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Daria A. Gaykalova, M.S., Ph.D.
Daria A. Gaykalova, M.S., Ph.D.
Assistant Professor of Otolaryngology - Head and Neck Surgery
Expertise: Cancer Genomics, Head and Neck Cancers, Human Papillomavirus Infections
Research Interests: Genetic and epigenetic alterations in head and neck cancer; Development of head and neck cancer biomarkers; Epigenetic mechanisms of transcription regulation; Cancer-specific transcription factor signatures; Molecular biology; Cancer biology; Translational research; High-throughput; Experimental therapeutics; Epigenetics; Chromatin structure; Alternative splicing ...read more
Dr. Gaykalova received her M.S. in molecular biology from Lomonosov Moscow State University and her Ph.D. in cellular and molecular pharmacology from the University of Medicine and Dentistry of New Jersey. She joined Johns Hopkins in 2009. Her lab is studying the functional role of epigenetics in transcriptional regulation of head and neck cancer progression.
- Assistant Professor of Otolaryngology - Head and Neck Surgery
Departments / Divisions
- M.S., Moscow State University (Russia) (2005)
- Ph.D., Robert Wood Johnson Medical School - Piscataway (New Jersey) (2009)
Research & Publications
In my lab, we define the functional role of epigenetics in transcriptional regulation of head and neck squamous cell carcinoma (HNSCC) progression. To evaluate the whole-genome distribution of various histone marks, we are using chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-Seq) methodology for primary tissues recently developed in my lab. My research group was the first to demonstrate the cancer-specific distribution of H3K4me3 and H3K27ac marks and their role in cancer-related gene expression in HNSCC. The research of my team showed that an aberrant chromatin alteration is a central event in carcinogenesis, and the therapeutic control of chromatin structure can prevent the primary of secondary cancerization. Furthermore, our preliminary data further suggest that the differential enrichment of these disease-specific histone marks and DNA methylation correlate with alternative splicing events (ASE) formation. For this project, we employed a novel bioinformatical tool for the detection of cancer-specific ASEs. Through thorough functional validation of the individual ASEs, we demonstrated that each of them has a unique mechanism of malignant transformation of the cells. Due to high disease-specificity, ASEs represent the perfect biomarkers and the neoantigens that have direct application to clinical practice.
Technology Expertise KeywordsHNSCC, ChIP-Seq, RNA-Seq, chromatin, transcription, alternative splicing
Selected PublicationsView all on Pubmed
Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Bahman A, Skaist A, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan S, Favorov AV, Califano JA, Fertig EJ*, Gaykalova DA*. Integrated analysis of whole-genome ChIP-Seq and RNA-Sequencing data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks. Cancer Res. 2017 Sep 25. pii: canres.0833.2017. doi: 10.1158/0008-5472.CAN-17-0833. [Epub ahead of print]. PMID: 28947419.*Equal Contribution.
Guo T, Sakai A, Afsari B, Considine M, Danilova L, Favorov AV, Kelley DZ, Flam EL, Khan Z, Wheelan S, Gutkind S, Fertig EJ*, Gaykalova DA*, Califano JA*. Definition of Alternative Splice Expression in HPV-related oropharyngeal cancer includes a novel functional splice variant of AKT3. Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21. PMID: 28733453. *Equal contribution
Faraji F, Zaidi M, Fakhry C, Gaykalova DA. Molecular Mechanisms of Human Papillomavirus-Related Carcinogenesis in Head and Neck Cancer. Microbes Infect. 2017 Sep - Oct;19(9-10):464-475. doi: 10.1016/j.micinf.2017.06.001. Epub 2017 Jun 12. PMID: 28619685
Kagohara LT†, Stein-O'Brien G†, Kelley DZ, Flam EL, Wick H, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA*, and Fertig EJ*. Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis. Brief Funct Genomics. 2017 Aug 11. doi: 10.1093/bfgp/elx018. [Epub ahead of print]. PMID: 28968850. †*Equal Contribution.
