Johnathan R. Whetstine, PhD

Johnathan Whetstine

This Fox Chase professor participates in the Undergraduate Summer Research Fellowship
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Research Program

Key Awards

Lung Cancer Discovery Award
American Lung Association
2014, 2017, 2019


Lab Overview

Epigenetic Mechanisms Driving Copy Gain, Amplifications and Drug Resistance


  • We are asking what cellular cues or exposures are involved in driving copy gain of regions promoting drug resistance and tumorigenesis. These same questions are being extended to other clinically relevant amplified oncogenes. 
  • We are identifying all known signaling and epigenetic-related pathways involved in driving copy gain and amplifications.
  • We are identifying the epigenetic states associated with the genome that have a propensity to undergo copy number changes.
  • We are screening for factors that will allow these copy gains to be inherited.
  • We are collaborating with clinicians to establish the optimal patients for using epigenetic therapies targeting pathways promoting copy gain and drug resistance.
Epigenetic Mechanisms Impacting Cancer Therapy


  • We are assessing whether there are other chromatin regulators involved in protein synthesis.
  • We are determining whether other chromatin factors enhance mTOR inhibitor sensitivity or other cancer therapies.
  • We are studying other coding SNPs in chromatin modifiers that impact drug response and patient stratification.
  • We use genetic features or molecular mechanisms downstream of chromatin regulators to stratify and optimally treat cancer patients. 
Epigenetic Mechanisms Regulating Cell Cycle Progression



  • We are using next generation sequencing strategies to map the epigenome during cell cycle.
  • We are identifying chromatin and non-coding RNAs that are regulating cell cycle progression.​


The Whetstine laboratory studies how chromatin factors control gene expression and genome stability. These types of studies were initiated by studying a specific class of chromatin regulators, JmjC-containing histone demethylases, that Dr. Whetstine was involved in discovering. While interrogating demethylase function, the Whetstine laboratory uncovered the first enzyme (KDM4A- histone tri-demethylase) responsible for generating extrachromosomal transient site-specific copy gains (TSSGs) of drug resistant oncogenes. Dr. Whetstine’s team is further interrogating these same relationships with other chromatin/epigenetic modifiers and DNA amplification events occurring in cancer and other diseases. His laboratory aims to provide mechanistic insights into extrachromosomal DNA amplification generation and the associated heterogeneity within cell populations, while identifying biomarkers to both predict and target copy gain events driving human diseases (Figure 1). The Whetstine laboratory is addressing the genomic features (epigenome and 3D genome organization) that are responsible for increasing the propensity of regions to rereplicate and amplify during S phase. Similar studies are also being conducted to better understand the role that chromatin control has in modulating DNA replication, transcription and genome integrity. The laboratory leverages a range of cytological, biochemical, genomic and epigenomic approaches to address DNA amplification control and DNA replication.

The Whetstine laboratory also addresses whether modulation of epigenetic factors provides novel therapeutic options across tumors (e.g., conventional chemotherapy and immune checkpoint therapy). His team is evaluating the expression levels, copy gains or losses, mutational and polymorphic repertoire in malignancies, as well as posttranslational regulatory mechanisms for epigenetic factors and how they relate to various tumor types. The Whetstine laboratory evaluates the impact that these events have on drug response and ability to stratify patients. These studies resulted in the identification of KDM4A associated copy gains as described above, as well as the identification of novel enzyme function for demethylases and association with chemotherapeutic response in lung cancer. Comparable studies are now being extended into additional chromatin modifying enzymes.

Key publications highlighting discoveries from the Whetstine Laboratory:

  • Black, J.C., Manning, A., Van Rechem, C., Kim, J., Ladd, B., Cho, J., Pineda, C.M., Murphy, N., Daniels, D.L., Montagna, S., Lewis, P.W., Glass, K., Allis, C.D., Dyson, N.J., Getz, G., Whetstine, J.R. (2013) H3K9/36me3 Demethylase KDM4A Promotes Site-Specific Copy Gain and Re-replication of Regions Amplified in Tumors. Cell. 154, 541-555. PubMed PMID: 23871696; PubMed Central PMCID: PMC3832053.
  • Black, J.C., Atabakhsh, E., Kim J., Biette K.B., Van Rechem C., Ladd B., Burrowes P.d., Donado C., Mattoo H., Kleinstiver B.P., Song B., Andriani G., Joung J.K., Iliopoulos O., Montagna C., Pillai S., Getz G., Whetstine J.R. (2015) Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Genes and Development 29, 1018-1031. PubMed PMID: 25995187; PubMed Central PMCID: PMC4441050.
  • Van Rechem, C., Black, J.C., Greninger, P., Zhao, Y., Donado, C., Burrowes, P.D., Ladd, B., Christiani, D.C., Benes, C.H., and Whetstine, J.R. (2015) A Coding Single Nucleotide Polymorphism in Lysine Demethylase KDM4A Associates with Increased Sensitivity to mTOR Inhibitors. Cancer Discov. 5, 245-254. PubMed PMID: 25564517; PubMed Central PMCID: PMC4355226.
  • Mishra, S., Van Rechem, C., Pal, S., Clarke, T.L., Chakraborty, D., Mahan, S., Black, J.C., Murphy, S.E., Lawrence, M.S., Daniels, D.L., Whetstine, J.R. (2018) Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell 174, 803-817. PubMed PMID: 30057114; PubMed Central PMCID: PMC6212369.
  • Clarke, T.L., Tang, R., Chakraborty, D., Van Rechem, C., Ji, F., Mishra, S., Ma, A., Kaniskan, H.U., Jin, J., Lawrence, M.S., Sadreyev, R.I., Whetstine, J.R. (2020) Histone Lysine Methylation Dynamics Control EGFR DNA Copy Number Amplification. Cancer Discov. 10, 306-325.PubMed PMID: 31776131.
  • Cancer Discovery, February 2020
  • An issue and review describing: Methylation- A Multifaceted Modification

