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Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS. Nat Protoc 2023; 18:3690-3731. [PMID: 37989764 PMCID: PMC10961825 DOI: 10.1038/s41596-023-00892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/21/2023] [Indexed: 11/23/2023]
Abstract
Non-negative matrix factorization (NMF) is an unsupervised learning method well suited to high-throughput biology. However, inferring biological processes from an NMF result still requires additional post hoc statistics and annotation for interpretation of learned features. Here, we introduce a suite of computational tools that implement NMF and provide methods for accurate and clear biological interpretation and analysis. A generalized discussion of NMF covering its benefits, limitations and open questions is followed by four procedures for the Bayesian NMF algorithm Coordinated Gene Activity across Pattern Subsets (CoGAPS). Each procedure will demonstrate NMF analysis to quantify cell state transitions in a public domain single-cell RNA-sequencing dataset. The first demonstrates PyCoGAPS, our new Python implementation that enhances runtime for large datasets, and the second allows its deployment in Docker. The third procedure steps through the same single-cell NMF analysis using our R CoGAPS interface. The fourth introduces a beginner-friendly CoGAPS platform using GenePattern Notebook, aimed at users with a working conceptual knowledge of data analysis but without a basic proficiency in the R or Python programming language. We also constructed a user-facing website to serve as a central repository for information and instructional materials about CoGAPS and its application programming interfaces. The expected timing to setup the packages and conduct a test run is around 15 min, and an additional 30 min to conduct analyses on a precomputed result. The expected runtime on the user's desired dataset can vary from hours to days depending on factors such as dataset size or input parameters.
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Affiliation(s)
- Jeanette A I Johnson
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ashley P Tsang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jacob T Mitchell
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David L Zhou
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Julia Bowden
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Emily Davis-Marcisak
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas Sherman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ted Liefeld
- Department of Medicine, Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Melanie Loth
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Loyal A Goff
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA
- Single Cell Training and Analysis Center, Johns Hopkins University, Baltimore, MD, USA
| | - Jacquelyn W Zimmerman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Kinny-Köster
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Pablo Tamayo
- Department of Medicine, Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Jill P Mesirov
- Department of Medicine, Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Michael Reich
- Department of Medicine, Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Single Cell Training and Analysis Center, Johns Hopkins University, Baltimore, MD, USA.
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA.
| | - Genevieve L Stein-O'Brien
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Convergence Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA.
- Single Cell Training and Analysis Center, Johns Hopkins University, Baltimore, MD, USA.
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Cierpikowski P, Leszczyszyn A, Bar J. The Role of Hedgehog Signaling Pathway in Head and Neck Squamous Cell Carcinoma. Cells 2023; 12:2083. [PMID: 37626893 PMCID: PMC10453169 DOI: 10.3390/cells12162083] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth leading malignancy worldwide, with a poor prognosis and limited treatment options. Molecularly targeted therapies for HNSCC are still lacking. However, recent reports provide novel insights about many molecular alterations in HNSCC that may be useful in future therapies. Therefore, it is necessary to identify new biomarkers that may provide a better prediction of the disease and promising targets for personalized therapy. The poor response of HNSCC to therapy is attributed to a small population of tumor cells called cancer stem cells (CSCs). Growing evidence indicates that the Hedgehog (HH) signaling pathway plays a crucial role in the development and maintenance of head and neck tissues. The HH pathway is normally involved in embryogenesis, stem cell renewal, and tissue regeneration. However, abnormal activation of the HH pathway is also associated with carcinogenesis and CSC regulation. Overactivation of the HH pathway was observed in several tumors, including basal cell carcinoma, that are successfully treated with HH inhibitors. However, clinical studies about HH pathways in HNSCC are still rare. In this review, we summarize the current knowledge and recent advances regarding the HH pathway in HNSCC and discuss its possible implications for prognosis and future therapy.
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Affiliation(s)
- Piotr Cierpikowski
- Department of Maxillofacial Surgery, The Ludwik Rydygier Specialist Hospital, Osiedle Zlotej Jesieni 1, 31-826 Krakow, Poland
| | - Anna Leszczyszyn
- Dental Surgery Outpatient Clinic, 4th Military Clinical Hospital, Weigla 5, 53-114 Wroclaw, Poland;
| | - Julia Bar
- Department of Immunopathology and Molecular Biology, Wroclaw Medical University, Bujwida 44, 50-345 Wroclaw, Poland
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Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ. Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species. Cell Syst 2020; 8:395-411.e8. [PMID: 31121116 DOI: 10.1016/j.cels.2019.04.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/24/2019] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
Analysis of gene expression in single cells allows for decomposition of cellular states as low-dimensional latent spaces. However, the interpretation and validation of these spaces remains a challenge. Here, we present scCoGAPS, which defines latent spaces from a source single-cell RNA-sequencing (scRNA-seq) dataset, and projectR, which evaluates these latent spaces in independent target datasets via transfer learning. Application of developing mouse retina to scRNA-Seq reveals intrinsic relationships across biological contexts and assays while avoiding batch effects and other technical features. We compare the dimensions learned in this source dataset to adult mouse retina, a time-course of human retinal development, select scRNA-seq datasets from developing brain, chromatin accessibility data, and a murine-cell type atlas to identify shared biological features. These tools lay the groundwork for exploratory analysis of scRNA-seq data via latent space representations, enabling a shift in how we compare and identify cells beyond reliance on marker genes or ensemble molecular identity.
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Affiliation(s)
- Genevieve L Stein-O'Brien
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Thomas Sherman
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Cristina Zibetti
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Sheng Liu
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - Carlo Colantuoni
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA; Center for Human Systems Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA; Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA; McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering and Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA.
