lncRNA DIRC3 regulates invasiveness and insulin-like growth factor signaling in thyroid cancer cells

Differentiated thyroid cancers (DTCs) are malignancies that demonstrate strong but largely uncharacterized heritability. Germline variants that influence the risk of DTCs localize in disrupted in renal carcinoma 3 (DIRC3), a poorly described long non-coding RNA gene. Here, we investigated the function of DIRC3 in DTCs. Using patient-matched thyroid tissue pairs and The Cancer Genome Atlas data, we established that DIRC3 is downregulated in DTCs, whereas high expression of DIRC3 in tumors may reduce the risk of cancer recurrence. DIRC3 transcripts were enriched in cell nuclei, where they upregulated insulin-like growth factor binding protein 5 (IGFBP5), a gene that modulates the cellular response to insulin-like growth factor 1 (IGF1). Silencing DIRC3 in thyroid cancer cell lines (MDA-T32 and MDA-T120) had a dichotomous phenotypic influence: augmented cell migration and invasiveness, reduced apoptosis, but abrogated the MTT reduction rate. Transcriptomic profiling and gene rescue experiments indicated the functional redundancy in the activities of DIRC3 and IGFBP5. Moreover, the reduced level of DIRC3 enhanced the susceptibility of thyroid cancer cells to IGF1 stimulation and promoted Akt signaling via downregulation of the IGFBP5 protein. In conclusion, DIRC3 expression alters the phenotype of thyroid cancer cells and regulates the activity of the IGFBP5/IGF1/Akt axis. Our findings suggest that an interplay between DIRC3 and IGF signaling may play a role in promoting thyroid carcinogenesis.

A comprehensive review on posttreatment surveillance in colorectal patients

Patients who undergo a potentially curative treatment of colorectal cancer are at risk of local recurrences, distant metastases, and metachronous neoplasms. Accordingly, these patients typically undergo a multimodal oncological surveillance aimed to detect relapses early, with an expectation of a higher rate of radical retreatments and better overall survival. Despite much research, the optimal diagnostic panel and the intensity of surveillance have not been well established. Evidence indicates, however, that more intensive follow‑up is unlikely to improve survival after a curative colorectal cancer surgery, chiefly due to the scarcity of recurrences suitable for salvage treatment. Typical surveillance recommended by guidelines includes regular physical examinations, computed tomography scans, serum carcinoembryonic antigen monitoring, and colonoscopy. The objective of this comprehensive review is to discuss different patterns of relapses observed in colorectal cancer patients, present diagnostic options, and summarize different strategies and recommendations of the posttreatment surveillance.

Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) exhibits a different composition of epigenetic alterations. In this study, we identified differentially methylated regions (DMRs) with potential utility in screening for HPV-positive OPSCC. Genome wide DNA methylation was measured using methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) in 50 HPV-positive OPSCC tissues and 25 normal tissues. Fifty-one DMRs were defined with maximal methylation specificity to cancer samples. The Cancer Genome Atlas (TCGA) methylation array data was used to evaluate the performance of the proposed candidates. Supervised hierarchical clustering of 51 DMRs found that HPV-positive OPSCC had significantly higher DNA methylation levels compared to normal samples, and non-HPV-related head and neck squamous cell carcinoma (HNSCC). The methylation levels of all top 20 DNA methylation biomarkers in HPV-positive OPSCC were significantly higher than those in normal samples. Further confirmation using quantitative methylation specific PCR (QMSP) in an independent set of 24 HPV-related OPSCCs and 22 controls showed that 16 of the 20 candidates had significant higher methylation levels in HPV-positive OPSCC samples compared with controls. One candidate, OR6S1, had a sensitivity of 100%, while 17 candidates (KCNA3, EMBP1, CCDC181, DPP4, ITGA4, BEND4, ELMO1, SFMBT2, C1QL3, MIR129-2, NID2, HOXB4, ZNF439, ZNF93, VSTM2B, ZNF137P and ZNF773) had specificities of 100%. The prediction accuracy of the 20 candidates rang from 56.2% to 99.8% by receiver operating characteristic analysis. We have defined 20 highly specific DMRs in HPV-related OPSCC, which can potentially be applied to molecular-based detection tests and improve disease management.

Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy

A majority of cancers fail to respond to immunotherapy with antibodies targeting immune checkpoints, such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) or programmed death-1 (PD-1)/PD-1 ligand (PD-L1). Cancers frequently express transforming growth factor-β (TGFβ), which drives immune dysfunction in the tumor microenvironment by inducing regulatory T cells (Tregs) and inhibiting CD8⁺ and T_H1 cells. To address this therapeutic challenge, we invent bifunctional antibody-ligand traps (Y-traps) comprising an antibody targeting CTLA-4 or PD-L1 fused to a TGFβ receptor II ectodomain sequence that simultaneously disables autocrine/paracrine TGFβ in the target cell microenvironment (a-CTLA4-TGFβRIIecd and a-PDL1-TGFβRIIecd). a-CTLA4-TGFβRIIecd is more effective in reducing tumor-infiltrating Tregs and inhibiting tumor progression compared with CTLA-4 antibody (Ipilimumab). Likewise, a-PDL1-TGFβRIIecd exhibits superior antitumor efficacy compared with PD-L1 antibodies (Atezolizumab or Avelumab). Our data demonstrate that Y-traps counteract TGFβ-mediated differentiation of Tregs and immune tolerance, thereby providing a potentially more effective immunotherapeutic strategy against cancers that are resistant to current immune checkpoint inhibitors.

