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Daria A. Gaykalova, M.S., Ph.D.

Daria A. Gaykalova, M.S., Ph.D.

Photo of Dr. Daria A. Gaykalova, M.S., Ph.D.
  • Assistant Professor of Otolaryngology - Head and Neck Surgery


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 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. more


  • Assistant Professor of Otolaryngology - Head and Neck Surgery
  • Assistant Professor of Oncology

Departments / Divisions

Centers & Institutes



  • Ph.D., Robert Wood Johnson Medical School - Piscataway (New Jersey) (2009)
  • M.S., Moscow State University (Russia) (2005)

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 Keywords

HNSCC, ChIP-Seq, RNA-Seq, chromatin, transcription, alternative splicing

Selected Publications

View 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
Phone: 410-614-2745

Academic Affiliations & Courses

Courses and Syllabi

  • BioTech 39
    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)

Professional Activities

  • 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
  • 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

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)
    Gdansk University
  • 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)
    Rutgers University
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