Maarouf A. Saad

Transcriptome sequencing uncovers novel long noncoding and small nucleolar RNAs dysregulated in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma persists as one of the most common and deadly malignancies, with early detection and effective treatment still posing formidable challenges. To expand our currently sparse knowledge of the noncoding alterations involved in the disease and identify potential biomarkers and therapeutic targets, we globally profiled the dysregulation of small nucleolar and long noncoding RNAs in head and neck tumors. Using next-generation RNA-sequencing data from 40 pairs of tumor and matched normal tissues, we found 2808 long noncoding RNA (lncRNA) transcripts significantly differentially expressed by a fold change magnitude ≥2. Meanwhile, RNA-sequencing analysis of 31 tumor-normal pairs yielded 33 significantly dysregulated small nucleolar RNAs (snoRNA). In particular, we identified two dramatically down-regulated lncRNAs and one down-regulated snoRNA whose expression levels correlated significantly with overall patient survival, suggesting their functional significance and clinical relevance in head and neck cancer pathogenesis. We confirmed the dysregulation of these noncoding RNAs in head and neck cancer cell lines derived from different anatomic sites, and determined that ectopic expression of the two lncRNAs inhibited key EMT and stem cell genes and reduced cellular proliferation and migration. As a whole, noncoding RNAs are pervasively dysregulated in head and squamous cell carcinoma. The precise molecular roles of the three transcripts identified warrants further characterization, but our data suggest that they are likely to play substantial roles in head and neck cancer pathogenesis and are significantly associated with patient survival.

The non-coding landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is an aggressive disease marked by frequent recurrence and metastasis and stagnant survival rates. To enhance molecular knowledge of HNSCC and define a non-coding RNA (ncRNA) landscape of the disease, we profiled the transcriptome-wide dysregulation of long non-coding RNA (lncRNA), microRNA (miRNA), and PIWI-interacting RNA (piRNA) using RNA-sequencing data from 422 HNSCC patients in The Cancer Genome Atlas (TCGA). 307 non-coding transcripts differentially expressed in HNSCC were significantly correlated with patient survival, and associated with mutations in TP53, CDKN2A, CASP8, PRDM9, and FBXW7 and copy number variations in chromosomes 3, 5, 7, and 18. We also observed widespread ncRNA correlation to concurrent TP53 and chromosome 3p loss, a compelling predictor of poor prognosis in HNSCCs. Three selected ncRNAs were additionally associated with tumor stage, HPV status, and other clinical characteristics, and modulation of their expression in vitro reveals differential regulation of genes involved in epithelial-mesenchymal transition and apoptotic response. This comprehensive characterization of the HNSCC non-coding transcriptome introduces new layers of understanding for the disease, and nominates a novel panel of transcripts with potential utility as prognostic markers or therapeutic targets.

Alcohol-dysregulated miR-30a and miR-934 in head and neck squamous cell carcinoma.

BackgroundAlcohol consumption is a well-established risk factor for head and neck squamous cell carcinoma (HNSCC); however, the molecular mechanisms by which alcohol promotes HNSCC pathogenesis and progression remain poorly understood. Our study sought to identify microRNAs that are dysregulated in alcohol-associated HNSCC and investigate their contribution to the malignant phenotype.MethodUsing RNA-sequencing data from 136 HNSCC patients, we compared the expression levels of 1,046 microRNAs between drinking and non-drinking cohorts. Dysregulated microRNAs were verified by qRT-PCR in normal oral keratinocytes treated with biologically relevant doses of ethanol and acetaldehyde. The most promising microRNA candidates were investigated for their effects on cellular proliferation and invasion, sensitivity to cisplatin, and expression of cancer stem cell genes. Finally, putative target genes were identified and evaluated in vitro to further establish roles for these miRNAs in alcohol-associated HNSCC.ResultsFrom RNA-sequencing analysis we identified 8 miRNAs to be significantly upregulated in alcohol-associated HNSCCs. qRT-PCR experiments determined that among these candidates, miR-30a and miR-934 were the most highly upregulated in vitro by alcohol and acetaldehyde. Overexpression of miR-30a and miR-934 in normal and HNSCC cell lines produced up to a 2-fold increase in cellular proliferation, as well as induction of the anti-apoptotic gene BCL-2. Upon inhibition of these miRNAs, HNSCC cell lines exhibited increased sensitivity to cisplatin and reduced matrigel invasion. miRNA knockdown also indicated direct targeting of several tumor suppressor genes by miR-30a and miR-934.ConclusionsAlcohol induces the dysregulation of miR-30a and miR-934, which may play crucial roles in HNSCC pathogenesis and progression. Future investigation of the alcohol-mediated pathways effecting these transformations will prove valuable for furthering the understanding and treatment of alcohol-associated HNSCC.