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Guo T, Zambo KDA, Zamuner FT, Ou T, Hopkins C, Kelley DZ, Wulf HA, Winkler E, Erbe R, Danilova L, Considine M, Sidransky D, Favorov A, Florea L, Fertig EJ, Gaykalova DA. Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma. Epigenetics 2020; 15:959-971. [PMID: 32164487 DOI: 10.1080/15592294.2020.1741757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV+ OPSCC) represents a unique disease entity within head and neck cancer with rising incidence. Previous work has shown that alternative splicing events (ASEs) are prevalent in HPV+ OPSCC, but further validation is needed to understand the regulation of this process and its role in these tumours. In this study, eleven ASEs (GIT2, CTNNB1, MKNK2, MRPL33, SIPA1L3, SNHG6, SYCP2, TPRG1, ZHX2, ZNF331, and ELOVL1) were selected for validation from 109 previously published candidate ASEs to elucidate the post-transcriptional mechanisms of oncogenesis in HPV+ disease. In vitro qRT-PCR confirmed differential expression of 9 of 11 ASE candidates, and in silico analysis within the TCGA cohort confirmed 8 of 11 candidates. Six ASEs (MRPL33, SIPA1L3, SNHG6, TPRG1, ZHX2, and ELOVL1) showed significant differential expression across both methods. Further evaluation of chromatin modification revealed that ASEs strongly correlated with cancer-specific distribution of acetylated lysine 27 of histone 3 (H3K27ac). Subsequent epigenetic treatment of HPV+ HNSCC cell lines (UM-SCC-047 and UPCI-SCC-090) with JQ1 not only induced downregulation of cancer-specific ASE isoforms, but also growth inhibition in both cell lines. The UPCI-SCC-090 cell line, with greater ASE expression, also showed more significant growth inhibition after JQ1 treatment. This study confirms several novel cancer-specific ASEs in HPV+OPSCC and provides evidence for the role of chromatin modifications in regulation of alternative splicing in HPV+OPSCC. This highlights the role of epigenetic changes in the oncogenesis of HPV+OPSCC, which represents a unique, unexplored target for therapeutics that can alter the global post-transcriptional landscape.
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Affiliation(s)
- Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Kristina Diana A Zambo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Fernando T Zamuner
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Tingting Ou
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Christopher Hopkins
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Dylan Z Kelley
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Hildegard A Wulf
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Eli Winkler
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Rossin Erbe
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Ludmila Danilova
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Michael Considine
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Alexander Favorov
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Liliana Florea
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University , Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Applied Mathematics and Statistics, Johns Hopkins University , Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine , MD, Baltimore, USA
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA
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Chen L, Xu J, Li SC. DeepMF: deciphering the latent patterns in omics profiles with a deep learning method. BMC Bioinformatics 2019; 20:648. [PMID: 31881818 PMCID: PMC6933662 DOI: 10.1186/s12859-019-3291-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND With recent advances in high-throughput technologies, matrix factorization techniques are increasingly being utilized for mapping quantitative omics profiling matrix data into low-dimensional embedding space, in the hope of uncovering insights in the underlying biological processes. Nevertheless, current matrix factorization tools fall short in handling noisy data and missing entries, both deficiencies that are often found in real-life data. RESULTS Here, we propose DeepMF, a deep neural network-based factorization model. DeepMF disentangles the association between molecular feature-associated and sample-associated latent matrices, and is tolerant to noisy and missing values. It exhibited feasible cancer subtype discovery efficacy on mRNA, miRNA, and protein profiles of medulloblastoma cancer, leukemia cancer, breast cancer, and small-blue-round-cell cancer, achieving the highest clustering accuracy of 76%, 100%, 92%, and 100% respectively. When analyzing data sets with 70% missing entries, DeepMF gave the best recovery capacity with silhouette values of 0.47, 0.6, 0.28, and 0.44, outperforming other state-of-the-art MF tools on the cancer data sets Medulloblastoma, Leukemia, TCGA BRCA, and SRBCT. Its embedding strength as measured by clustering accuracy is 88%, 100%, 84%, and 96% on these data sets, which improves on the current best methods 76%, 100%, 78%, and 87%. CONCLUSION DeepMF demonstrated robust denoising, imputation, and embedding ability. It offers insights to uncover the underlying biological processes such as cancer subtype discovery. Our implementation of DeepMF can be found at https://github.com/paprikachan/DeepMF.
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Affiliation(s)
- Lingxi Chen
- City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China
| | - Jiao Xu
- City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China
| | - Shuai Cheng Li
- City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China.
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6
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Flam EL, Danilova L, Kelley DZ, Stavrovskaya E, Guo T, Considine M, Qian J, Califano JA, Favorov A, Fertig EJ, Gaykalova DA. Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer. Sci Rep 2019; 9:15034. [PMID: 31636280 PMCID: PMC6803762 DOI: 10.1038/s41598-019-51018-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/16/2019] [Indexed: 12/30/2022] Open
Abstract
Current literature suggests that epigenetically regulated super-enhancers (SEs) are drivers of aberrant gene expression in cancers. Many tumor types are still missing chromatin data to define cancer-specific SEs and their role in carcinogenesis. In this work, we develop a simple pipeline, which can utilize chromatin data from etiologically similar tumors to discover tissue-specific SEs and their target genes using gene expression and DNA methylation data. As an example, we applied our pipeline to human papillomavirus-related oropharyngeal squamous cell carcinoma (HPV + OPSCC). This tumor type is characterized by abundant gene expression changes, which cannot be explained by genetic alterations alone. Chromatin data are still limited for this disease, so we used 3627 SE elements from public domain data for closely related tissues, including normal and tumor lung, and cervical cancer cell lines. We integrated the available DNA methylation and gene expression data for HPV + OPSCC samples to filter the candidate SEs to identify functional SEs and their affected targets, which are essential for cancer development. Overall, we found 159 differentially methylated SEs, including 87 SEs that actively regulate expression of 150 nearby genes (211 SE-gene pairs) in HPV + OPSCC. Of these, 132 SE-gene pairs were validated in a related TCGA cohort. Pathway analysis revealed that the SE-regulated genes were associated with pathways known to regulate nasopharyngeal, breast, melanoma, and bladder carcinogenesis and are regulated by the epigenetic landscape in those cancers. Thus, we propose that gene expression in HPV + OPSCC may be controlled by epigenetic alterations in SE elements, which are common between related tissues. Our pipeline can utilize a diversity of data inputs and can be further adapted to SE analysis of diseased and non-diseased tissues from different organisms.
