will focus specifically in urine of UCC patients with a known exposure to arsenic, as well as urine with matched tumor tissue. Appropriate cohort with age and gender matched controls needs to be tested for alterations of a panel of miRNAs expression to determine its clinical utility.

Citation Format: Christina Michailidi, Tal Hadar, Kaitlyn Zenner, Mark Schoenberg, George Netto, David Sidransky, Mohammad O. Hoque. Exposure to arsenic and miRNA deregulation: a potential non-invasive screening tool for urothelial cell carcinoma. [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 4193. doi:10.1158/1538-7445.AM2013-4193

Abstract 655: Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma

Urothelial Cell Carcinoma (UCC) is the second most common genitourinary malignant disease in the USA, and tobacco smoking is the major known risk factor for UCC development. Exposure to carcinogens, such as those contained in tobacco smoke, is known to directly or indirectly damage DNA, causing mutations, chromosomal deletion events and epigenetic alterations in UCC. Molecular studies have shown that chromosome 9 alterations and P53, RAS, RB and PTEN mutations are among the most frequent events in UCC. Recent studies suggested that continuous tobacco carcinogen exposure drives and enhances the selection of epigenetically altered cells in UCC, predominantly in the invasive form of the disease. However, the sequence of molecular events that lead to UCC after exposure to tobacco smoke is not well understood.

To elucidate molecular events that lead to UCC oncogenesis and progression after tobacco exposure, we developed an in vitro cellular model for smoking induced UCC. SV-40 immortalized normal HUC1 human bladder epithelial cells were continuously exposed to 0.1% cigarette smoke extract (CSE) until transformation occurred. Morphological alterations and increased cell proliferation of non-malignant urothelial cells were observed after 4 months of treatment with CSE. Anchorage-independent growth assessed by soft agar assay and increase in the migratory and invasive potential was observed in urothelial cells after 6 months of CSE treatment. By performing a PCR mRNA expression array specific to the PI3K-AKT pathway, we found 26 genes were up-regulated and 22 genes were down-regulated after 6 months of CSE exposure of HUC cells. Among the altered genes, PTEN, FOXO1, MAPK1 and PDK1 were down-regulated in the transformed cells while AKT1, AKT2, HRAS, RAC1 were up-regulated. Validation by RT-PCR and western blot analysis was then performed. Furthermore, genome-wide methylation analysis revealed MCAM, DCC and HIC1 are hypermethylated in CSE treated urothelial cells when compared to non-CSE exposed cells. The methylation status of these genes was validated using Quantitative Methylation Specific PCR (QMSP), confirming an increase in methylation of CSE treated urothelial cells compared untreated controls. Therefore, our findings suggest that a tobacco signature could emerge from distinctive patterns of genetic and epigenetic alterations and can be identified using an in vitro cellular model for the development of smoking induced cancer.

Citation Format: Enrico Munari, Mariana Brait, Cynthia LeBron, Maartje G. Noordhuis, Shahnaz Begum, Christina Michailidi, Nilda Gonzalez-Roibon, Leonel Maldonado, Tanusree Sen, Rafael Guerrero-Preston, Leslie Cope, Paola Parrella, Vito Michele Fazio, Patrick K. Ha, George Netto, David Sidransky, Mohammad O. Hoque. Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma . [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 655. doi:10.1158/1538-7445.AM2013-655

Abstract 690: Potential biomarkers for the prediction of urothelial cell carcinoma recurrence

Background: Over 90% of bladder cancer cases in the western world present as urothelial cell carcinoma (UCC). Superficial UCC is the most common subtype at the time of detection (around 75%) and usually treated by trans-urethral resection (TUR). Twenty-percent of the previous 75% will be cured after TUR and up to 70% will recur at least once every 5 years even after complete TUR; the remaining progress to muscle invasion and higher stages with a poor prognosis. Currently there are no well validated markers that can discern the tumors that will recur from those that will not. The purpose of this study is to identify methylation based biomarkers to stratify patients with a higher risk of recurrence.

Materials and Methods: Methylation biomarker analysis was performed retrospectively in tumors from 38 UCC patients;18 non-recurrent and 20 recurrent. Using Quantitative Methylation Specific PCR (QMSP), we analyzed the promoter region of 9 genes (ARF, TIMP3, RAR-β, NID2, CCNA1, VGF, AIM1, CALCA and CCND2) in primary UCC tissues. The association of promoter methylation of these genes to recurrence was performed using Fisher Exact and/or Chi-square test. In vitro functional studies of two highly relevant genes (CCNA1 and CCND2) in several urothelial cancer cell lines were performed to have a better understanding of the role of these genes in UCC genesis.