Alcohol-dysregulated microRNAs in hepatitis B virus-related hepatocellular carcinoma

Alcohol consumption and chronic hepatitis B virus (HBV) infection are two well-established risk factors for Hepatocellular carcinoma (HCC); however, there remains a limited understanding of the molecular pathway behind the pathogenesis and progression behind HCC, and how alcohol promotes carcinogenesis in the context of HBV+ HCC. Using next-generation sequencing data from 130 HCC patients and 50 normal liver tissues, we identified a panel of microRNAs that are significantly dysregulated by alcohol consumption in HBV+ patients. In particular, two microRNAs, miR-944 and miR-223-3p, showed remarkable correlation with clinical indication and genomic alterations. We confirmed the dysregulation of these two microRNAs in liver cell lines treated by alcohol and acetaldehyde, and showed that manipulation of miR-223-3p and miR-944 expression induces significant changes in cellular proliferation, sensitivity to doxorubicin, and the expression of both direct-binding and downstream mRNA targets. Together, the results of this study suggest that alcohol consumption in HBV+ HCCs regulates microRNAs that likely play previously uncharacterized roles in the alcohol-associated carcinogenesis of HCC, and future studies of these microRNAs may be valuable for furthering the understanding and treatment of alcohol and HBV-associated HCC.

Performance of PROMIS Global-10 compared with legacy instruments in patients with shoulder arthritis

BACKGROUND The Patient-Reported Outcomes Measurement Information System (PROMIS) Global-10 measures physical and mental health and provides an estimated EuroQol-5 Dimension (EQ-5D) score. The purpose of this study was to determine the correlation between the PROMIS Global-10 and several gold-standard legacy measures to validate its overall performance and usefulness in patients with shoulder arthritis. METHODS The study prospectively enrolled 161 patients with shoulder arthritis before treatment. Each patient completed the PROMIS, EQ-5D, American Shoulder and Elbow Surgeons (ASES) Assessment Form, Single Assessment Numeric Evaluation (SANE), and Western Ontario Osteoarthritis of the Shoulder (WOOS) Index. Spearman correlations were calculated, and Bland-Altman agreement tests were conducted between estimated EQ-5D scores from the PROMIS and actual EQ-5D scores. Ceiling and floor effects were determined. RESULTS Correlation between the PROMIS and EQ-5D was excellent (0.72, P < .001). However, agreement for estimated EQ-5D ranged from 0.37 below to 0.36 above actual EQ-5D scores. Correlation of the PROMIS physical score was good with the ASES score (0.57, P < .001) and poor with the SANE score (0.23, P = .0045) and WOOS score (0.11, P = .3743). Correlation of the PROMIS mental score was poor when compared with all patient-reported outcome instruments investigated (ASES score, 0.26 [P = .0012]; SANE score, 0.13 [P = .1004]; and WOOS score, 0.09 [P = .4311]). No floor or ceiling effects were observed. CONCLUSION PROMIS Global-10 physical scores show excellent correlation with the EQ-5D. However, the PROMIS Global-10 cannot replace actual EQ-5D scores for cost-effectiveness assessment in this population because of the large variance in agreement between actual and PROMIS Global-10-estimated EQ-5D scores. PROMIS Global-10 physical scores showed good correlation with the ASES score but poor correlation with other gold-standard patient-reported outcome instruments, suggesting that it is an inappropriate instrument for outcome measurement in populations with shoulder arthritis.