Gaykalova DA*, Zizkova V, Guo T, Tiscareno I, Wei Y, Vatapalli R, Hennessey PT, Ahn J, Danilova L, Khan Z, Bishop JA, Gutkind JS, Koch WM, Westra WH, Fertig EJ, Ochs MF, Califano JA*. Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC. Oncotarget. 2017 Feb 28;8(9):15349-15363. doi: 10.18632/oncotarget.14856. PMID: 28146432. *Corresponding authors
Hypermethylated Gene Markers for Head and Neck Cancer
Patent # 14/381,489
We have detected the panel of differentially methylated genes in head and neck cancers, which can be used as disease biomarkers
Methods and Agent for Modulating the RNA Polymerase II-Histone Surface
Patent # 12/952,295
We have described the RNA Polymerase II-Histone surface interactions and methods/agents that can modulate them
Contact for Research Inquiries
The Johns Hopkins University School of Medicine
1550 Orleans Street
Cancer Research Building II
Baltimore, MD 21231 map
Academic Affiliations & Courses
Courses and Syllabi
2015 - 2016
Activities & Honors
- Cervical Cancer SPORE Pilot Grant Award, NIH, 2017
- NIH Exploratory/Developmental Research Grant Award (R21), NIDCR, 2015
- Head and Neck Cancer SPORE Career Enhancement Grant Award, NIH, 2015
- Head and Neck Cancer SPORE Pilot Grant Award, NIH, 2014
- American Head and Neck Society Pilot Grant Award, AHNS, 2012
- 2009 Best Publication by a Graduate Student, UMDNJ, 2010
- Young Investigator Award, UMDNJ, 2006 - 2009
- Financial Aid Award, Genetics Society of America, 2008
- Conference Travel Award, UMDNJ, 2006 - 2008
- Magna Cum Laude, MSU, 2005
- American Association for Cancer Research (AACR)
- American Head and Neck Society (AHNS)
- R01/R21 Grant Reviewer, Oral, Dental, and Craniofacial Sciences Study Section, NIH, 2016
- Grant Reviewer, The Voelcker Fund, Texas, 2015
- Award Committee member, Toby Eagle Foundation, Baltimore, 2015
- Judge, The North Jersey Regional Science Fair, Picataway, 2008 - 2009
- Cell Line Bank Leader, Cell Line Bank, Baltimore, 2009
- Tissue Bank Advisor, Tissue Bank, Baltimore, 2014
- Peer Reviewer, Clinical Epigenetics, Cancer Letters, Oral Oncology, Scientific Reports, International Journal of Cancer, Head and Neck Journal, and PloS One Journal, 2013
- Scientific Mentor for postdocs, medical residents and students, Wet-lab research, Baltimore, 2009
Mentoring (total 18 people): M.D. residents; Ph.D. postdocs; M.D., Ph.D., M.S. students, undergraduate students.
Videos & Media
Lectures and Presentations
Analysis of alternative splice expression in human papillomavirus-related oropharyngeal cancers
Invited talk , Workshop , The International workshop on cancer neoantigen science , Gdansk (Poland) (09/21/2017)
Integrated analysis of whole-genome ChIP-Seq and RNA-Sequencing data of primary tumor samples associates HPV integration sites with open chromatin marks
Invited talk , International conference , The Future of Biomedicine , Vladivostok (Russia) (09/12/2017)
Integrated analysis of whole-genome ChIP-Seq and RNA-Sequencing data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks
Invited talk , Seminar , Viral Oncology Interest Group Seminar , Baltimore (01/10/2017)
Cancer-related transcriptional regulation and alternative splicing events in HPV+ HNSCC
Invited talk , Seminar , San Diego (02/19/2016)
University of California, San Diego
Epigenetics. Histone Code. ChIP
Lecture , Workshop , BioTech 39: Epigenetics Workshop , Bethesda (12/05/2016)
Cancer epigenetics. DNA Methylation. Cancer Diagnostics
Invited talk , Lecture , Vladivostok (Russia) (06/12/2016)
The Discovery Of Differentially Methylated Super-enhancer Elements In HPV-related Oropharyngeal Squamous Cell Carcinoma
Invited talk , International Conference , AHNS 9th International Conference on Head and Neck Cancer , Seattle (07/25/2016)
Histones. Role and Analysis. ChIP
Lecture , Workshop , BioTech 39: Epigenetics Workshop , Bethesda (04/02/2016)
How to Design a Quantitative Methylation Specific PCR (QMSP) Experiment
Lecture , Workshop , BioTech 39: Epigenetics Workshop , Bethesda (12/04/2015)
The discovery of prospective HNSCC drivers via integrative analysis of epigenetic and transcriptional alterations in primary tissues
Invited talk , World Congress , 5th IFHNOS World Congress and AHNS Annual Meeting , New York (07/01/2014)
Nucleosomal Barrier Formation/Histone Survival during Pol II Transcription
Invited talk , Conference , National Postdoc Appreciation Day Symposium , Piscataway (09/14/2009)