Results: By establishing an empiric cutoff value, the frequencies of methylation in recurrent and non-recurrent UCC respectively are: CCND2 11/19 (58%) and 1/18 (5.5%) (p=0.001,); CCNA1 10/20 (50%) and 3/18 (16%) (p=0.043); NID2 13/20 (65%) and 4/18 (22%) (p=0.01); and, CALCA 8/20 (40%) and 2/18 (11%) (p=0.067). Functional studies of CCNA1 and CCND2 revealed that these genes are inactivated by promoter methylation and have anti-proliferative properties. To assess the potential use of these genes as biomarkers in bodily fluids, we analyzed their promoter methylation in urines from UCC patients and controls. By establishing an empiric cutoff, we found CCND2, CCNA1 and CALCA being significantly more methylated in urine of UCC patients than controls. The methylation frequency of CCND2, CCNA1 and CALCA is 51/148 (34%), 57/82 (69%) and 99/148 (67%), respectively for UCC patients urines, and 3/65(5%), 10/60 (17%) and 20/65(31%) for control urines, respectively.

Conclusion: Our findings depict the relevance of promoter methylation of CCND2, CCNA1, NID2 and CALCA genes for predicting recurrence in patients with UCC and the potential utility for detecting UCC in urine. Future studies using a larger cohort will provide us a better understanding of the molecular alterations associated with UCC in order to develop a reliable tool for outcome prediction and recurrence.

Citation Format: Christina Michailidi, Leonel Maldonado, Mariana Brait, Luciana Schultz, Jong Chul Park, David Sidransky, George Netto, Mohammad O. Hoque. Potential biomarkers for the prediction of urothelial cell carcinoma recurrence. [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 690. doi:10.1158/1538-7445.AM2013-690

Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma

Urothelial cell carcinoma (UCC) is the second most common genitourinary malignant disease in the USA, and tobacco smoking is the major known risk factor for UCC development. Exposure to carcinogens, such as those contained in tobacco smoke, is known to directly or indirectly damage DNA, causing mutations, chromosomal deletion events and epigenetic alterations in UCC. Molecular studies have shown that chromosome 9 alterations and P53, RAS, RB and PTEN mutations are among the most frequent events in UCC. Recent studies suggested that continuous tobacco carcinogen exposure drives and enhances the selection of epigenetically altered cells in UCC, predominantly in the invasive form of the disease. However, the sequence of molecular events that leads to UCC after exposure to tobacco smoke is not well understood. To elucidate molecular events that lead to UCC oncogenesis and progression after tobacco exposure, we developed an in vitro cellular model for smoking-induced UCC. SV-40 immortalized normal HUC1 human bladder epithelial cells were continuously exposed to 0.1% cigarette smoke extract (CSE) until transformation occurred. Morphological alterations and increased cell proliferation of non-malignant urothelial cells were observed after 4 months (mo) of treatment with CSE. Anchorage-independent growth assessed by soft agar assay and increase in the migratory and invasive potential was observed in urothelial cells after 6 mo of CSE treatment. By performing a PCR mRNA expression array specific to the PI3K-AKT pathway, we found that 26 genes were upregulated and 22 genes were downregulated after 6 mo of CSE exposure of HUC1 cells. Among the altered genes, PTEN, FOXO1, MAPK1 and PDK1 were downregulated in the transformed cells, while AKT1, AKT2, HRAS, RAC1 were upregulated. Validation by RT-PCR and western blot analysis was then performed. Furthermore, genome-wide methylation analysis revealed MCAM, DCC and HIC1 are hypermethylated in CSE-treated urothelial cells when compared with non-CSE exposed cells. The methylation status of these genes was validated using quantitative methylation-specific PCR (QMSP), confirming an increase in methylation of CSE-treated urothelial cells compared to untreated controls. Therefore, our findings suggest that a tobacco signature could emerge from distinctive patterns of genetic and epigenetic alterations and can be identified using an in vitro cellular model for the development of smoking-induced cancer.

Hypermethylation of genes detected in urine from Ghanaian adults with bladder pathology associated with Schistosoma haematobium infection

PURPOSE

Schistosoma haematobium is associated with chronic bladder damage and may subsequently induce bladder cancer in humans, thus posing a serious threat where the parasite is endemic. Here we evaluated aberrant promoter DNA methylation as a potential biomarker to detect severe bladder damage that is associated with schistosomiasis by analyzing urine specimens.