  • Lysine Demethylase 4A (KDM4A) regulates translation and impacts mTOR therapeutic response

  • Hypoxia Controls Epigenetic Programs Driving Amplification

  • MicroRNAs Control site-specific copy gains

  • There is an epigenetic addressing system for defining site-specific DNA rereplication and amplifications

    Educational Background

    • Postdoctoral Fellow, Epigenetics/Pathology, Harvard Medical School, Cambridge, MA, 2002-07
    • PhD, Pharmacology, Wayne State University, Detroit, MI, 2002
    • Graduate Researcher, Laboratory of Dr. Larry H. Matherly, Department of Pharmacology, Wayne State University, Detroit, MI 1999-2002


    • American Association for Cancer Research
    • American Society of Biochemist and Molecular Biologist 

    Honors & Awards

    • Lung Cancer Discovery Award, American Lung Association, 2014, 2017, 2019
    • Keynote Molecular Analysis for Personalized Therapy, 2016
    • MGH One Hundred,  Massachusetts General Hospital, 2016
    • Innovation Award, Alex Lemonade Stand Foundation, 2015
    • Leukemia and Lymphoma Society Scholar, The Leukemia and Lymphoma Society, 2014
    • Tepper Family MGH Research Scholar, Massachusetts General Hospital, 2014
    • Basic Research Scholar Award, American Cancer Society, 2013
    • Howard M. Goodman Prize, MGH, 2009
    • New Scholar Award, Ellison Medical Foundation, 2009

    Selected Publications

    Nakatani T., Lin J., Ji F., Ettinger A., Pontabry J., Tokoro M., Altamirano-Pacheco L., Fiorentino J., Mahammadov E., Hatano Y., Van Rechem C., Chakraborty D., Ruiz-Morales E.R., Arguello Pascualli P.Y., Scialdone A., Yamagata K., Whetstine J.R., Sadreyev R.I.,Torres-Padilla M.E., DNA replication fork speed underlies cell fate changes and promotes reprogramming. Nat Genet. 54(3): 318-327, 2022.PMC8920892.

    Van Rechem C., Ji F., Chakraborty D., Black J.C., Sadreyev R.I.,Whetstine J.R., Collective regulation of chromatin modifications predicts replication timing during cell cycle. Cell Rep. 37(1): 109799, 2021.PMC8530517.

    Capucine Van Rechem, Fei Ji, Sweta Mishra, Damayanti Chakraborty, Sedona E. Murphy, Megan E. Dillingham, Ruslan I. Sadreyev, Johnathan R. Whetstine, The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Volume 1863, Issue 10, 2020, 194624

    Clarke T.L., Tang R., Chakraborty D., Van Rechem C., Ji F., Mishra S., Ma A., Kaniskan H.U., Jin J., Lawrence M.S., Sadreyev R.I., Whetstine J.R., Histone lysine methylation dynamics control egfr DNA copy number amplification. Cancer Discov, 2019. 26.370

    Etchegaray J.P., Zhong L., Li C., Henriques T., Ablondi E., Nakadai T., Van Rechem C., Ferrer C., Ross K.N., Choi J.E., Samarakkody A., Ji F., Chang A., Sadreyev R.I., Ramaswamy S., Nechaev S., Whetstine J.R., Roeder R.G., Adelman K., Goren A., Mostoslaysky R., The histone deacetylase sirt6 restrains transcription elongation via promoter-proximal pausing. Mol Cell. 75(4): 683-699 e7, 2019. 14.548

    Whetstine J.R., Prc2 plays red light, green light with mhc-i and cd8(+) t cells. Cancer Cell. 36(4): 343-345, 2019. 23.916

    Mishra S, Van Rechem C, Pal S, Clarke TL, Chakraborty D, Mahan SD, Black JC, Murphy SE, Lawrence MS, Daniels DL, Whetstine JR.
    Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications, Cell. 2018 Aug 9

    Guarner, A., Morris, R., Korenjak, M., Boukhali, M., Zappia, M.P., Van Rechem, C., Whetstine, J.R.,
    Ramaswamy, S., Zou, L., Frolov, M.V., Haas, W., Dyson, N.J. (2017) E2F/DP Prevents Cell-Cycle
    Progression in Endocycling Fat Body Cells by Suppressing dATM Expression. Dev. Cell 43, 689-703.

