An atlas of gastric PIWI-interacting RNA transcriptomes and their utility for identifying signatures of gastric cancer recurrence

The poor survival and recurrence rate in gastric adenocarcinoma highlights the need for cancer gene discovery. Towards this end, we globally assessed the expression of an emerging class of small non-coding RNAs, called PIWI-interacting RNAs (piRNAs). We analysed the transcriptomes of 358 non-malignant stomach tissue and gastric adenocarcinoma samples, and found that nearly half of the expressed piRNAs were overexpressed in tumours. Our gastric piRNA atlas showed that most piRNAs were embedded in protein-coding sequences rather than known piRNA clusters. Furthermore, we identified a three-piRNA signature associated with recurrence-free survival. In this proof-of-principle study, we demonstrate the potential clinical utility of piRNAs in gastric cancer.

Abstract A21: MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma

Introduction: MiR-106a and miR-106b are paralogs of the oncogenic miR-17~92, and have been associated with poor outcome and metastasis in several solid tumors. Their role in lung cancer is relatively unexplored. We characterized the expression of miR-106a and miR-106b in a clinical cohort of lung adenocarcinoma (AC) tumors and assessed their ability to regulate growth and metastasis in cell models.

Methods: MicroRNA (miRNA) expression was deduced from small RNA sequencing data derived from clinical lung AC specimens (60 localized, 27 with lymph node invasion) and paired non-malignant tissues. MiR-106a and miR-106b overexpression vectors and controls were stably transfected into immortalized non-malignant Human Bronchial Epithelial Cells (HBECs) and stage I AC cell lines with epithelial expression patterns by lentiviral delivery. Migration and invasion was assessed by Boyden chamber assay, while cell proliferation was assessed by BrdU incorporation assay. Expression of epithelial-to-mesenchymal transition (EMT) markers and other proteins of interest were assessed by Western Blot. Clinical associations in an external cohort were derived using publically available TCGA data.

Results: MiR-106a and miR-106b were significantly overexpressed in lung AC with lymph node invasion. Overexpression of miR-106a and miR-106b significantly increased proliferation of lung AC cell lines, and was associated with decreased levels of predicted target, p21. AC cell lines displayed a marked increase in metastatic phenotypes in vitro, and were associated with increased mesenchymal and decreased epithelial markers, characteristic of EMT. Importantly, tumors with high expression of both miR-106a and miR-106b and mesenchymal marker vimentin had significantly poorer outcome.

Conclusions: MiR-106a and miR-106b are overexpressed in metastatic lung AC. Lung AC cell models indicate these miRNAs are metastatic agonists, affecting the metastatic potential of cells at least in part via induction of EMT. A deeper characterization of this observation may reveal therapeutic intervention points, or, with the development of miRNA therapeutics, miR-106a/b may be promising targets to prevent or treat metastatic disease.

Citation Format: Katey SS Enfield, David A. Rowbotham, Alice Holly, Christine Anderson, Kevin W. Ng, Brenda de Carvalho Minatel, Graham Dellaire, Chiara Pastrello, Igor Jurisica, Calum MacAulay, Stephen Lam, Wan L. Lam. MiR-106a and miR-106b affect growth and metastasis of lung adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A21.

Abstract B26: OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer

Background: Lung cancer represents an enormous health burden, representing the most common cause of cancer death worldwide. The poor therapeutic outcome is largely due to a complex molecular background as well as late stage diagnosis, with most patients presenting unresectable local tumors, or metastatic disease. While mutations of driver genes is a well-known mechanism, approximately half of all non-small cell lung cancer (NSCLC) tumors harbor no known clinically relevant oncogenic drivers, emphasizing the need to explore alternative mechanisms such as non-coding RNAs (ncRNAs). Natural antisense transcripts (NATS) are ncRNAs that are expressed from the opposite strand of coding mRNAs. These genes overlap with, and are often involved in the regulation of their sense counterparts. NATs can recruit regulatory complexes to their transcriptional locus, leading to silencing of transcription and have recently been described in cancer to silence tumor suppressor genes. NATs are quite prevalent as it is estimated that 25-40% of genes display overlapping transcription, however only a few NATs have been characterized, emphasizing the need to explore these ncRNAs in the context of NSCLC.

