Paul Knoepfler, Ph.D.
633A Shriners Hospital
Sacramento Campus

The Knoepfler Lab is interested in epigenetics in stem cells and cancer. We use cutting edge molecular, cellular and developmental biology methods as well as genomic and gene editing technologies to answer key open questions in these areas of research. We are particularly interested now in the roles of three factors normally in stem cells and during tumorigenesis: histone variant H3.3, the MYC family, and DPPA4. How do these factors link the epigenome to cellular behaviors and tissue growth?

Our big picture goal is to impact human health through novel discoveries that catalyze new treatments for cancer and advances in translational stem cell biology.

For more information please visit the Knoepfler lab homepage at:

Kim M, Knoepfler PS. Anticipated impact of stem cell and other cellular medicine clinical trials for COVID-19. Regen Med. 2021 Jun 11. doi: 10.2217/rme-2021-0025. Epub ahead of print. PMID: 34114493.

Klein RH, Knoepfler PS. Stem cell models help crack regional oncohistone codes driving childhood gliomas. Cell Stem Cell. 2021 May 6;28(5):785-787. doi: 10.1016/j.stem.2021.04.013. PMID: 33961758.

Chen, KY., Bush, K., Klein, R.H. et al. Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling. Commun Biol 3, 363 (2020).

Rapid change of a cohort of 570 unproven stem cell clinics in the USA over 3 years. Knoepfler PS. Regen Med. 2019 Aug 28. doi: 10.2217/rme-2019-0064. [Epub ahead of print] PMID: 31456478

Gene editing: sloppy definitions mislead. Knoepfler P. Nature. 2018 Dec;564(7736):345. doi: 10.1038/d41586-018-07802-2. No abstract available. PMID: 30568213

Mapping and driving the stem cell ecosystem. Knoepfler PS. Regen Med. 2018 Oct;13(7):845-858. doi: 10.2217/rme-2018-0056. Epub 2018 Oct 5. PMID: 30289055

Genomic functions of developmental pluripotency associated factor 4 (Dppa4) in pluripotent stem cells and cancer. Klein RH, Tung PY, Somanath P, Fehling HJ, Knoepfler PS. Stem Cell Res. 2018 Jul 19;31:83-94. doi: 10.1016/j.scr.2018.07.009. [Epub ahead of print]

Too Much Carrot and Not Enough Stick in New Stem Cell Oversight Trends. Knoepfler PS. Cell Stem Cell. 2018 Jul 5;23(1):18-20. doi: 10.1016/j.stem.2018.06.004. Epub 2018 Jun 21.

The FDA and the US direct-to-consumer marketplace for stem cell interventions: a temporal analysis. Knoepfler PS, Turner LG., Regen Med. 2018 Jan 12. doi: 10.2217/rme-2017-0115. [Epub ahead of print]

ERBB3-Binding Protein (EBP1) is a novel DPPA4 cofactor in human pluripotent cells. Somanath P, Bush KM, Knoepfler PS., Stem Cells. 2018 Jan 12. doi: 10.1002/stem.2776. [Epub ahead of print]

Priyanka Somanath, Rachel Herndon Klein, Paul S. Knoepfler. CRISPR-mediated HDAC2 disruption identifies two distinct classes of target genes in human cells. PLOS. 2017 October 5,

Martinez-Cerdeno V, Barrilleaux B, McDonough A, Ariza J, Yuen B, Somanath P, Le C, Steward C, Horton K, Knoepfler P. Behavior of xeno-transplanted undifferentiated human induced pluripotent stem cells is impacted by microenvironment without evidence of tumorsStem Cells Dev. 2017 Jul 10. doi: 10.1089/scd.2017.0059.

To CRISPR and beyond: the evolution of genome editing in stem cells. Chen KY, Knoepfler PS., Regen Med. 2016 Dec;11(8):801-816. PMID: 27905217

Turner L, Knoepfler P. Selling Stem Cells in the USA: Assessing the Direct-to-Consumer Industry. Cell Stem Cell. 2016 Jun 29. pii: S1934-5909(16)30157-6. doi: 10.1016/j.stem. 2016.06.007. [Epub ahead of print] PubMed PMID: 27374789.

Review of Stem Cell Dialogues by Sheldon Krimsky(1). Knoepfler PS. Am J Bioeth. 2016 Apr;16(4):W12-3. doi: 10.1080/15265161.2016.1145756.

When patients reach out, scientists should reach back carefully. Knoepfler PS. Nat Med. 2016 Mar 3;22(3):230. doi: 10.1038/nm0316-230.

Reviewing post-publication peer review. Knoepfler P., Trends Genet. 2015 May;31(5):221-3. doi: 10.1016/j.tig.2015.03.006. Epub 2015 Apr 4.

From bench to FDA to bedside: US regulatory trends for new stem cell therapies. Knoepfler PS., Adv Drug Deliv Rev. 2015 Mar;82-83C:192-196. doi: 10.1016/j.addr.2014.12.001. Epub 2014 Dec 7. Review.

Histone H3.3 regulates dynamic chromatin states during spermatogenesis. Yuen BT, Bush KM, Barrilleaux BL, Cotterman R, Knoepfler PS. Development. 2014 Aug 19. pii: dev.106450. [Epub ahead of print]

Miz-1 Activates Gene Expression via a Novel Consensus DNA Binding Motif.. Barrilleaux BL, Burow D, Lockwood SH, Yu A, Segal DJ, Knoepfler PS. PLoS One. 2014 Jul 1;9(7):e101151. doi: 10.1371/journal.pone.0101151. eCollection 2014.