MATERIALS AND METHODS

A quantitative methylation-specific PCR (QMSP) assay was used to examine the methylation status of seven genes (RASSF1A, RARβ2, RUNX3, TIMP3, MGMT, P16, ARF) in 57 urine samples obtained from volunteers that include infected and uninfected by S. haematobium from an endemic region. The Fishers Exact Test and Logistic Regression analysis were used to evaluate the methylation status with bladder damage (as assessed by ultrasound examination) in subjects with S. haematobium infection.

RESULTS

RASSF1A and TIMP3 were significant to predict severe bladder damage both in univariate (p = 0.015 and 0.023 respectively) and in multivariate (p = 0.022 and 0.032 respectively) logistic regression analysis. Area under the receiver operator characteristic curves (AUC-ROC) for RASSF1A and TIMP3 to predict severe bladder damage were 67.84% and 63.73% respectively. The combined model, which used both RASSF1A and TIMP3 promoter methylation, resulted in significant increase in AUC-ROC compared to that of TIMP3 (77.55% vs. 63.73%.29; p = 0.023).

CONCLUSIONS

In this pilot study, we showed that aberrant promoter methylation of RASSF1A and TIMP3 are present in urine sediments of patients with severe bladder damage associated with S. haematobium infection and that may be used to develop non-invasive biomarker of S. haematobium exposure and early molecular risk assessmentof neoplastic transformation.

Cigarette smoke induces methylation of the tumor suppressor gene NISCH

We have previously identified a putative tumor suppressor gene, NISCH, whose promoter is methylated in lung tumor tissue as well as in plasma obtained from lung cancer patients. NISCH was observed to be more frequently methylated in smoker lung cancer patients than in non-smoker lung cancer patients. Here, we investigated the effect of tobacco smoke exposure on methylation of the NISCH gene. We tested methylation of NISCH after oral keratinocytes were exposed to mainstream and side stream cigarette smoke extract in culture. Methylation of the promoter region of the NISCH gene was also evaluated in plasma obtained from lifetime non-smokers and light smokers (<20 pack/year), with and without lung tumors, and heavy smokers (20+ pack/year) without disease. Promoter methylation of NISCH was tested by quantitative fluorogenic real-time PCR in all samples. Promoter methylation of NISCH occurred after exposure to mainstream tobacco smoke as well as to side stream tobacco smoke in normal oral keratinocyte cell lines. NISCH methylation was also detected in 68% of high-risk, heavy smokers without detectable tumors. Interestingly, in light smokers, NISCH methylation was present in 69% of patients with lung cancer and absent in those without disease. Our pilot study indicates that tobacco smoke induces methylation changes in the NISCH gene promoter before any detectable cancer. Methylation of the NISCH gene was also found in lung cancer patients' plasma samples. After confirming these findings in longitudinally collected plasma samples from high-risk populations (such as heavy smokers), examining patients for hypermethylation of the NISCH gene may aid in identifying those who should undergo additional screening for lung cancer.

Correlation between BRAF mutation and promoter methylation of TIMP3, RARβ2 and RASSF1A in thyroid cancer

Our aim was to comprehensively analyze promoter hypermethylation of a panel of novel and known methylation markers for thyroid neoplasms and to establish their relationship with BRAF mutation and clinicopathologic parameters of thyroid cancer. A cohort of thyroid tumors, consisting of 44 cancers and 44 benign thyroid lesions, as well as 15 samples of adjacent normal thyroid tissue, was evaluated for BRAF mutation and promoter hypermethylation. Genes for quantitative methylation specific PCR (QMSP) were selected by a candidate gene approach. Twenty-two genes were tested: TSHR, RASSF1A, RARβ2, DAPK, hMLH1, ATM, S100, p16, CTNNB1, GSTP1, CALCA, TIMP3, TGFßR2, THBS1, MINT1, CTNNB1, MT1G, PAK3, NISCH, DCC, AIM1 and KIF1A. The PCR-based "mutector assay" was used to detect BRAF mutation. All p values reported are two sided. Considerable overlap was seen in the methylation markers among the different tissue groups. Significantly higher methylation frequency and level were observed for KIF1A and RARß2 in cancer samples compared with benign tumors. A negative correlation between BRAF mutation and RASSF1A methylation, and a positive correlation with RARß2 methylation were observed in accordance with previous results. In addition, positive correlation with TIMP3 and a marginal correlation with DCC methylation were observed. The present study constitutes a comprehensive promoter methylation profile of thyroid neoplasia and shows that results must be analyzed in a tissue-specific manner to identify clinically useful methylation markers. Integration of genetic and epigenetic changes in thyroid cancer will help identify relevant biologic pathways that drive its development.

AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy

PURPOSE

To evaluate the prognostic significance of six epigenetic biomarkers (AIM1, CDH1, KIF1A, MT1G, PAK3, and RBM6 promoter hypermethlation) in a homogeneous group of prostate cancer patients, following radical prostatectomy (RP).

PATIENTS AND METHODS

Biomarker analyses were performed retrospectively on tumors from 95 prostate cancer patients all with a Gleason score of 3 + 4 = 7 and a minimum follow-up period of 8 years. Using Quantitative Methylation Specific PCR (QMSP), we analyzed the promoter region of six genes in primary prostate tumor tissues. Time to any progression was the primary endpoint and development of metastatic disease and/or death from prostate cancer was a secondary endpoint. The association of clinicopathological and biomolecular risk factors to recurrence was performed using the Log-rank test and Cox proportional hazards model for multivariate analysis. To identify independent prognostic factors, a stepwise selection method was used.

RESULTS

At a median follow-up time of 10 years, 48 patients (50.5%) had evidence of recurrence: Biochemical/PSA relapse, metastases, or death from prostate cancer. In the final multivariate analysis for time to progression, the significant factors were: Older age, HR = 0.95 (95% CI: 0.91, 1.0) (P = 0.03), positive lymph nodes HR = 2.11 (95% CI: 1.05, 4.26) (P = 0.04), and decreased hypermethylation of AIM1 HR = 0.45 (95% CI: 0.2, 1.0) (P = 0.05).

CONCLUSIONS

Methylation status of AIM1 in the prostate cancer specimen may predict for time to recurrence in Gleason 3 + 4 = 7 patients undergoing prostatectomy. These results should be validated in a larger and unselected cohort.

Abstract 4035: Inactivation of the putative tumor suppressor gene AGTR1 by promoter hypermethylation in primary human cancer

Introduction: Primary human cancers are thought to arise from genetic and epigenetic alterations of tumor suppressor genes and oncogenes. Transcriptional and DNA copy-number studies have improved our understanding and classification of solid tumors. Recent studies have established that like mutation, methylation-mediated gene silencing often leads to tumorigenesis. The aim of this study was to comprehensively explore the “ovarian cancer methylome” and to validate the novel methylation marker AGTR1 in a large independent series of ovarian cancer samples. Patients and methods: Fifteen ovarian cancer samples and 10 normal ovarian surface epithelium brushings were hybridized to Affymetrix U133 plus 2.0 arrays. Furthermore, 3 normal ovarian and 3 isogenic (resistant and sensitive to chemotherapy) ovarian cancer cell lines, with or without treatment with a demethylating agent were hybridized to the same array. Selection of cancer specific methylated genes was based on differential expression between normal and cancer samples, with cancer samples having lower expression than normal samples, and upregulation in cancer cell lines after treatment with a demethylating agent. A number of selected genes that showed low or no expression in primary cancer tissues and re-expressed after treatment with a demethylating agent were then tested for promoter methylation by bisulfite sequencing. Quantitative methylation specific PCR (QMSP) was developed for the AGRT1 gene and tested in a total of 353 ovarian cancer, 17 ovarian cystadenoma and 16 ovarian borderline tumor samples. Results: Fourteen primary ovarian tumor DNA samples were available from the samples that were hybridized for expression array analysis. Twelve out of 14 samples were methylated for AGRT1 which is inversely correlated with expression from our array analysis. We then tested 13 normal ovarian epithelium samples and no methylation was detected in any of the samples. Validation in a large independent set of samples confirmed that ovarian cancer samples (207/353, 53%) were more frequently methylated than ovarian cystadenoma (3/17, 18%; P=0.004). Conclusion: We have identified a set of potential tumor suppressor genes by a comprehensive discovery approach to uncover the cancer methylome. Among these genes, AGTR1 methylation was identified as a potential cancer specific methylated gene that may hold promise for further studies to establish it as a biomarker. Functional studies are warranted to evaluate the biologic role of AGTR1 methylation in the carcinogenic process of solid tumors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4035. doi:1538-7445.AM2012-4035