Hypothesis: We hypothesize NATs of NSCLC-related genes are deregulated in NSCLC.

Methods: We performed RNAseq and miRNAseq on a set of 65 NSCLC tumors including 36 adenocarcinomas and 29 squamous cell carcinomas as well as matched non-malignant lung tissue. A sign rank test was used to identify NATs with significantly altered expression between tumor and matched normal. Survival analysis was done using a Cox Proportional hazard model, as well as the Kaplan-Meier method.

Results: We have identified a NAT of OIP5, a lung cancer oncogene required for chromatin segregation, to be significantly underexpressed, while its sense counterpart, OIP5 mRNA, is significantly overexpressed. We also find that expression of both OIP5 and OIP5-AS1 has a significant impact on 5 year survival. These findings suggest that deregulation of OIP5 through its antisense RNA may represent a novel mechanism regulating tumor phenotypes in NSCLC.

Citation Format: Greg L. Stewart, Katey SS Enfield, David A. Rowbotham, Roland Hubaux, Victor Martinez, Stephen Lam, Wan Lam. OIP5-Antisense 1, a long noncoding RNA deregulated in non-small cell lung cancer. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr B26.

Arsenic, asbestos and radon: emerging players in lung tumorigenesis

The cause of lung cancer is generally attributed to tobacco smoking. However lung cancer in never smokers accounts for 10 to 25% of all lung cancer cases. Arsenic, asbestos and radon are three prominent non-tobacco carcinogens strongly associated with lung cancer. Exposure to these agents can lead to genetic and epigenetic alterations in tumor genomes, impacting genes and pathways involved in lung cancer development. Moreover, these agents not only exhibit unique mechanisms in causing genomic alterations, but also exert deleterious effects through common mechanisms, such as oxidative stress, commonly associated with carcinogenesis. This article provides a comprehensive review of arsenic, asbestos, and radon induced molecular mechanisms responsible for the generation of genetic and epigenetic alterations in lung cancer. A better understanding of the mode of action of these carcinogens will facilitate the prevention and management of lung cancer related to such environmental hazards.

Abstract B21: The paralogous microRNA clusters, miR-17-92 and miR-106-25, are specifically overexpressed in metastatic non-small cell lung carcinomas

Background: Lung cancer is the cause of the most cancer-related deaths worldwide, with poor survival being largely attributed to late stage of disease at diagnosis and frequent metastasis. Understanding the mechanisms by which lung tumors metastasize could enable the development of anti-metastatic interventions or more specific therapeutics for metastatic disease. MicroRNAs (miRNAs) are major regulators of gene expression and control a wide range of cellular processes involved in metastasis, including apoptosis and cell cycle progression. Recently, increased expression of two paralogous miRNA clusters, miR-17-92 and miR-106b-25, was tied to control of these functions through antagonizing transforming growth factor-β (TGFβ) signaling. A tumor suppressive cytokine, TGFβ regulates cell cycle progression and apoptosis through activation of p21 and BIM, respectively. However, evidence suggests this regulation can be repressed by the overexpression of these microRNA clusters to promote tumor progression. To this end, we sought to determine whether or not expression of these clusters was increased in non-small cell lung cancer (NSCLC) cases positive for nodal or distant metastases compared to those with only locally invasive disease.