Epigenetic mechanisms of tumorigenicity manifesting in stem cells. Tung PY, Knoepfler PS. Oncogene. Jun 16;0. doi: 10.1038/onc.2014.172. [Epub ahead of print]

Histone H3.3 Mutations: A Variant Path to Cancer. BTK Yuen, PS Knoepfler. Cancer cell 2013 24 (5), 567-574.

Identification of DPPA4 and DPPA2 as a Novel Family of Pluripotency‐Related Oncogenes. PY Tung, NV Varlakhanova, PS Knoepfler. STEM CELLS 2013 31 (11), 2330-2342.

Key Action Items for the Stem Cell Field: Looking Ahead to 2014. PS Knoepfler. Stem cells and development. 2013

Scientists: you really need to get out of the lab more. Knoepfler PS. Nat Med. 2013 Sep 6;19(9):1086. doi: 10.1038/nm0913-1086.

Chromatin immunoprecipitation assays for myc and N-myc. Barrilleaux BL, Cotterman R, Knoepfler PS. The Myc Gene, 2013 117-133.

Automation of Library Preparation for High-resolution ChIP-seq Profiling. IM Henry, R Cotterman, P Knoepfler, L Comai, RW Kim, H O'Geen. Journal of Biomolecular Techniques. 2013. JBT 24 (Suppl), S45.

Laskowski AI and Knoepfler PS. Myc binds the pluripotency factor Utf1 through the basic-helix-loop-helix leucine zipper domain. Biochemical and biophysical research communications.2013

Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development. Bush KM, Yuen BT, Barrilleaux BL, Riggs JW, O Geen H, Cotterman R, Knoepfler PS. Epigenetics Chromatin. 2013 Apr 9;6(1):7.

Riggs JW, 
Barrilleaux B, 
Varlakhanova N, 
Bush K, 
Chan V, 
and Knoepfler PS. Induced pluripotency and oncogenic transformation are related processes. Stem Cells & Dev. 2013 Jan 1;22(1):37-50.

Knoepfler PS. Call for fellowship programs in stem cell-based regenerative and cellular medicine: new stem cell training is essential for physicians. Regen Med. 2013 Mar;8(2):223-5.

Meissen JK, Yuen BTK, Kind T, Riggs JW, Barupala DK, KnoepflerPK*, and Fiehn O*. Induced pluripotent stem cells show metabolomic differences to embryonic stem cells in polyunsaturated phosphatidylcholines and primary metabolism. PLoS One 2012;7(10):e46770. *co-corresponding authors.

Laskowski AI and KnoepflerPS. Utf1: Goldilocks for ESC bivalency. Cell Stem Cell 2012; Dec 7;11(6):732-4.

Pshenichnaya I, Schouwey K, Armaro M, Larue L, Knoepfler PS, Eisenman RN, Trumpp A, Delmas V, and Beermann F. Constitutive gray hair in Mice induced by Melanocyte-specific deletion of c-Myc. Pigment Cell Melanoma Res. 2012 Mar 15.

Martínez-Cerdeño V, Lemen JM, Chan V, Wey A, Lin W, Dent SR, and Knoepfler PS. N-Myc and GCN5 regulate significantly overlapping transcriptional programs in neural stem cells. PLoS One. 2012;7(6):e39456.

Knoepfler PS. Key anticipated regulatory issues for clinical use of human induced pluripotent stem cells. Regenerative Medicine. 2012; Sep;7(5):713-20.

Dominguez-Frutos E., Lopez Hernandez I., Vendrell V., Gallozzi M., Gutsche K., Sharpe J., Knoepfler PS, Eisenman RN, Trumpp A., and Schimmang T. N-myc controls proliferation, morphogenesis and patterning of the inner ear. J. NeuroSci. 2011 31(19):7178-89.

Barrilleaux B. and Knoepfler PSInducing iPS cells to escape the dish. Cell Stem Cell. 2011 Aug 5;9(2):103-11.

Varlakhanova NV, Cotterman RF, Bradnam K, Korf I, and Knoepfler PS. Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics & Chromatin. 2011 Nov 4;4(1):20.

Knoepfler PS. My Year As A Stem Cell Blogger. Nature. 2011 Jul 27;475(7357):425.

Barrilleaux B. and Knoepfler PS. Overexpression of oncogenes in human cells using ecotropic lentivirus for enhanced biosafety. J Vis Exp. 2011 Jul 24;(53). pii: 2822

Domínguez-Frutos E, López-Hernández I, Vendrell V, Neves J, Gallozzi M, Gutsche K, Quintana L, Sharpe J, Knoepfler PS, Eisenman RN, Trumpp A, Giráldez F, Schimmang T. N-myc Controls Proliferation, Morphogenesis, and Patterning of the Inner Ear. J. Neurosci 2011 31(19): 7178-7189.

  • Leukemia & Lymphoma Society Special Fellowship, 2002-2005
  • Howard Temin Award, NCI, 2005-2010
  • Brain Tumor Society Award: 2007-8 Steven C. Higgins Leadership Chair of Research
  • March of Dimes Basil O'Conner Starter Scholar Award, 2008-9.
  • CIRM New Faculty Award: 2009-2014
  • National Institute of Health
  • CA Institute for Regenerative Medicine
  • National Cancer Institute Howard Temin Award Grant
  • St. Baldrick's Foundation
  • MCB 213, Developmental Biology
  • CHA 402, Cell and Tissue Biology
  • CHA 199, Undergraduate Research
  • NSC 290C, Research Conference in Neuroscience
  • NSC 299, Graduate Research