    Mishra, S., and Whetstine, J.R. (2016) Different Facets of Copy Number Changes: Permanent,
    Transient, and Adaptive. Molecular and Cellular Biology 36, 1050-1063

    Denu, J. (2016) Expression level of the histone demethylase KDM4A is regulated by microRNAs. J.
    Biol. Chem. 291... Expand

    Additional Publications

    Dr. Whetstine on PubMed

    • Cancer Discovery, February 2020
    • An issue and review describing: Methylation- A Multifaceted Modification

    • Lysine Demethylase 4A (KDM4A) regulates translation and impacts mTOR therapeutic response

    • Hypoxia Controls Epigenetic Programs Driving Amplification

    • MicroRNAs Control site-specific copy gains

    • There is an epigenetic addressing system for defining site-specific DNA rereplication and amplifications

      Open Positions

      About the Position

      The Whetstine Laboratory at the Fox Chase Cancer Center is hiring highly ambitious and self-motivated Postdoctoral Fellows in Cancer Epigenetics. The laboratory uses state-of-the-art technologies and collaborations with leading scientist and clinicians to address the following areas: (1) the identification and characterization of epigenetic mechanisms driving extrachromosomal DNA amplification and chromosomal rearrangement, therapeutic resistance and tumor heterogeneity; (2) the impact of cancer-associated epigenetic factor variants (mutations and germline) on drug responses; and (3) the direct role of chromatin factors in regulating cell division, especially DNA replication. Some example publications addressing these areas of interest are: Black et al. (2010) Mol Cell; Black et al. (2013) Cell; Van Rechem et al. (2015) Cancer Discovery; Mishra et al. (2018) Cell; Clarke et al. (2020) Cancer Discov.; van Rechem et al. (2021) Cell Reports; Gray et al. (2023) Cell.

      Learn more about the laboratory research in the Whetstine laboratory.

      The Whetstine laboratory seeks candidates that published peer reviewed manuscripts and that have strong expertise in molecular biology, cancer biology, biochemistry, genomics, epigenomics and/or chromatin biology. 

      The Whetstine laboratory is a member of the Cancer Epigenetics Institute (CEI) at Fox Chase. The institute provides trainees unparalleled access to world-leaders in epigenetics as well as opportunities to interact with editors and industry leaders. CEI also has an annual symposium that brings leaders in the area of epigenetics from both academia and industry so that new advances are discussed. There are poster sessions and opportunities for travel awards at the annual symposium as well. Trainees also have ample opportunities to present their findings to colleagues in CEI and across FCCC.  CEI aims to enhance each trainee’s opportunity for networking and exposure to leading science so they have an optimal opportunity to develop their career path.

      About the Training Environment

      As one of the four original cancer centers to receive comprehensive designation from the National Cancer Institute, Fox Chase Cancer Center has been at the forefront of cancer research for almost 90 years. We are home to excellent research facilities, top clinicians and scientists, and outstanding patient care. Our singular focus on cancer, which couples discovery science with state of the art clinical care and population health, remains the foundation of our work.

      The scientist training programs at Fox Chase Cancer Center provide professional development opportunities in four core areas identified as crucial for successful careers in science, research, and health care including communication, leadership, teaching, and mentorship. Upon joining the program, graduate students and postdocs develop individual development plans to help guide their growth. Training throughout the year is supplemented with free professional development opportunities, including a robust ‘How To’ series, writing courses, networking, mentorship, and teaching opportunities, a trainee-led seminar series, a trainee-led annual Research Conference, and more. Postdocs at Fox Chase Cancer Center are supported by the Temple University Postdoc Association and the Office of Academic Affairs at Fox Chase, and are compensated with competitive pay and benefits.

      In addition to the robust training program, scientists at Fox Chase Cancer Center benefit from being part of the rich scientific and biotech environment in the Philadelphia region. Many of our former trainees are now employees (and contacts) at nearby institutions and companies, including The Wistar Institute, Merk, GSK, AACR, and numerous others.

      To Apply

      Email a CV, cover letter that states research interest(s) and goals, and the name of at least three references to [email protected].


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      This Fox Chase professor participates in the Undergraduate Summer Research Fellowship
      Learn more about Research Volunteering.