Abstract 5451: Arsenic induced altered pathways in bladder cancer

Background: Urine excretion is the primary route for arsenic elimination. The bladder may thus be exposed to higher concentrations of arsenic due to the bioconcentration of urine by the kidneys. The molecular etiology of cancer linked to arsenic exposure is complex and multiple factors have been described as playing a role in this process. Although there is extensive epidemiologic evidence of increased risk for the development of urothelial cell carcinoma (UCC) associated with arsenic exposure, the mechanisms by which arsenic participates in tumorigenesis are not fully elucidated. Materials and Methods: To prepare in vitro model we chronically exposed immortalized normal human bladder cell line (HUC-1) to arsenic. Briefly, HUC1 cells were cultured in 25cm flask in F12K complete medium with or without 1µM As2O3. Medium and arsenic was changed every two days. Cells were sub-cultured as necessary and frozen down each month for future studies. Morphology differences were monitored over the entire treatment schedule, using a light microscope. Cell growth was monitored by MTT assay. Tumorigenic properties were analyzed by soft agar and invasion assay. Expression of several key molecules of PI3K-AKT signaling pathway was determined by western blot analysis. Results: At 6 months arsenic treated HUC1 cells started to became more rounded and had a tendency to pile on to one another. MTT was performed for each month of treatment in order to determine any changes in cell proliferation due to arsenic treatment. As expected the growth of the HUC1 cells was increased in a time dependent manner after arsenic treatment. Anchorage independent growth was evaluated using soft agar assay. Colonies were observed only in arsenic treated cells and the number of colonies was gradually increased with longer period of treatment. Similarly invaded cells were determined only in arsenic treated cells after 8 months. Withdrawal of arsenic for 2.5 months from 8 and 10 months arsenic treated cells does not reverse the tumorigenic properties. Western Blot analysis of AKT pathway genes, PTEN decreased and AKT and mTOR increased in arsenic treated HUC cells. Conclusion: Our study suggests that the exposure of HUC-1 to arsenic rapidly induces a multifaceted dedifferentiation program characterized by increased cell proliferation, anchorage independent growth and invasion, a motive that is also present after the end of the arsenic treatment indicating that such a manifestation seems to be irreversible. Further studies are needed in order to delineate the molecular effect of arsenic exposal to primary urothelial cancer tissue collected from patients exposed to arsenic. Studies are in progress to understand the mechanisms that induce this tumorigenic properties and potential stem cells activities in arsenic exposed urothelial cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5451. doi:1538-7445.AM2012-5451

Detection of promoter hypermethylation in salivary rinses as a biomarker for head and neck squamous cell carcinoma surveillance

PURPOSE

Hypermethylation of tumor suppressor gene promoters has been found in head and neck squamous carcinoma (HNSCC) and other solid tumors. We evaluated these alterations in pretreatment salivary rinses from HNSCC patients by using real-time quantitative methylation-specific PCR (Q-MSP).

EXPERIMENTAL DESIGN

Pretreatment saliva DNA samples from HNSCC patients were evaluated for patterns of hypermethylation by using Q-MSP. Target tumor suppressor gene promoter regions were selected based on a previous study describing a screening panel for HNSCC in a high-risk population subjects. The selected genes were: DAPK, DCC, MINT-31, TIMP-3, p16, MGMT, CCNA1.

RESULTS

We analyzed the panel in a cohort of 61 HNSCC patients. Thirty-three of the analyzed patients (54.1%) showed methylation of at least one of the selected genes in the saliva DNA. Pretreatment methylated saliva DNA was not significantly associated with tumor site (P = 0.209) nor clinical stage (P = 0.299). However, local disease control and overall survival were significantly lower in patients presenting hypermethylation in saliva rinses (P = 0.010 and P = 0.015, respectively). Multivariate analysis confirmed that this hypermethylation pattern remained as an independent prognostic factor for local recurrence (HR = 12.2; 95% CI = 1.8-80.6; P = 0.010) and overall survival (HR = 2.8; 95% CI = 1.2-6.5; P = 0.016).

CONCLUSIONS

We were able to confirm an elevated rate of promoter hypermethylation in HNSCC saliva of patients by using a panel of gene promoters previously described as methylated specifically in HNSCC. Detection of hypermethylation in pretreatment saliva DNA seems to be predictive of local recurrence and overall survival. This finding has potential to influence treatment and surveillance of HNSCC patients.

Integrated, genome-wide screening for hypomethylated oncogenes in salivary gland adenoid cystic carcinoma

PURPOSE

Salivary gland adenoid cystic carcinoma (ACC) is a rare malignancy that is poorly understood. To look for relevant oncogene candidates under the control of promoter methylation, an integrated, genome-wide screen was conducted.

