Mark R. Charbonneau, PhD

Biotechnology R&D leader with cross-functional expertise in live biotherapeutic drug development, computational biology, and biomarker assay development.


About

Mark is a first-generation college graduate who received a B.S. in microbiology at Michigan State University, before obtaining a PhD in computational and systems biology at Washington University in St. Louis in the lab of Jeffrey I. Gordon, MD. Currently, Mark leads the Translational Sciences team at Synlogic, Inc, a biotechnology company pioneering the development of engineered live bacterial therapeutics. His team connects the dots between preclinical data and human biology, with the goal of predicting the impacts of engineered bacterial therapeutics on disease biology. He has demonstrated cross-functional expertise in live biotherapeutic drug development, mechanistic modeling, computational biology, and biomarker assay development. Mark integrates technical acumen and emotional intelligence to build high-functioning teams and foster innovation.

Professional Skills

  • Excellent written and oral communication
  • Building value through innovation
  • Project team management and leadership
  • Cross-functional collaboration
  • People management and coaching
  • Microbiome research
  • Mechanistic model construction
  • Germ-free animal models
  • Biomarker assay development
  • Data analysis and statistics
  • Next Generation Sequencing
  • Python Programming

Professional Experience

  • Senior Director, Head of Translational Sciences | Synlogic, Inc | Jul 2021 - Present

    - Fulfilled dual roles of Alliance director and Research Project Leader for IBD therapeutic development collaboration with global pharma partner.
    2021
  • Director, Head of Quantitative Biology | Synlogic, Inc | Jan 2020 - Jun 2021

    - Chaired Synlogic research leadership team, responsible for setting research goals and budget, allocating resources to align with corporate priorities, and representing research function to executive leadership team.

    - Advanced early research projects through key development milestones, including progression of an enteric hyperoxaluria program (SYNB8802) from program nomination through IND-enabling studies in nine months.

    - Built mechanistic computational models to predict function of synthetic biotics for the treatment of phenylketonuria (SYNB1618) and enteric hyperoxaluria (SYNB8802) in healthy subjects and patients to drive strategic decisions for clinical development.
    2020
  • Associate Director, Head of Quantitative Biology | Synlogic, Inc | Feb 2019 - Dec 2019

    - Led a functional R&D team of eight, responsible for sample bioanalysis, in vitro assay development, and mathematical modeling, and managed the efficient delivery of high-quality data to key stakeholders.

    - Coordinated development, qualification/validation, and execution of LC-MS/MS based biomarker assays and clinical microbiology protocols to meet aggressive clinical development timelines (SYNB1618 and SYNB1891 programs).

    - Established and led a collaboration with the US Air Force Research Laboratory 711th Human Performance Wing to demonstrate blood phenylalanine lowering, using human organ-on-a-chip technology, by a synthetic biotic for the treatment of phenylketonuria.
    2019
  • Senior Scientist | Synlogic, Inc. | Aug 2017 - Feb 2019

    - Developed in vitro gastrointestinal simulation (IVS) assays to elucidate engineered bacterial strain function in the physiological conditions of the human gastrointestinal environment.

    - Deployed IVS model to demonstrate activity of lyophilized synthetic biotic drug substance (SYNB1618, SYNB1020) and to identify a novel in vivo biomarker of SYNB1618 activity (phenyllactic acid).

    - Established a partnership with the Broad Institute of MIT and Harvard to enable RNAseq-based transcriptional profiling of synthetic biotics under simulated gastrointestinal conditions.
    2017
  • Scientist - Senior Scientist | Matatu, Inc. | Jan 2016 - Jul 2017

    - Designed, implemented, and optimized next generation sequencing (NGS) based computational pipelines to identify and determine engraftment of putative growth-promoting bacterial strains in agricultural swine.

    - Developed juvenile gnotobiotic (germ-free) mouse models to define the growth-promoting properties of consortia comprised of primary bacterial isolates.
    2016
  • PhD Candidate | Washington University in St Louis | Jul 2010 - Dec 2015

    - Investigated the role of human milk oligosaccharides in promoting healthy growth by interaction with infant gut microbiota using gnotobiotic (germ-free) mouse and piglet models of undernutrition.