Bifunctional immune checkpoint-targeted antibody-ligand traps that simultaneously disable TGFβ enhance the efficacy of cancer immunotherapy

A majority of cancers fail to respond to immunotherapy with antibodies targeting immune checkpoints, such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) or programmed death-1 (PD-1)/PD-1 ligand (PD-L1). Cancers frequently express transforming growth factor-β (TGFβ), which drives immune dysfunction in the tumor microenvironment by inducing regulatory T cells (Tregs) and inhibiting CD8+ and TH1 cells. To address this therapeutic challenge, we invent bifunctional antibody-ligand traps (Y-traps) comprising an antibody targeting CTLA-4 or PD-L1 fused to a TGFβ receptor II ectodomain sequence that simultaneously disables autocrine/paracrine TGFβ in the target cell microenvironment (a-CTLA4-TGFβRIIecd and a-PDL1-TGFβRIIecd). a-CTLA4-TGFβRIIecd is more effective in reducing tumor-infiltrating Tregs and inhibiting tumor progression compared with CTLA-4 antibody (Ipilimumab). Likewise, a-PDL1-TGFβRIIecd exhibits superior antitumor efficacy compared with PD-L1 antibodies (Atezolizumab or Avelumab). Our data demonstrate that Y-traps counteract TGFβ-mediated differentiation of Tregs and immune tolerance, thereby providing a potentially more effective immunotherapeutic strategy against cancers that are resistant to current immune checkpoint inhibitors.

Abstract 734: Improved detection of salivary glands’ RNA markers in saliva samples

RNA based liquid biopsy in saliva could be part of the diagnostic process and surveillance in patients with Salivary Gland Tumors. There is no established approach for saliva markers in salivary gland tumors. These tumors occur approximately in one out of 100,000 adults per year in the USA. We aim to develop a method to identify RNA shed specifically from the salivary glands.The two most common salivary gland malignancies harbor frequent gene fusions, which may be candidate RNA based markers. In mucoepidermoid carcinoma, the MECT1-MAML2 fusion. In adenoid cystic carcinoma, either a MYB-NFIB or MYBL1-NFIB fusion. We identified collection and processing methods to be tested on healthy individuals’ saliva samples. We compared three saliva stimulation methods: Chewing Gum, Tabasco and Vitamin C powder with unstimulated collected saliva; and also utilized different processing and RNA extraction procedures: Trizol based: QIAzol method (Qiagen), RNEasy saliva protecting reagent (Qiagen), OrageneRNA (DNA Genotek), and mirVana Kit (ThermoFisher). We evaluated the RNA´s quantity and quality with Spectrophotometer and Agilent’s 2100 Bio analyzer. We identified two salivary gland specifically highly expressed genes (HTN3 and CA6) to be analyzed by quantitative RT-PCR. We have collected and processed 221 samples and analysis is ongoing. Bio analyzer showed that RNA from the unstimulated collected saliva has a higher concentration than stimulated saliva. Unstimulated saliva is expected to contain mucosa cells, bacteria and rests of food, therefore those could also be RNA sources. When saliva’s RNA is protected by either of the buffers tested, the RIN scores (RNA Integrity Number) obtained by Bio analyzer are higher. Based on our preliminary data, stimulation with either Tabasco, Chewing Gum or Vitamin C followed by RNA stabilization with the OrageneRNA kit and extraction with Trizol resulted in the highest quality and specificity of the RNA for its salivary gland origin. Unstimulated collection followed by the same processing generates a greater RNA yield. This saliva RNA is likely contaminated with RNA form squamous cells, bacteria and food residues, which may decrease the sensitivity of the specific gene expression of HTN3 and CA6. Once established how to best collect and protect saliva for the extraction of nucleic acids originated from the salivary glands, we anticipate accelerating the path to clinically highly demanded kits for the surveillance of salivary gland cancer patients. We plan to prospectively collect samples from Salivary gland tumor patients with the chosen method and evaluate tumor related markers. The detection of tumor markers in bodily fluids will open a new avenue for the diagnosis and the clinical management of patients with this type of tumor. Moreover, our work creates the possibility of a liquid biopsy-based detection of several disease-specific alterations identified in different types of salivary gland tumors.

