Honors & Awards

  • Siebel Scholar, Siebel Scholars Foundation (2021)
  • Lavidge and McKinley Interdisciplinary Fellow, BioX (2017-2020)

All Publications

  • Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS. Analytical chemistry Brower, K. K., Khariton, M., Suzuki, P. H., Still, C. 2., Kim, G., Calhoun, S. G., Qi, L. S., Wang, B., Fordyce, P. M. 2020


    In the past five years, droplet microfluidic techniques have unlocked new opportunities for the high-throughput genome-wide analysis of single cells, transforming our understanding of cellular diversity and function. However, the field lacks an accessible method to screen and sort droplets based on cellular phenotype upstream of genetic analysis, particularly for large and complex cells. To meet this need, we developed Dropception, a robust, easy-to-use workflow for precise single-cell encapsulation into picoliter-scale double emulsion droplets compatible with high-throughput screening via fluorescence-activated cell sorting (FACS). We demonstrate the capabilities of this method by encapsulating five standardized mammalian cell lines of varying sizes and morphologies as well as a heterogeneous cell mixture of a whole dissociated flatworm (5-25 mum in diameter) within highly monodisperse double emulsions (35 mum in diameter). We optimize for preferential encapsulation of single cells with extremely low multiple-cell loading events (<2% of cell-containing droplets), thereby allowing direct linkage of cellular phenotype to genotype. Across all cell lines, cell loading efficiency approaches the theoretical limit with no observable bias by cell size. FACS measurements reveal the ability to discriminate empty droplets from those containing cells with good agreement to single-cell occupancies quantified via microscopy, establishing robust droplet screening at single-cell resolution. High-throughput FACS screening of cellular picoreactors has the potential to shift the landscape of single-cell droplet microfluidics by expanding the repertoire of current nucleic acid droplet assays to include functional phenotyping.

    View details for DOI 10.1021/acs.analchem.0c02499

    View details for PubMedID 32900183

  • Neural Progenitor Cells Alter Chromatin Organization and Neurotrophin Expression in Response to 3D Matrix Degradability. Advanced healthcare materials Madl, C. M., LeSavage, B. L., Khariton, M., Heilshorn, S. C. 2020: e2000754


    Neural progenitor cells (NPCs) are promising therapeutic candidates for nervous system regeneration. Significant efforts focus on developing hydrogel-based approaches to facilitate the clinical translation of NPCs, from scalable platforms for stem cell production to injectable carriers for cell transplantation. However, fundamental questions surrounding NPC-hydrogel interactions remain unanswered. While matrix degradability is known to regulate the stemness and differentiation capacity of NPCs, how degradability impacts NPC epigenetic regulation and secretory phenotype remains unknown. To address this question, NPCs encapsulated in recombinant protein hydrogels with tunable degradability are assayed for changes in chromatin organization and neurotrophin expression. In high degradability gels, NPCs maintain expression of stem cell factors, proliferate, and have large nuclei with elevated levels of the stemness-associated activating histone mark H3K4me3. In contrast, NPCs in low degradability gels exhibit more compact, rounded nuclei with peripherally localized heterochromatin, are non-proliferative yet non-senescent, and maintain expression of neurotrophic factors with potential therapeutic relevance. This work suggests that tuning matrix degradability may be useful to direct NPCs toward either a more-proliferative, stem-like phenotype for cell replacement therapies, or a more quiescent-like, pro-secretory phenotype for soluble factor-mediated therapies.

    View details for DOI 10.1002/adhm.202000754

    View details for PubMedID 32743903

  • 'Chromatic' neuronal jamming in a primitive brain Nature Physics Khariton, M., Kong, X., Qin, J., Wang, B. 2020
  • Mechanically resolved imaging of bacteria using expansion microscopy. PLoS biology Lim, Y., Shiver, A. L., Khariton, M., Lane, K. M., Ng, K. M., Bray, S. R., Qin, J., Huang, K. C., Wang, B. 2019; 17 (10): e3000268


    Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (muExM) in which bacterial cells are physically expanded prior to imaging. We find that expansion patterns depend on the structural and mechanical properties of the cell wall, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of muExM to distinguish species through an in vitro defined community of human gut commensals and in vivo imaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.

    View details for DOI 10.1371/journal.pbio.3000268

    View details for PubMedID 31622337

  • Locked Expansion Microscopy to in Situ Analyze Microbial Communities Lim, Y., Khariton, M., Bray, S., Ng, K., Shiver, A., Huang, K. C., Wang, B. CELL PRESS. 2018: 532A
  • Nanoengineered Osteoinductive and Elastomeric Scaffolds for Bone Tissue Engineering ACS BIOMATERIALS SCIENCE & ENGINEERING Kerativitayanan, P., Tatullo, M., Khariton, M., Joshi, P., Perniconi, B., Gaharwar, A. K. 2017; 3 (4): 590–600
  • Maintenance of neural progenitor cell stemness in 3D hydrogels requires matrix remodelling. Nature materials Madl, C. M., LeSavage, B. L., Dewi, R. E., Dinh, C. B., Stowers, R. S., Khariton, M., Lampe, K. J., Nguyen, D., Chaudhuri, O., Enejder, A., Heilshorn, S. C. 2017; 16 (12): 1233–42


    Neural progenitor cell (NPC) culture within three-dimensional (3D) hydrogels is an attractive strategy for expanding a therapeutically relevant number of stem cells. However, relatively little is known about how 3D material properties such as stiffness and degradability affect the maintenance of NPC stemness in the absence of differentiation factors. Over a physiologically relevant range of stiffness from ∼0.5 to 50 kPa, stemness maintenance did not correlate with initial hydrogel stiffness. In contrast, hydrogel degradation was both correlated with, and necessary for, maintenance of NPC stemness. This requirement for degradation was independent of cytoskeletal tension generation and presentation of engineered adhesive ligands, instead relying on matrix remodelling to facilitate cadherin-mediated cell-cell contact and promote β-catenin signalling. In two additional hydrogel systems, permitting NPC-mediated matrix remodelling proved to be a generalizable strategy for stemness maintenance in 3D. Our findings have identified matrix remodelling, in the absence of cytoskeletal tension generation, as a previously unknown strategy to maintain stemness in 3D.

    View details for PubMedID 29115291