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Affiliation(s)
- Emily L Flam
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Ludmila Danilova
- Division of Oncology Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dylan Z Kelley
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Elena Stavrovskaya
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, Russia.,Institute for Information Transmission Problems, RAS, Moscow, 127994, Russia
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Michael Considine
- Division of Oncology Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Joseph A Califano
- Department of Surgery, Head and Neck Cancer Center, University of California, San Diego, California, USA
| | - Alexander Favorov
- Division of Oncology Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elana J Fertig
- Division of Oncology Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
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Terlecki-Zaniewicz L, Lämmermann I, Latreille J, Bobbili MR, Pils V, Schosserer M, Weinmüllner R, Dellago H, Skalicky S, Pum D, Almaraz JCH, Scheideler M, Morizot F, Hackl M, Gruber F, Grillari J. Small extracellular vesicles and their miRNA cargo are anti-apoptotic members of the senescence-associated secretory phenotype. Aging (Albany NY) 2019; 10:1103-1132. [PMID: 29779019 PMCID: PMC5990398 DOI: 10.18632/aging.101452] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/10/2018] [Indexed: 12/15/2022]
Abstract
Loss of functionality during aging of cells and organisms is caused and accompanied by altered cell-to-cell communication and signalling. One factor thereby is the chronic accumulation of senescent cells and the concomitant senescence-associated secretory phenotype (SASP) that contributes to microenvironment remodelling and a pro-inflammatory status. While protein based SASP factors have been well characterized, little is known about small extracellular vesicles (sEVs) and their miRNA cargo. Therefore, we analysed secretion of sEVs from senescent human dermal fibroblasts and catalogued the therein contained miRNAs. We observed a four-fold increase of sEVs, with a concomitant increase of >80% of all cargo miRNAs. The most abundantly secreted miRNAs were predicted to collectively target mRNAs of pro-apoptotic proteins, and indeed, senescent cell derived sEVs exerted anti-apoptotic activity. In addition, we identified senescence-specific differences in miRNA composition of sEVs, with an increase of miR-23a-5p and miR-137 and a decrease of miR-625-3p, miR-766-3p, miR-199b-5p, miR-381-3p, miR-17-3p. By correlating intracellular and sEV-miRNAs, we identified miRNAs selectively retained in senescent cells (miR-21-3p and miR-17-3p) or packaged specifically into senescent cell derived sEVs (miR-15b-5p and miR-30a-3p). Therefore, we suggest sEVs and their miRNA cargo to be novel, members of the SASP that are selectively secreted or retained in cellular senescence.
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Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics 2019; 17:49-63. [PMID: 28968850 PMCID: PMC5860551 DOI: 10.1093/bfgp/elx018] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Daria A Gaykalova
- Corresponding authors: Daria A. Gaykalova, Otolaryngology - Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, Rm 574, CRBII Baltimore, MD 21231, USA. Tel.: +1 410 614 2745; Fax: +1 410 614 1411; E-mail: ; Elana J. Fertig, Assistant Professor of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University, 550 N Broadway, 1101 E Baltimore, MD 21205, USA. Tel.: +1 410 955 4268; Fax: +1 410 955 0859; E-mail:
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Kanazawa T, Misawa K, Shinmura K, Misawa Y, Kusaka G, Maruta M, Sasaki T, Watanabe Y, Carey TE. Promoter methylation of galanin receptors as epigenetic biomarkers for head and neck squamous cell carcinomas. Expert Rev Mol Diagn 2019; 19:137-148. [PMID: 30640567 DOI: 10.1080/14737159.2019.1567334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION While remarkable progress has been made in standard treatments for head and neck squamous cell carcinomas (HNSCCs), the long-term survival remains at an unsatisfactory 40-50%. To improve the survival rate, biomarkers for optimal treatment selection and prognostic prediction, as well as novel, low-toxicity treatment strategies, are required. Galanin receptor (GALR) 1 and GALR2 are well-studied tumor suppressors in HNSCCs. Compared with other clinicopathological factors, the epigenetic variants of GALRs have been found to be the most powerful markers to predict the prognosis of HNSCC patients. Areas covered: This review outlines the functions and signaling pathways of GALRs and explains the potential of GALR promoter methylation as a biomarker for HNSCC prognosis. We also summarize recent developments in promoter methylation studies in HNSCC and indicate future directions for GALR promoter methylation studies. Expert commentary: GALR studies have highlighted two major aspects with implications in HNSCC - that G-protein coupled receptors (GPCRs) act as tumor suppressor genes and that GALR promoter methylation is significantly related to the carcinogenesis of HNSCC. The findings of GALR studies can be applied to studies on other GPCRs and further in-depth DNA methylation studies. Deeper insights into GPCR epigenetics are expected to markedly improve HNSCC treatment.
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Affiliation(s)
- Takeharu Kanazawa
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan.,b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Kiyoshi Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Kazuya Shinmura
- d Department of Tumor Pathology , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Yuki Misawa
- c Department of Otolaryngology/Head and Neck Surgery , Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Gen Kusaka
- e Department of Neurosurgery , Jichi Medical University Saitama Medical Center , Saitama , Saitama , Japan
| | - Mikiko Maruta
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Toru Sasaki
- b Department of Otolaryngology-Head and Neck Surgery , Jichi Medical University , Shimotsuke , Japan
| | - Yusuke Watanabe
- a Department of Otolaryngology-Head and Neck Surgery , International University of Health and Welfare , Tokyo , Japan
| | - Thomas E Carey
- f Laboratory of Head and Neck Center Biology, Department of Otolaryngology, Head and Neck Surgery , The University of Michigan , Ann Arbor , MI , USA
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10
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Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Enter the Matrix: Factorization Uncovers Knowledge from Omics. Trends Genet 2018; 34:790-805. [PMID: 30143323 PMCID: PMC6309559 DOI: 10.1016/j.tig.2018.07.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022]
Abstract
Omics data contain signals from the molecular, physical, and kinetic inter- and intracellular interactions that control biological systems. Matrix factorization (MF) techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in applications ranging from pathway discovery to timecourse analysis. We review exemplary applications of MF for systems-level analyses. We discuss appropriate applications of these methods, their limitations, and focus on the analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with MF enables discovery from high-throughput data beyond the limits of current biological knowledge - answering questions from high-dimensional data that we have not yet thought to ask.
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Affiliation(s)
- Genevieve L Stein-O'Brien
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Raman Arora
- Department of Computer Science, Institute for Data Intensive Engineering and Science, Johns Hopkins University, Baltimore, MD, USA
| | - Aedin C Culhane
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Alexander V Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA; Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, PA, USA; Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, PA, USA
| | - Loyal A Goff
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifeng Li
- Digital Technologies Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Aloune Ngom
- School of Computer Science, University of Windsor, Windsor, ON, Canada
| | - Michael F Ochs
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ, USA
| | - Yanxun Xu
- Department of Applied Mathematics and Statistics, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Elana J Fertig
- Department of Oncology, Division of Biostatistics and Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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11
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Stein-O’Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance. Genome Med 2018; 10:37. [PMID: 29792227 PMCID: PMC5966898 DOI: 10.1186/s13073-018-0545-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients' treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. METHODS To determine the dynamics of these molecular changes, we obtained high throughput omics data (RNA-sequencing and DNA methylation) weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. The CoGAPS unsupervised algorithm was used to determine the dynamics of the molecular changes associated with resistance during the time course of resistance development. RESULTS CoGAPS was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically. CONCLUSIONS Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize the resistant phenotype. These genes include FGFR1, which was associated with EGFR inhibitors resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. This understanding of the time course progression of molecular changes in acquired resistance is important for the development of alternative treatment strategies that would introduce appropriate selection of new drugs to treat cancer before the resistant phenotype develops.