Abstract 4426: Alcohol consumption and hepatitis B-associated microRNAs in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) affects more than 500,000 new patients each year and is characterized by fast growing, heterogeneous tumors and low five-year survival rates. Despite the identification of HCC risk factors, including alcohol consumption and chronic hepatitis B (HBV) infection, early diagnosis of HCC and molecular understanding of how these risk factors promote HCC both individually and in combination remain elusive. microRNAs (miRNAs), non-coding transcripts ~22 nt in length, have emerged as central mediators of post-transcriptional and translational gene regulation, and have been increasingly implicated in the initiation and progression of many cancers, including HCC. However, the dysregulation profile of miRNAs in HCCs of varying etiologies remains largely unexplored. To identify dysregulated miRNAs specifically associated with alcohol use or with HBV in HCC patients, we analyzed next-generation RNA-sequencing data from 234 HCCs in The Cancer Genome Atlas (TCGA). Through differential expression analyses on cohorts stratified by alcohol consumption and HBV status, we discovered 10 miRNAs specifically dysregulated in alcohol-associated HCCs and 251 miRNAs specifically dysregulated in HBV-associated HCCs (FDR Note: This abstract was not presented at the meeting. Citation Format: Pin Xue Li, Hao Zheng, Maarouf A. Saad, Angela E. Zou, Xiaoqi Wang, James G. Kwok, Avinaash Korrapati, Yuanhao Qu, Thomas K. Honda, Jessica Wang-Rodriguez, Weg M. Ongkeko. Alcohol consumption and hepatitis B-associated microRNAs in hepatocellular carcinoma [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 4426. doi:10.1158/1538-7445.AM2017-4426

Abstract 977: RNA-sequencing analysis implicates novel non-coding RNAs in human papillomavirus-associated head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is an aggressive disease marked by frequent recurrence and metastasis and stagnant survival rates. Given the recent emergence of human papillomavirus (HPV) as a major etiological factor in head and neck cancers, there exists a pressing need to better resolve the molecular heterogeneity of HNSCCs, define more precise diagnostic and prognostic tools, and develop a wider repertoire of targeted therapies. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), have been increasingly viewed as promising sources of insight into cancer onset and progression, with their diverse regulatory roles, tissue specificity, and aberrant expression in various human diseases now established by a multitude of studies. Using RNA-sequencing data from 466 HNSCC patients in The Cancer Genome Atlas (TCGA), we sought to investigate the transcriptome-wide dysregulation of both classes of ncRNAs in HPV-associated HNSCCs. Differential expression analyses controlled for patient smoking status revealed 5 lncRNAs and 9 miRNAs exhibiting significantly altered regulation between HPV-negative and HPV-positive HNSCC tumors (FDR Citation Format: Angela E. Zou, Aswini R. Krishnan, Yinan Xuan, Maarouf A. Saad, Avinaash Korrapati, Sunil J. Advani, Jessica Wang-Rodriguez, Weg Ongkeko. RNA-sequencing analysis implicates novel non-coding RNAs in human papillomavirus-associated head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 977.

Abstract 4069: The carcinogenic effects of electronic cigarettes in oral cancer

Alcohol consumption, tobacco use, and human papillomavirus infection have been well-established as the primary risk factors for head and neck squamous cell carcinoma (HNSCC). However, the surge in popularity of e-cigarettes (e-cigs) has prompted speculation of e-cig use potentially emerging as a new risk factor. With previous research on the safety of e-cigs still collectively inconclusive, a comprehensive study of the carcinogenicity of these devices remains urgently necessary. We therefore investigated the potential genotoxic, cytotoxic, and invasive and migratory effects of e-cig vapor exposure on human epithelial cells. A panel of normal epithelial and head and neck cancer cell lines was treated with 0.5%, 1.0%, and 2.0% by volume e-cig vapor from two popular e-cig brands, over periods ranging from 24 hours to 4 weeks. Neutral comet assay and immunostaining for γ-H2AX foci revealed significant induction of DNA double-stranded breaks (up to 3-fold increase, p Citation Format: Avinaash Korrapati, Vicky Yu, Maarouf A. Saad, Mehran Rahimy, Yinan Xuan, Angela Zou, Aswini Krishnan, Kevin Brumund, Weg M. Ongkeko. The carcinogenic effects of electronic cigarettes in oral cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4069.