EXPERIMENTAL DESIGN

Global demethylation of normal salivary gland cell strains using 5-aza-2'-deoxycytidine (5-aza-dC) and trichostatin A (TSA), followed by expression array analysis was conducted. ACC-specific expression profiling was generated using expression microarray analysis of primary ACC and normal samples. Next, the two profiles were integrated to identify a subset of genes for further validation of promoter demethylation in ACC versus normal. Finally, promising candidates were further validated for mRNA, protein, and promoter methylation levels in larger ACC cohorts. Functional validation was then conducted in cancer cell lines.

RESULTS

We found 159 genes that were significantly re-expressed after 5-aza-dC/TSA treatment and overexpressed in ACC. After initial validation, eight candidates showed hypomethylation in ACC: AQP1, CECR1, C1QR1, CTAG2, P53AIP1, TDRD12, BEX1, and DYNLT3. Aquaporin 1 (AQP1) showed the most significant hypomethylation and was further validated. AQP1 hypomethylation in ACC was confirmed with two independent cohorts. Of note, there was significant overexpression of AQP1 in both mRNA and protein in the paraffin-embedded ACC cohort. Furthermore, AQP1 was upregulated in 5-aza-dC/TSA-treated SACC83. Finally, AQP1 promoted cell proliferation and colony formation in SACC83.

CONCLUSIONS

Our integrated, genome-wide screening method proved to be an effective strategy for detecting novel oncogenes in ACC. AQP1 is a promising oncogene candidate for ACC and is transcriptionally regulated by promoter hypomethylation.

Abstract 3910: An integrated genomic and epigenomic approach for identification of novel disease-related regions and genes in bladder cancer progression

Different pathways drive bladder cancer distinct presentations, such as superficial papillary (Ta) when compared to carcinoma in situ (Cis) or muscle invasive tumors. Although multiple chromosomal alterations have been identified, the specific genes and loci driving the distinct pathways remain largely unknown. In part this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high-resolution genome-wide method, Affymetrix 250K Nsp1 SNP mapping arrays, to screen for somatic DNA copy number variation (CNV) among 49 bladder tumors [17 (35%) clinical stage 1 (15 Ta and 2 Cis), 11 (23%) stage 2, 15 (31%) stage 3 and 6 to be classified] samples and corresponding normals (lymphocytes from the same patient). GeneChip Genotyping analysis software (GTYPE v4.0), Partek Genomic SuiteTM and Hidden Markov model assuming diploid copy for normal samples were employed to infer the CNV estimates. We utilized a genomic segmentation algorithm (requiring a minimum of 10 probes) to characterize significantly higher or lower intensity ratios into cancer specific CNV regions. A threshold of &gt; 3 (gains, amplifications) and &lt; 1.25 (losses, deletions) was used to categorize altered regions. Genome Wide CNV analysis were determined in different groups of comparison (tumor versus normal, superficial vs muscle-invasive stages, Ta vs Cis). Furthermore, to identify the genes that are inactivated one allele by methylation and the other allele by deletion, we performed genome-wide methylation analysis on a subset of these samples by Illumina Methylation Bead Array containing over 27,000 CpG sites, focused on the promoter regions of 14,495 genes. Significant major alterations were seen on chromosome 6q, 8p, 8q, 9p, 9q, 5p, 12p, 12q, 18p, 18q and 20q. We also identified novel small deletions and amplifications throughout the genome. Amplification of loci 6q21-22 (NKAIN2 and FRK), 9q22 (PHF2) and 11p15 (OR51F2) and deletion of loci 11p15 (MRGPRX1), 16p23 (ADAMTS18), 11q15 (MCT2) and 14q11 (DAD1) were observed in superficial Ta compared to Cis. Interestingly, among the 366 CpG probes classified as significantly methylated in the bladder cancer samples, ADAMTS18 was also present. This gene is a disintegrin and metalloproteinase with thrombospondin motifs and has been reported to be epigenetically inactivated in tumors other than bladder cancer, including nasopharyngeal, esophageal, gastric, colorectal and pancreatic cancers. Genetic alterations have also being described: deletions in breast cancer as well as somatic mutations in melanoma. Our initial findings strengthen ADAMTS18 potential's of being a candidate gene related to bladder tumorigenesis. The integration of genetic and epigenetic alterations may lead to a comprehensive knowledge of the biology of bladder cancer and will open up fertile avenue for further research.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3910. doi:10.1158/1538-7445.AM2011-3910