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Affiliation(s)
- Genevieve Stein-O’Brien
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
| | - Luciane T. Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
| | - Sijia Li
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
| | - Manjusha Thakar
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
| | - Ruchira Ranaweera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology-Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Haixia Cheng
- Department of Surgery - Otolaryngology–Head and Neck Surgery, University of Utah, |Salt Lake City, UT USA
| | - Michael Considine
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
| | - Sandra Schmitz
- Head and Neck Surgery Unit, St Luc University Hospital, Brussels, Belgium
| | - Alexander V. Favorov
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
- Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ludmila V. Danilova
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
- Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Joseph A. Califano
- Department of Surgery, UC San Diego Moores Cancer Center, La Jolla, CA USA
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD USA
| | - Daria A. Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD USA
| | - Christine H. Chung
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL USA
| | - Elana J. Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD USA
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12
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Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics 2018; 33:1892-1894. [PMID: 28174896 DOI: 10.1093/bioinformatics/btx058] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/27/2017] [Indexed: 12/24/2022] Open
Abstract
Summary Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF solutions can obscure biomarkers. Therefore, we developed a novel patternMarkers statistic to extract genes for biological validation and enhanced visualization of NMF results. Finding novel and unbiased gene markers with patternMarkers requires whole-genome data. Therefore, we also developed Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS), the first robust whole genome Bayesian NMF using the sparse, MCMC algorithm, CoGAPS. Additionally, a manual version of the GWCoGAPS algorithm contains analytic and visualization tools including patternMatcher, a Shiny web application. The decomposition in the manual pipeline can be replaced with any NMF algorithm, for further generalization of the software. Using these tools, we find granular brain-region and cell-type specific signatures with corresponding biomarkers in GTEx data, illustrating GWCoGAPS and patternMarkers ascertainment of data-driven biomarkers from whole-genome data. Availability and Implementation PatternMarkers & GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license. Contact gsteinobrien@jhmi.edu or ccolantu@jhmi.edu or ejfertig@jhmi.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Genevieve L Stein-O'Brien
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jacob L Carey
- Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Wai Shing Lee
- Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michael Considine
- Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alexander V Favorov
- Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Vavilov Institute of General Genetics, Moscow, Russia.,Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Emily Flam
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sijia Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Luigi Marchionni
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas Sherman
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA
| | - Shawn Sivy
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ronald D McKay
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Michael F Ochs
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA
| | - Carlo Colantuoni
- Department of Neurology and Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Institute for Genome Sciences, University of Maryland School of Medicine
| | - Elana J Fertig
- Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA
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13
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Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics 2018. [PMID: 28968850 DOI: 10.1101/114025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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14
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NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma. Sci Rep 2017; 7:17064. [PMID: 29213088 PMCID: PMC5719078 DOI: 10.1038/s41598-017-17298-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022] Open
Abstract
Chromatin modifying enzymes are frequently mutated in cancer, resulting in widespread epigenetic deregulation. Recent reports indicate that inactivating mutations in the histone methyltransferase NSD1 define an intrinsic subtype of head and neck squamous cell carcinoma (HNSC) that features pronounced DNA hypomethylation. Here, we describe a similar hypomethylated subtype of lung squamous cell carcinoma (LUSC) that is enriched for both inactivating mutations and deletions in NSD1. The ‘NSD1 subtypes’ of HNSC and LUSC are highly correlated at the DNA methylation and gene expression levels, featuring ectopic expression of developmental transcription factors and genes that are also hypomethylated in Sotos syndrome, a congenital disorder caused by germline NSD1 mutations. Further, the NSD1 subtype of HNSC displays an ‘immune cold’ phenotype characterized by low infiltration of tumor-associated leukocytes, particularly macrophages and CD8+ T cells, as well as low expression of genes encoding the immunotherapy target PD-1 immune checkpoint receptor and its ligands. Using an in vivo model, we demonstrate that NSD1 inactivation results in reduced T cell infiltration into the tumor microenvironment, implicating NSD1 as a tumor cell-intrinsic driver of an immune cold phenotype. NSD1 inactivation therefore causes epigenetic deregulation across cancer sites, and has implications for immunotherapy.
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15
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Zhu L, Su F, Xu Y, Zou Q. Network-based method for mining novel HPV infection related genes using random walk with restart algorithm. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2376-2383. [PMID: 29197659 DOI: 10.1016/j.bbadis.2017.11.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/03/2017] [Accepted: 11/26/2017] [Indexed: 12/27/2022]
Abstract
The human papillomavirus (HPV), a common virus that infects the reproductive tract, may lead to malignant changes within the infection area in certain cases and is directly associated with such cancers as cervical cancer, anal cancer, and vaginal cancer. Identification of novel HPV infection related genes can lead to a better understanding of the specific signal pathways and cellular processes related to HPV infection, providing information for the development of more efficient therapies. In this study, several novel HPV infection related genes were predicted by a computation method based on the known genes involved in HPV infection from HPVbase. This method applied the algorithm of random walk with restart (RWR) to a protein-protein interaction (PPI) network. The candidate genes were further filtered by the permutation and association tests. These steps eliminated genes occupying special positions in the PPI network and selected key genes with strong associations to known HPV infection related genes based on the interaction confidence and functional similarity obtained from published databases, such as STRING, gene ontology (GO) terms and KEGG pathways. Our study identified 104 novel HPV infection related genes, a number of which were confirmed to relate to the infection processes and complications of HPV infection, as reported in the literature. These results demonstrate the reliability of our method in identifying HPV infection related genes. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Fangchu Su
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - YaoChen Xu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Quan Zou
- School of Computer Science and Technology, TianJin University, Tianjin 300350, China.
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16
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Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC. Oncotarget 2017; 8:15349-15363. [PMID: 28146432 PMCID: PMC5362490 DOI: 10.18632/oncotarget.14856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/16/2017] [Indexed: 01/23/2023] Open
Abstract
Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have accelerated the genome-wide characterization of HNSCC. However, comprehensive pipelines with statistical algorithms that account for HNSCC biology and perform independent confirmatory and functional validation of candidates are needed to identify the most biologically relevant genes. We applied outlier statistics to high throughput gene expression data, and identified 76 top-scoring candidates with significant differential expression in tumors compared to normal tissues. We identified 15 epigenetically regulated candidates by focusing on a subset of the genes with a negative correlation between gene expression and promoter methylation. Differential expression and methylation of 3 selected candidates (BANK1, BIN2, and DTX1) were confirmed in an independent HNSCC cohorts from Johns Hopkins and TCGA (The Cancer Genome Atlas). We further performed functional evaluation of NOTCH regulator, DTX1, which was downregulated by promoter hypermethylation in tumors, and demonstrated that decreased expression of DTX1 in HNSCC tumors maybe associated with NOTCH pathway activation and increased migration potential.