Citation Format: Adrian D. Schubert, Evgeny Izumchenko, Piotr T. Wysocki, David Sidransky, Mariana Brait. Improved detection of salivary glands’ RNA markers in saliva samples [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 734. doi:10.1158/1538-7445.AM2017-734

Comparative mutational landscape analysis of patient-derived tumour xenografts

Background:

Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted next-generation sequencing-based approaches offer promising diagnostic capabilities, there are still limitations. There is a pressing clinical need for a well-validated, rapid, cost-effective mutation profiling system in patient specimens. Given their speed and cost-effectiveness, quantitative PCR mutation detection techniques are well suited for the clinical environment. The qBiomarker mutation PCR array has high sensitivity and shorter turnaround times compared with other methods. However, a direct comparison with existing viable alternatives are required to assess its true potential and limitations.

Methods:

In this study, we evaluated a panel of 117 patient-derived tumour xenografts by the qBiomarker array and compared with other methods for mutation detection, including Ion AmpliSeq sequencing, whole-exome sequencing and droplet digital PCR.

Results:

Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics.

Conclusions:

This large-scale direct comparison and validation of currently available mutation detection approaches is extremely relevant for the current scenario of precision medicine and will lead to informed choice of screening methodologies, especially in lower budget conditions or time frame limitations.

Common pathway signature in lung and liver fibrosis

Fibrosis, a progressive accumulation of extracellular matrix components, encompasses a wide spectrum of distinct organs, and accounts for an increasing burden of morbidity and mortality worldwide. Despite the tremendous clinical impact, the mechanisms governing the fibrotic process are not yet understood, and to date, no clinically reliable therapies for fibrosis have been discovered. Here we applied Regeneration Intelligence, a new bioinformatics software suite for qualitative analysis of intracellular signaling pathway activation using transcriptomic data, to assess a network of molecular signaling in lung and liver fibrosis. In both tissues, our analysis detected major conserved signaling pathways strongly associated with fibrosis, suggesting that some of the pathways identified by our algorithm but not yet wet-lab validated as fibrogenesis related, may be attractive targets for future research. While the majority of significantly disrupted pathways were specific to histologically distinct organs, several pathways have been concurrently activated or downregulated among the hepatic and pulmonary fibrosis samples, providing new evidence of evolutionary conserved pathways that may be relevant as possible therapeutic targets. While future confirmatory studies are warranted to validate these observations, our platform proposes a promising new approach for detecting fibrosis-promoting pathways and tailoring the right therapy to prevent fibrogenesis.

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.

Abstract 4844: High throughput detection of PRKD1 mutations in salivary gland tumors using in situ mutation detection in tissue microarrays

Recently, unique activating mutations in PRKD1 were observed in salivary gland polymorphous low-grade adenocarcinoma (PLGA). PRKD1 is a serine-threonine kinase that participates in important cell functions such as survival, adhesion, and migration. PLGA is a salivary gland tumor that usually shows indolent clinical presentation. Due to morphological similarities within different subtypes of salivary gland neoplasms, differential diagnosis may be puzzling. Although salivary gland cancer is a rare disease (around 3,000 new cases per year in the USA), the gravity of the disease should not be undermined. Currently, the salivary gland cancer biology is poorly understood. Comprehending the molecular biology of this cancer is instrumental in improving the diagnosis and prognostic prediction of this disease. Our goal is to assess the incidence of c.2130A>T and c.2130A>C PRKD1 mutations in different salivary gland tumors by a high throughput mutation detection technique. We first assessed the c.2130 PRKD1 point mutations in 8 PLGA cases using conventional Sanger sequencing. Hotspot mutations were present in 75% (6/8) of the samples. Subsequently, we built tissue microarrays slides that included the following: 5 PLGA, 54 adenoid cystic carcinomas, 30 mucoepidermoid carcinomas, 14 acinic cell carcinomas, 6 adenocarcinomas not otherwise specified, 34 pleomorphic adenocarcinomas, 3 mammary analogue secretory carcinomas, and 1 salivary duct carcinoma. Additional sample collection is ongoing. We optimized a recently described in situ mutation detection to directly visualize single mutations with microscopy in fixed cells and tissue sections. The technique is based on in situ proximity ligation assays that utilize sequence specific probes. Ligation of the padlock probe will only occur if there is a perfect match between the probe and the target. The probes are labeled with fluorophores that allow generated signals to be visualized as bright spots with a fluorescence microscope. This technique allows exact quantification of the detected target molecules while identifying each individual signal (mutant or wild type) within the tissue sections. Once the methodology is validated to detect these mutations, it will allow us to quickly analyze a cohort of salivary gland neoplasms which have been already prepared as tumor microarrays. Additionally, this technique will open new avenues to analyze other mutations in different tumor cohorts already prepared as tumor microarray slides. In the context of salivary gland tumors, differentiating distinct primary tumors subtypes and/ or metastasis from primary tumors with other sites of origin would be invaluable for clinical decisions.

Citation Format: Piotr T. Wysocki, William H. Westra, Shahnaz Begum, David Sidransky, Mariana Brait. High throughput detection of PRKD1 mutations in salivary gland tumors using in situ mutation detection in tissue microarrays. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4844. doi:10.1158/1538-7445.AM2015-4844