Methods: A panel of 41 non-metastatic NSCLCs and a panel of 28 NSCLCs with nodal or distant metastases were collected along with paired adjacent non-malignant tissues. Expression analysis of miRNAs was conducted in these specimens using Illumina GaXII small RNA sequencing technologies. Matched tumor and normal miRNA normalized read count comparisons were performed for each miRNA in the miR-17-92 (miR-17, miR-18a, miR-19a, miR-20a, miR-19b-1, miR-92a-1) and miR-106b-25 (miR-106b, miR-93, miR-25) clusters (Wilcoxon Signed-Rank test p<0.05). Only those miRNAs that were significantly overexpressed and displayed a minimum average expression fold change of 2 were further investigated.

Results: The significant overexpression of several miRNAs occurred specifically in the metastatic cohort, and included miR-20a, miR-92a-1, miR-106b and miR-93. miR-18a and miR-19a were significantly overexpressed in both tumor cohorts as compared to matched normal tissue; however, expression levels were substantially higher in the metastatic cohort and increased by 9.5 and 3 fold, respectively. miR-17 and miR-19b-1 were upregulated in both cohorts to a similar level, while expression of miR-25 was not significantly altered.

Conclusion: miRNAs in the miR-17-92 and miR-106b-25 clusters, save miR-25, were significantly overexpressed in NSCLC cases positive for nodal or distant metastases. There was an overall trend of increasing involvement of miRNAs from these clusters moving from NSCLC cases without metastases to those with metastases, suggesting upregulation of these miRNAs is involved in the metastatic process.

Citation Format: Katey SS Enfield, Stephen Lam, Wan L. Lam. The paralogous microRNA clusters, miR-17-92 and miR-106-25, are specifically overexpressed in metastatic non-small cell lung carcinomas [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr B21.

Abstract A26: DNA copy number alterations deregulate expression of miRNAs in lung adenocarcinoma

Background: Lung cancer represents an enormous health burden, representing the most common cause of cancer death worldwide, with a five-year survival of less than 15%. microRNAs (miRNAs) have emerged as major players in lung cancer oncogenesis, displaying both oncogenic and tumor suppressive functions. DNA copy number (CN) amplification of oncogenes is a major molecular mechanism driving cancer, and like protein coding genes, CN alterations can influence miRNA expression levels. We hypothesize that DNA copy number gain modulates the expression of miRNAs important to cancer cell growth, and that integrative analysis can identify these cancer driving miRNAs.

Methods: Global gene dosage profiles for 46 lung adenocarcinoma and paired adjacent non-malignant tissues were generated by array comparative genomic hybridization. miRNA sequencing analysis was performed on this same panel of tumors and matched non-malignant tissues using Illumina GAXII small RNA sequencing technologies. CN and expression were correlated for each miRNA (Spearman's correlation >0.3, p<0.05) and expression of each significant miRNA was compared between tumors with and without CN gain (U-test p<0.05). To select for miRNAs that most likely play a role in cancer we compared the expression between tumor and matched normal and selected for miRNAs with a fold change of at least 2 in tumors as compared to normal tissues.

Results: We identified a panel of miRNAs in lung adenocarcinoma whose expression deregulation was associated with CN alteration. These miRNAs were found to be gained in >15% of tumors and underwent at least a 2 fold greater increase in expression in tumors compared to matched normal tissues. This study identified several miRNAs known to play a role in cancer including miR-141, known to be highly upregulated in lung and ovarian cancer, and miR-301a, upregulated in invasive early cervical cancer. In addition we identified several novel miRNAs that have not yet been implicated in cancer.

Conclusion: Here we identify a panel of miRNAs that are selectively gained at the genomic level to alter expression in lung adenocarcinoma. Several of these miRNAs have been previously shown to have oncogenic properties in many cancer types including lung cancer and may be potentially useful as therapeutic targets. In addition we identify several miRNAs that have not been previously reported in lung cancer. Future characterization of these miRNAs may lead to increased knowledge of adenocarcinoma oncogenesis.

Citation Format: Greg L. Stewart, Katey SS Enfield, Stephen Lam, Wan Lam. DNA copy number alterations deregulate expression of miRNAs in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A26.