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17
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Kumar A, Sarode SC, Sarode GS, Majumdar B, Patil S, Sharma NK. Beyond gene dictation in oral squamous cell carcinoma progression and its therapeutic implications. TRANSLATIONAL RESEARCH IN ORAL ONCOLOGY 2017. [DOI: 10.1177/2057178x17701463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ajay Kumar
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sachin C Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Gargi S Sarode
- Department of Oral Pathology, Dr D.Y. Patil Dental College and Research, Pimpri, Pune, Maharashtra, India
| | - Barnali Majumdar
- Department of Oral Pathology and Microbiology, Bhojia Dental College and Hospital, Baddi, Himachal Pradesh, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Nilesh Kumar Sharma
- Cancer and Translational Research Lab, Dr D.Y. Patil Biotechnology and Bioinformatics Institute, Dr D.Y. Patil Vidyapeeth, Pune, Maharashtra, India
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18
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Brennan K, Koenig JL, Gentles AJ, Sunwoo JB, Gevaert O. Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype. EBioMedicine 2017; 17:223-236. [PMID: 28314692 PMCID: PMC5360591 DOI: 10.1016/j.ebiom.2017.02.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is broadly classified into HNSCC associated with human papilloma virus (HPV) infection, and HPV negative HNSCC, which is typically smoking-related. A subset of HPV negative HNSCCs occur in patients without smoking history, however, and these etiologically 'atypical' HNSCCs disproportionately occur in the oral cavity, and in female patients, suggesting a distinct etiology. To investigate the determinants of clinical and molecular heterogeneity, we performed unsupervised clustering to classify 528 HNSCC patients from The Cancer Genome Atlas (TCGA) into putative intrinsic subtypes based on their profiles of epigenetically (DNA methylation) deregulated genes. HNSCCs clustered into five subtypes, including one HPV positive subtype, two smoking-related subtypes, and two atypical subtypes. One atypical subtype was particularly genomically stable, but featured widespread gene silencing associated with the 'CpG island methylator phenotype' (CIMP). Further distinguishing features of this 'CIMP-Atypical' subtype include an antiviral gene expression profile associated with pro-inflammatory M1 macrophages and CD8+ T cell infiltration, CASP8 mutations, and a well-differentiated state corresponding to normal SOX2 copy number and SOX2OT hypermethylation. We developed a gene expression classifier for the CIMP-Atypical subtype that could classify atypical disease features in two independent patient cohorts, demonstrating the reproducibility of this subtype. Taken together, these findings provide unprecedented evidence that atypical HNSCC is molecularly distinct, and postulates the CIMP-Atypical subtype as a distinct clinical entity that may be caused by chronic inflammation.
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Affiliation(s)
- K Brennan
- Department of Medicine, Stanford University, United States
| | - J L Koenig
- Department of Medicine, Stanford University, United States
| | - A J Gentles
- Department of Medicine, Stanford University, United States
| | - J B Sunwoo
- Department of Otolaryngology-Head and Neck Surgery, Stanford University, United States
| | - O Gevaert
- Department of Medicine, Stanford University, United States.
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19
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Reduced proliferation and colony formation of head and neck squamous cell carcinoma (HNSCC) after dual targeting of EGFR and hedgehog pathways. Cancer Chemother Pharmacol 2017; 79:411-420. [PMID: 28110457 DOI: 10.1007/s00280-017-3239-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE The hedgehog signalling pathway (Hh) is frequently active in head and neck squamous cell carcinoma (HNSCC). Overexpressed Hh associates with poor prognosis. The Hh inhibitor vismodegib targets smoothened, and based on molecular data, may prevent resistance to EGFR targeting. METHODS To elucidate potential roles of vismodegib in HNSCC therapy, its sole effects and those combined with cisplatin, docetaxel, and cetuximab on HNSCC cell lines were assessed by MTT metabolisation and BrdU incorporation. Colony formation (CF) of primary HNSCC cells was studied utilizing the FLAVINO-protocol. Combinatory effects were analysed regarding antagonism, additivity or synergism. Associations between the ex vivo detected mode of action of vismodegib with other treatments related to patient characteristics were assessed and progression-free survival (PFS) in patient groups compared using Kaplan-Meier curves. RESULTS Vismodegib suppressed BrdU incorporation significantly stronger than MTT turnover; CF was significantly inhibited at ≥20 µM vismodegib while concentrations <20 µM acted hormetic. Combining 20 µM vismodegib plus docetaxel (T), cisplatin (P), and cetuximab (E), additively enhanced anti-tumoral activity in HNSCC samples from patients with superior PFS highlighting a potential role for ex-vivo testing of this combination for use as a prognostic classifier. CONCLUSION We provide ex-vivo evidence for vismodegib's potential in HNSCC therapies, especially if combined with cetuximab, cisplatin and docetaxel.
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20
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Hess J. Predictive Factors for Outcome and Quality of Life in HPV-Positive and HPV-Negative HNSCC. Recent Results Cancer Res 2017; 206:233-242. [PMID: 27699543 DOI: 10.1007/978-3-319-43580-0_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Infection with high-risk types of the human papilloma virus (HPV) is an etiological risk factor for oropharyngeal squamous cell carcinoma (OPSCC) and associated with a better response to therapy and improved survival. A better understanding of the molecular principles underlying the differences in clinical behavior could pave the way to establish more effective and less toxic therapy for HPV-positive OPSCC and their HPV-negative counterparts. Compelling experimental evidence demonstrates that extensive global reprogramming of epigenetic profiles is as important as genetic mutations during neoplastic transformation and malignant progression, including HPV-positive OPSCC. In this chapter, the current knowledge on HPV-related alterations in DNA methylation, histone modification, and chromosome remodeling will be summarized and assessment of cancer-related profiles will be discussed as a valuable tool to gain important diagnostic or prognostic information for therapeutic decision-making and clinical management of HNSCC patients.
