Professional Education

  • Doctor of Philosophy, University of Michigan Ann Arbor (2016)
  • Master of Science in Engr, University of Michigan Ann Arbor (2013)
  • Bachelor of Science, Purdue University (2010)

Stanford Advisors


All Publications

  • Tailoring dendrimer conjugates for biomedical applications: the impact of altering hydrophobicity JOURNAL OF NANOPARTICLE RESEARCH Holl, M., Dougherty, C. A., Vaidyanathan, S. 2018; 20 (10)
  • Uridine Depletion and Chemical Modification Increase Cas9 mRNA Activity and Reduce Immunogenicity without HPLC Purification. Molecular therapy. Nucleic acids Vaidyanathan, S., Azizian, K. T., Haque, A. K., Henderson, J. M., Hendel, A., Shore, S., Antony, J. S., Hogrefe, R. I., Kormann, M. S., Porteus, M. H., McCaffrey, A. P. 2018; 12: 530?42


    The Cas9/guide RNA (Cas9/gRNA) system is commonly used for genome editing. mRNA expressing Cas9 can induce innate immune responses, reducing Cas9 expression. First-generation Cas9 mRNAs were modified with pseudouridine and 5-methylcytosine to reduce innate immune responses. We combined four approaches to produce more active, less immunogenic second-generation Cas9 mRNAs. First, we developed a novel co-transcriptional capping method yielding natural Cap 1. Second, we screened modified nucleotides in Cas9 mRNA to identify novel modifications that increase Cas9 activity. Third, we depleted the mRNA of uridines to improve mRNA activity. Lastly, we tested high-performance liquid chromatography (HPLC) purification to remove double-stranded RNAs. The activity of these mRNAs was tested in cell lines and primary human CD34+ cells. Cytokines were measured in whole blood and mice. These approaches yielded more active and less immunogenic mRNA. Uridine depletion (UD) most impacted insertion or deletion (indel) activity. Specifically, 5-methoxyuridine UD induced indel frequencies as high as 88% (average± SD= 79%± 11%) and elicited minimal immune responses without needing HPLC purification. Our work suggests that uridine-depleted Cas9 mRNA modified with 5-methoxyuridine (without HPLC purification) or pseudouridine may be optimal for the broad use of Cas9 both invitro and invivo.

    View details for PubMedID 30195789

  • Global Transcriptional Response to CRISPR/Cas9-AAV6-Based Genome Editing in CD34+ Hematopoietic Stem and Progenitor Cells. Molecular therapy : the journal of the American Society of Gene Therapy Cromer, M. K., Vaidyanathan, S. n., Ryan, D. E., Curry, B. n., Lucas, A. B., Camarena, J. n., Kaushik, M. n., Hay, S. R., Martin, R. M., Steinfeld, I. n., Bak, R. O., Dever, D. P., Hendel, A. n., Bruhn, L. n., Porteus, M. H. 2018


    Genome-editing technologies are currently being translated to the clinic. However, cellular effects of the editing machinery have yet to be fully elucidated. Here, we performed global microarray-based gene expression measurements on human CD34+ hematopoietic stem and progenitor cells that underwent editing. We probed effects of the entire editing process as well as each component individually, including electroporation, Cas9 (mRNA or protein) with chemically modified sgRNA, and AAV6 transduction. We identified differentially expressed genes relative to control treatments, which displayed enrichment for particular biological processes. All editing machinery components elicited immune, stress, and apoptotic responses. Cas9 mRNA invoked the greatest amount of transcriptional change, eliciting a distinct viral response and global transcriptional downregulation, particularly of metabolic and cell cycle processes. Electroporation also induced significant transcriptional change, with notable downregulation of metabolic processes. Surprisingly, AAV6 evoked no detectable viral response. We also found Cas9/sgRNA ribonucleoprotein treatment to be well tolerated, in spite of eliciting a DNA damage signature. Overall, this data establishes a benchmark for cellular tolerance of CRISPR/Cas9-AAV6-based genome editing, ensuring that the clinical protocol is as safe and efficient as possible.

    View details for PubMedID 30005866

  • Priming Human Repopulating Hematopoietic Stem and Progenitor Cells for Cas9/sgRNA Gene Targeting Molecular Therapy Nucleic Acids Charlesworth, C. T., Camarena, J., Cromer, M. K., Vaidyanathan, S., Bak, R. O., Carte, J. M., Potter, J., Dever, D. P., Porteus, M. H. 2018; 12: 89-104

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