    - Characterized the compositional, transcriptional, and metabolic responses of infant gut bacterial communities to human milk oligosaccharides.
    2010

Education

  • PhD, Computational and Systems Biology | 2010 - 2015
    Washington University in Saint Louis, Saint Louis, MO
    Advisor: Jeffrey I. Gordon, MD
    2015
  • BS, Microbiology and Molecular Genetics | 2006 - 2009
    Michigan State University, East Lansing, MI
    Advisors: James M. Tiedje, PhD and C.A. Reddy, PhD
    GPA: 4.0
    2009

Professional Training

Synlogic Learning Series: Coaching, Synlogic, Inc. | 2021

Synlogic Learning Series: Career Development, Synlogic, Inc. | 2021

The Business of Biotechnology: Advanced Concepts, RA Capital Management | 2020

Influential Leadership Fundamentals, Synlogic, Inc. | 2018

Machine Learning, Coursera.org | 2017

Publications

Charbonneau MR, Denney WS, Horvath N, Cantarella P, Castillo MJ, Puurunen MK, and Brennan AM. Modeling the impact of an engineered bacterial therapeutic on plasma phenylalanine in healthy subjects and patients with phenylketonuria. Commun Biol 4, 898. (2021). https://doi.org/10.1038/s42003-021-02183-1

Puurunen MK, Vockley J, Searle S, Sacharow S, Phillips J, Denney WS, Goodlett B, Wagner DA, Blankstein L, Castillo MJ, Charbonneau MR, Isabella VM, Sethuraman V, Riese R, Kurtz CB, and Brennan AM. Safety and pharmacodynamics of an engineered E. coli Nissle for the treatment of phenylketonuria: a first-in-human study. Nat Metab. (2021). https://doi.org/10.1038/s42255-021-00430-7

Nelson MT*, Charbonneau MR*, Coia HG, Castillo MJ, Holt C, Greenwood ES, Robinson PJ, Merrill EA, Lubkowicz D, Mauzy CA. Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip. Nat. Comms. 12, 2805. (2021).

Charbonneau MR, Isabella VM, Li N, and Kurtz CB. Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat. Comms. 11, 1738. (2020).

Kurtz CB, Millet YA, Puurunen MK, Perreault M, Charbonneau MR, Isabella VM, Kotula JW, Antipov E, Dagon Y, Denney WS, Wagner DA, West KA, Degar AJ, Brennan AM, and Miller PF. An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans. Sci. Transl. Med. 11(475), eaau7975. (2019).

Charbonneau MR, Blanton LV, DiGiulio DB, Relman DA, Lebrilla CB, Mills DA, and Gordon JI. A microbial perspective of human developmental biology. Nature 535, 48-55. (2016).

Blanton LV, Barratt MJ, Charbonneau MR, Ahmed T, and Gordon JI. Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics. Science 352(6293), 1533. (2016).

Charbonneau MR, O’Donnell D, Blanton LV, Totten SM, Davis, JCC, Barratt MJ, Cheng J, Guruge J, Talcott M, Bain JR, Muehlbauer MJ, Ilkayeva O, Wu C, Struckmeyer T, Barile D, Mangani C, Jorgensen J, Fan Y-M, Maleta K, Dewey KG, Ashorn P, Newgard CB, Lebrilla C, Mills DA, and Gordon JI. Sialylated milk glycans promote growth in gnotobiotic mice and pigs with a stunted Malawian infant gut microbiota. Cell 164(5), 859–871 (2016).

Blanton LV, Charbonneau MR, Salih T, Barratt MJ, Venkatesh S, Ilkayeva O, Subramanian S, Manary MJ, Trehan I, Jorgensen JM, Fan Y-M, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Maleta KM, Newgard CB, Ashorn P, Dewey KG, and Gordon JI. Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351(6275), aad3311. (2016).

Faith JJ, Guruge JL, Charbonneau MR, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, and Gordon JI. The long-term stability of the human gut microbiota. Science 341(6141), 1237439 (2013).

Invited Presentations

Microbiome Movement Drug Development Summit | 2021
Development of a Synthetic Biotic for the Treatment of Enteric Hyperoxaluria

Keystone Symposium: Harnessing the Microbiome for Disease Prevention and Therapy | 2021
Development of a Synthetic Biotic for the Treatment of Enteric Hyperoxaluria

International Conference on Microbiome Engineering | 2020
Development of a Synthetic Biotic for the Treatment of Enteric Hyperoxaluria

International Conference on Microbiome Engineering | 2019
Development of an Engineered Therapeutic E. coli Nissle for the Treatment of Phenylketonuria.

Keystone Symposium on Manipulation of the Gut Microbiota for Metabolic Health | 2018
A Genetically Engineered E. coli Nissle to Prevent Hyperammonemia in Urea Cycle Disorders (UCDs).

Joint Meeting of the German and Japanese Societies of Developmental Biologists | 2017
Childhood undernutrition: a microbial view of human postnatal development.

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