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Affiliation(s)
- Jochen Hess
- Department of Otolaryngology, Head and Neck Surgery, University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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21
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Krishnan AR, Korrapati A, Zou AE, Qu Y, Wang XQ, Califano JA, Wang-Rodriguez J, Lippman SM, Hovell MF, Ongkeko WM. Smoking status regulates a novel panel of PIWI-interacting RNAs in head and neck squamous cell carcinoma. Oral Oncol 2016; 65:68-75. [PMID: 28109471 DOI: 10.1016/j.oraloncology.2016.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/30/2016] [Accepted: 12/17/2016] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Smoking remains a primary etiological factor in head and neck squamous cell carcinoma (HNSCC). Given that non-coding RNAs (ncRNAs), including PIWI-interacting RNAs (piRNAs), have emerged as mediators of initiation and progression in head and neck malignancies, we undertook a global study of piRNA expression patterns in smoking-associated HNSCC. MATERIALS AND METHODS Using RNA-sequencing data from 256 current smoker and lifelong nonsmoker samples in The Cancer Genome Atlas (TCGA), we analyzed the differential expression patterns of 27,127 piRNAs across patient cohorts stratified by tobacco use, with HPV16 status and tumor status taken into account. We correlated their expression to clinical characteristics and to smoking-induced alterations of PIWI proteins, the functional counterparts of piRNAs. Finally, we correlated our identified piRNAs and PIWI proteins to known chromosomal aberrations in HNSCC to understand their wider-ranging genomic effects. RESULTS AND CONCLUSION Our analyses implicated a 13-member piRNA panel in smoking-related HNSCC, among which NONHSAT123636 and NONHSAT113708 associated with tumor stage, NONHSAT067200 with patient survival, and NONHSAT081250 with smoking-altered PIWIL1 protein expression. 6 piRNAs as well as PIWIL1 correlated with genomic alterations common to HNSCC, including TP53 mutation, TP53-3p co-occurrence, and 3q26, 8q24, and 11q13 amplification. Collectively, our findings provide novel insights into the etiology-specific piRNA landscape of smoking-induced HNSCC.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Avinaash Korrapati
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Angela E Zou
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Yuanhao Qu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Xiao Qi Wang
- Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Jessica Wang-Rodriguez
- Veterans Administration Medical Center and Department of Pathology, University of California, San Diego, La Jolla, CA, United States.
| | - Scott M Lippman
- Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States.
| | - Melbourne F Hovell
- Graduate School of Public Health, San Diego State University, San Diego, CA, United States.
| | - Weg M Ongkeko
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
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22
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Enzenhofer E, Parzefall T, Haymerle G, Schneider S, Kadletz L, Heiduschka G, Pammer J, Oberndorfer F, Wrba F, Loader B, Grasl MC, Perisanidis C, Erovic BM. Impact of Sonic Hedgehog Pathway Expression on Outcome in HPV Negative Head and Neck Carcinoma Patients after Surgery and Adjuvant Radiotherapy. PLoS One 2016; 11:e0167665. [PMID: 27918595 PMCID: PMC5137890 DOI: 10.1371/journal.pone.0167665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 11/17/2016] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION HPV positive patients suffering from head and neck cancer benefit from intensified radiotherapy when applied as a primary as well as an adjuvant treatment strategy. However, HPV negative patients treated with surgery and adjuvant radiotherapy lack validated prognostic biomarkers. It is therefore important to define prognostic biomarkers in this particular patient population. Especially, ´high-risk groups´ need to be defined in order to adapt treatment protocols. Since dysregulation of the sonic hedgehog pathway plays an important role in carcinogenesis, we aimed to assess whether members of the sonic hedgehog-signaling pathway may act as prognostic factors in patients with HPV negative head and neck squamous cell carcinoma. MATERIALS AND METHODS In this prospective study, pretreatment tumor biopsies of patients with head and neck squamous cell carcinoma were taken during panendoscopy (2005 to 2008). All patients were treated with surgery and postoperative radiotherapy. After assessment of HPV and p16 status, protein expression profiles of the Sonic hedgehog-signaling pathway were determined by immunohistochemistry and tissue microarray analyses in 36 HPV negative tumor biopsies. Expression profiles of Sonic hedgehog, Indian hedgehog, Patched, Smoothened, Gli-1, Gli-2 and Gli-3 were correlated with patients´ clinical data, local-control rate, disease-free as well as overall survival. Data from The Cancer Genome Atlas databank were used for external validation of our results. RESULTS Gli-1 (p = 0.04) and Gli-2 (p = 0.02) overexpression was significantly linked to improved overall survival of HPV negative patients. Gli-2 (p = 0.04) overexpression correlated significantly with prolonged disease-free survival. Cox-multivariate analysis showed that overexpression of Gli-2 correlated independently (HR 0.40, 95% CI 0.16-0.95, p = 0.03) with increased overall survival. DISCUSSION Gli-1 and Gli-2 overexpression represents a substantial prognostic factor for overall and disease-free survival in patients with locally advanced HPV negative head and neck cancer undergoing surgery and postoperative radiotherapy.
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Affiliation(s)
- Elisabeth Enzenhofer
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Parzefall
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Georg Haymerle
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Sven Schneider
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Lorenz Kadletz
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Gregor Heiduschka
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Johannes Pammer
- Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Fritz Wrba
- Department of Clinical Pathology, Medical University of Vienna, Vienna, Austria
| | - Benjamin Loader
- Department of Otorhinolaryngology, Head and Neck Surgery, Rudolfstiftung, Vienna, Austria
| | - Matthäus Christoph Grasl
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Christos Perisanidis
- Department of Oral and Maxillofacial Surgery, Medical University of Vienna, Vienna, Austria
| | - Boban M. Erovic
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
- * E-mail:
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23
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Paluszczak J, Wiśniewska D, Kostrzewska-Poczekaj M, Kiwerska K, Grénman R, Mielcarek-Kuchta D, Jarmuż-Szymczak M. Prognostic significance of the methylation of Wnt pathway antagonists-CXXC4, DACT2, and the inhibitors of sonic hedgehog signaling-ZIC1, ZIC4, and HHIP in head and neck squamous cell carcinomas. Clin Oral Investig 2016; 21:1777-1788. [PMID: 27553089 PMCID: PMC5442212 DOI: 10.1007/s00784-016-1946-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022]
Abstract
Objectives Aberrations in Wnt and Shh signaling pathways are related to the pathogenesis of head and neck carcinomas, and their activation frequently results from epigenetic alterations. This study aimed to assess the frequency of methylation of negative regulators of Wnt signaling: CXXC4, DACT2, HDPR1, and FBXW11 and Shh signaling: HHIP, PTCH1, SUFU, ZIC1, and ZIC4 and correlate it with clinicopathological features in this group of patients. Materials and methods Methylation-specific PCR was used to detect gene promoter methylation, and real-time PCR was used to assess gene expression level. Results The analysis of the occurrence of gene promoter methylation in head and neck carcinoma cell lines indicated that CXXC4, DACT2, HHIP, ZIC1, and ZIC4 are methylated in these tumors. These genes were further analyzed in tumor sections from oral and laryngeal cancer patients. Gene methylation rate was higher in laryngeal tumors. The methylation index in tumor samples correlated with the overall survival in a subgroup of oral cancer patients who died of the disease. Moreover, ZIC4 methylation correlated with lymph node involvement in oral cancer patients. Conclusions Our findings corroborate that the activation of Wnt signaling in head and neck squamous cell carcinoma (HNSCC) is related to epigenetic silencing of its negative regulators. Moreover, the results indicate that the same mechanism of activation may operate in the case of Shh signaling. Clinical relevance The methylation of ZIC4 may be considered a new prognostic marker in oral cavity and oropharyngeal tumors. Further investigations should determine the diagnostic significance of methylation of ZIC4, HHIP, and DACT2 in head and neck carcinomas.
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Affiliation(s)
- Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781, Poznań, Poland.
| | - Dorota Wiśniewska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, ul. Święcickiego 4, 60-781, Poznań, Poland
| | | | - Katarzyna Kiwerska
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Reidar Grénman
- Department of Otorhinolaryngology, Head and Neck Surgery and Department of Medical Biochemistry, Turku University Central Hospital and Turku University, Turku, Finland
| | - Daniela Mielcarek-Kuchta
- Department of Otolaryngology and Laryngological Oncology, Poznan University of Medical Sciences, Poznań, Poland
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24
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Gaykalova DA, Vatapalli R, Wei Y, Tsai HL, Wang H, Zhang C, Hennessey PT, Guo T, Tan M, Li R, Ahn J, Khan Z, Westra WH, Bishop JA, Zaboli D, Koch WM, Khan T, Ochs MF, Califano JA. Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients. PLoS One 2015; 10:e0142148. [PMID: 26544568 PMCID: PMC4636259 DOI: 10.1371/journal.pone.0142148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 10/18/2015] [Indexed: 01/09/2023] Open
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is the fifth most common cancer, annually affecting over half a million people worldwide. Presently, there are no accepted biomarkers for clinical detection and surveillance of HNSCC. In this work, a comprehensive genome-wide analysis of epigenetic alterations in primary HNSCC tumors was employed in conjunction with cancer-specific outlier statistics to define novel biomarker genes which are differentially methylated in HNSCC. The 37 identified biomarker candidates were top-scoring outlier genes with prominent differential methylation in tumors, but with no signal in normal tissues. These putative candidates were validated in independent HNSCC cohorts from our institution and TCGA (The Cancer Genome Atlas). Using the top candidates, ZNF14, ZNF160, and ZNF420, an assay was developed for detection of HNSCC cancer in primary tissue and saliva samples with 100% specificity when compared to normal control samples. Given the high detection specificity, the analysis of ZNF DNA methylation in combination with other DNA methylation biomarkers may be useful in the clinical setting for HNSCC detection and surveillance, particularly in high-risk patients. Several additional candidates identified through this work can be further investigated toward future development of a multi-gene panel of biomarkers for the surveillance and detection of HNSCC.
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Affiliation(s)
- Daria A. Gaykalova
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Rajita Vatapalli
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Urology, Northwestern University, Chicago, Illinois, United States of America
| | - Yingying Wei
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Statistics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Hua-Ling Tsai
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Hao Wang
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Chi Zhang
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- University of Virginia, Department of Pathology, Charlottesville, Virginia, United States of America
| | - Patrick T. Hennessey
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Theresa Guo
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Marietta Tan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Ryan Li
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Julie Ahn
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Zubair Khan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - William H. Westra
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Justin A. Bishop
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - David Zaboli
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Wayne M. Koch
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Tanbir Khan
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Michael F. Ochs
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Department of Mathematics and Statistics, The College of New Jersey, Ewing, New Jersey, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology—Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland, United States of America
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, California, United States of America
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25
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Whang SN, Filippova M, Duerksen-Hughes P. Recent Progress in Therapeutic Treatments and Screening Strategies for the Prevention and Treatment of HPV-Associated Head and Neck Cancer. Viruses 2015; 7:5040-65. [PMID: 26393639 PMCID: PMC4584304 DOI: 10.3390/v7092860] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/17/2015] [Accepted: 08/27/2015] [Indexed: 12/11/2022] Open
Abstract
The rise in human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has elicited significant interest in the role of high-risk HPV in tumorigenesis. Because patients with HPV-positive HNSCC have better prognoses than do their HPV-negative counterparts, current therapeutic strategies for HPV+ HNSCC are increasingly considered to be overly aggressive, highlighting a need for customized treatment guidelines for this cohort. Additional issues include the unmet need for a reliable screening strategy for HNSCC, as well as the ongoing assessment of the efficacy of prophylactic vaccines for the prevention of HPV infections in the head and neck regions. This review also outlines a number of emerging prospects for therapeutic vaccines, as well as for targeted, molecular-based therapies for HPV-associated head and neck cancers. Overall, the future for developing novel and effective therapeutic agents for HPV-associated head and neck tumors is promising; continued progress is critical in order to meet the challenges posed by the growing epidemic.
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Affiliation(s)
- Sonia N Whang
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Maria Filippova
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
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26
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Gaykalova DA, Manola JB, Ozawa H, Zizkova V, Morton K, Bishop JA, Sharma R, Zhang C, Michailidi C, Considine M, Tan M, Fertig EJ, Hennessey PT, Ahn J, Koch WM, Westra WH, Khan Z, Chung CH, Ochs MF, Califano JA. NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma. Int J Cancer 2015; 137:1879-89. [PMID: 25857630 DOI: 10.1002/ijc.29558] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/27/2015] [Indexed: 12/29/2022]
Abstract
Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the effects of DNA methylation and copy number. Using this discovery pipeline, we determined that human papillomavirus-related (HPV+) and HPV- HNSCC differed significantly based on the activity levels of key TFs including AP1, STATs, NF-κB and p53. Immunohistochemical analysis confirmed that HPV- HNSCC is characterized by co-activated STAT3 and NF-κB pathways and functional studies demonstrate that this phenotype can be effectively targeted with combined anti-NF-κB and anti-STAT therapies. These discoveries correlate strongly with previous findings connecting STATs, NF-κB and AP1 in HNSCC. We identified five top-scoring pair biomarkers from STATs, NF-κB and AP1 pathways that distinguish HPV+ from HPV- HNSCC based on TF activity and validated these biomarkers on TCGA and on independent validation cohorts. We conclude that a novel approach to TF pathway analysis can provide insight into therapeutic targeting of patient subgroup for heterogeneous disease such as HNSCC.
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Affiliation(s)
- Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Judith B Manola
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Hiroyuki Ozawa
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Veronika Zizkova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Laboratory of Molecular Pathology, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Kathryn Morton
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Justin A Bishop
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Rajni Sharma
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Chi Zhang
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,University of Virginia, Charlottesville, VA
| | - Christina Michailidi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Michael Considine
- Division of Oncology Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Marietta Tan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Elana J Fertig
- Division of Oncology Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Patrick T Hennessey
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Mid-Michigan Ear, Nose, and Throat, East Lansing, MI
| | - Julie Ahn
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - William H Westra
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Zubair Khan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Christine H Chung
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Michael F Ochs
- Division of Oncology Biostatistics, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD.,Department of Mathematics and Statistics, The College of New Jersey, Ewing, NJ
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, MD
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27
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Mosquera Orgueira A. Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways. Front Genet 2015; 6:163. [PMID: 26029238 PMCID: PMC4429616 DOI: 10.3389/fgene.2015.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/10/2015] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is a frequent epigenetic mechanism that participates in transcriptional repression. Variations in DNA methylation with respect to gene expression are constant, and, for unknown reasons, some genes with highly methylated promoters are sometimes overexpressed. In this study we have analyzed the expression and methylation patterns of thousands of genes in five groups of cancer and normal tissue samples in order to determine local and genome-wide differences. We observed significant changes in global methylation-expression correlation in all the neoplasms, which suggests that differential correlation events are frequent in cancer. A focused analysis in the breast cancer cohort identified 1662 genes whose correlation varies significantly between normal and cancerous breast, but whose DNA methylation and gene expression patterns do not change substantially. These genes were enriched in cancer-related pathways and repressive chromatin features across various model cell lines, such as PRC2 binding and H3K27me3 marks. Substantial changes in methylation-expression correlation indicate that these genes are subject to epigenetic remodeling, where the differential activity of other factors break the expected relationship between both variables. Our findings suggest a complex regulatory landscape where a redistribution of local and large-scale chromatin repressive domains at differentially correlated genes (DCGs) creates epigenetic hotspots that modulate cancer-specific gene expression.
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28
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Pon JR, Marra MA. Driver and Passenger Mutations in Cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:25-50. [DOI: 10.1146/annurev-pathol-012414-040312] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Julia R. Pon
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3;
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3;
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4;
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29
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Koffler J, Sharma S, Hess J. Predictive value of epigenetic alterations in head and neck squamous cell carcinoma. Mol Cell Oncol 2014; 1:e954827. [PMID: 27308324 PMCID: PMC4905189 DOI: 10.1080/23723548.2014.954827] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 12/31/2022]
Abstract
Head and neck cancer collectively describes malignant tumors originating from the mucosal surface of the upper aerodigestive tract. These tumors pose a great threat to public health because of their high incidence and mortality. Traditional risk factors are tobacco and alcohol abuse. More recently, infection by high-risk types of human papilloma virus (HPV) has been identified as an additional risk factor, especially for oropharyngeal squamous cell carcinoma (OPSCC). Moreover, HPV-positive OPSCC is considered a distinct tumor entity with an improved clinical outcome compared to HPV-negative OPSCC. Epigenetic alterations act as key events in the pathogenesis of cancer and are of special interest for basic and translational oncology because of their reversible nature. This review provides a comprehensive summary of alterations of the epigenome in head and neck squamous cell carcinoma (HNSCC) with a focus on the methylome (hypomethylation and hypermethylation) and its predictive value in the evaluation of pathologic states and clinical outcome, or monitoring response rates to certain therapies.
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Affiliation(s)
- Jennifer Koffler
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg ; Heidelberg, Germany
| | - Sarika Sharma
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg ; Heidelberg, Germany
| | - Jochen Hess
- Section Experimental and Translational Head and Neck Oncology; Department of Otolaryngology; Head and Neck Surgery; University Hospital Heidelberg; Heidelberg, Germany; Research Group Molecular Mechanisms of Head and Neck Tumors; German Cancer Research Center (DKFZ); Heidelberg, Germany
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30
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Talukdar FR, Ghosh SK, Laskar RS, Kannan R, Choudhury B, Bhowmik A. Epigenetic pathogenesis of human papillomavirus in upper aerodigestive tract cancers. Mol Carcinog 2014; 54:1387-96. [PMID: 25213493 DOI: 10.1002/mc.22214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 02/06/2023]
Abstract
Human papillomavirus (HPV) has been recently associated with squamous cell carcinoma of upper aerodigestive tract (SCC of UADT), but its possible role in promoting aberrant methylation in these tumors has largely remained unexplored. Herein, we investigated the association of HPV with aberrant methylation in tumor-related genes/loci consisting of the classical CpG Island Methylator Phenotype (CIMP) panel markers (p16, MLH1, MINT1, MINT2, and MINT31) and other frequently methylated cancer-related genes (DAPK1, GSTP1, BRCA1, ECAD, and RASSF1) and survival of UDAT cancers. The study includes 219 SCC of UADT patients from different hospitals of Northeast India. Detection of HPV and aberrant promoter methylation was performed by PCR and Methylation Specific PCR respectively. Association study was conducted by Logistic regression analysis and overall survival analysis was done by Kaplan-Meier plot. HPV was detected in 37% of cases, with HPV-18 as the major high-risk sub-type. Although HPV presence did not seem to affect survival in overall UADT cancers, but was associated with a favourable prognosis in head and neck squamous cell carcinoma. Hierarchical clustering revealed three distinct clusters with different methylation profile and HPV presence. Among these, the CIMP-high subgroup exhibited the highest HPV positive cases (66%). Furthermore, multivariate analysis revealed a strong synergistic association of HPV and tobacco towards modulating promoter hypermethylation in UADT cancer (OR = 27.50 [95% CI = 11.51-88.03] for CIMP-high vs. CIMP-low). The present study proposes a potential role of HPV in impelling aberrant methylation in specific tumor related loci, which might contribute in the initiation and progression of SCC of UADT.
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Affiliation(s)
- Fazlur Rahman Talukdar
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Ruhina Shirin Laskar
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Ravi Kannan
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Biswadeep Choudhury
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Arup Bhowmik
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India
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