*co-corresponding authors
"Bisphenol A replacement chemicals, BPF and BPS, induce protumorigenic changes in human mammary gland organoid morphology and proteomeWinkler J, Liu P, Phong K, Hinrichs JH, Ataii N, Williams K, Hadler-Olsen E, Samson S, Gartner ZJ, Fisher S, Werb Z. PNAS (2022)
"Setting boundaries for tissue patterning" Huycke TR and Gartner ZJ. Science (2022)
"Single-Cell Protein Profiling by Microdroplet Barcoding and Next-Generation Sequencing" Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Single Cell Protein Analysis (book chapter) (2022)
"AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data" Thibodeau A, Eroglu A, McGinnis CS, Lawlor N, Nehar-Belaid D, Kursawe R, Marches R, Conrad DN, Kuchel GA, Gartner ZJ, Banchereau J, Stitzel ML, Cicek AE, Ucar D. Genome Biology (2021)
"Human microglia states are conserved across experimental models and regulate neural stem cell responses in chimeric organoids" Popova G, Soliman SS, Kim CN, Keefe MG, Hennick KH, Jain S, Li T, Tejera D, Shin D, Chhun BB, McGinnis CS, Speir M, Gartner ZJ, Mehta SB, Haeussler M, Hengen KB, Ransohoff RR, Piao X, Nowakowski TJ. Cell Stem Cell. (2021)
"Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids" Huang L, Desai D, Conrad DN, Leite NC, Akshinthala D, Lim CM, Gonzalez R, Muthuswamy LM, Gartner ZJ, Muthuswamy SK. Cell Stem Cell. (2021)
"EPH/EPHRIN regulates cellular organization by actomyosin contractility effects on cell contacts" Kindberg AA, Srivastava V, Muncie JM, Weaver VM, Gartner ZJ, Bush JO. J. Cell Bio. (2021)
"Simple, Affordable, and Modular Patterning of Cells using DNA" Cabral KA, Patterson DM, Scheideler OJ, Cole R, Abate AR, Schaffer DV, Sohn LL, Gartner ZJ. J. Vis. Exp. (2021)
"T cell circuits that sense antigen density with an ultrasensitive threshold" Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Pazmino MDPL, Tonai Y, Guzman AD, Makela A, Gartner ZJ, Lim WA. Science (2021)
"Expanding the Boundaries of Synthetic Development" Martyn I, Gartner ZJ. Developmental Biology (2021)
"High diversity droplet microfluidic libraries generated with a commercial liquid spotter" Zhang JQ, Siltanen CA, Dolatmoradi A, Sun C, Chang KC, Cole RH, Gartner ZJ, Abate AR. Scientific Reports (2021)
"No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells" McGinnis CS, Siegel DA, Xie G, Stone M, Gartner ZJ, Roan NR, Lee SA. BMC Biology (2021)
"Organoid models for mammary gland dynamics and breast cancer" Srivastava V, Huycke TR, Phong KT, Gartner ZJ. Curr Opin Cell Biol (2020)
"ZipSeq: Barcoding for Real-time Mapping of Single Cell Transcriptomes" Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF. Nature Methods (2020) [pdf]
"High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing" Zhang JQ, Chang KC, Liu L, Gartner ZJ, Abate AR. JoVE (2020) [pdf]
"Lactoferrin Reverses Methotrexate Driven Epithelial Barrier Defect by Inhibiting TGF-β Mediated Epithelial to Mesenchymal Transition" Wallach TE, Srivastava V, Reyes E, Klein OD, Gartner ZJ. (submitted)
"Linked optical
and gene expression profiling of single cells at high-throughput." Zhang JQ, Siltanen CA, Liu L, Chang KC, Gartner ZJ, Abate AR. Genome Bio. (2020) [pdf]
"Antibody-Drug Conjugates Targeting the Urokinase Receptor (uPAR) as a Possible Treatment of Aggressive Breast Cancer." Harel ET, Drake PM, Barfield RM, Lui I, Farr-Jones S, Van’t Veer L, Gartner ZJ, Green EM, Lourenço AL, Cheng Y, Hann BC, Rabuka D, Craik CS. Antibodies (2019) [pdf]
"Balancing Act: Cell Polarity and Shape Compete to Ensure Robust Development." Murrow LM, Gartner ZJ. Dev. Cell (2019) [pdf]
"Bioprinting in Space and Time." *Gartner Z, *Hughes A. Nature (2019) [pdf]
*co-corresponding authors
"Human organoids: a new dimension in cell biology." Lehmann R, Lee CM, Shugart EC, Benedetti M, Charo RA, Gartner Z, Hogan B, Knoblich J, Nelson CM, Wilson KM. Mol Biol Cell. (2019) [pdf]
"MULTI-seq: scalable sample multiplexing for single-cell RNA sequencing using lipid-tagged indices" McGinnis CS, Patterson DM, Winkler J, Hein MY, Srivastava S, Hu JL, Conrad DN, Murrow LM, Weissman JS, Werb Z, *Chow ED, *Gartner ZJ. Nature Methods (2019) [pdf]
*co-corresponding authors
"DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors" McGinnis CS, Murrow LM, Gartner ZJ. Cell Systems (2019) [pdf]
"Paracrine costimulation of IFN-γ signaling by integrins modulates CD8 T cell differentiation." select
Krummel MF, Mahale JN, Uhl LFK, Hardison EA, Mujal AM, Mazet JM, Weber RJ, Gartner ZJ, Gérard A. Proc Natl Acad Sci U S A (2018) [pdf]
"Cell-specific chemical delivery using a selective nitroreductase-nitroaryl pair" Gruber TD, Krishnamurthy C, Grimm JB, Tadross MR, Wysocki LM, Gartner ZJ, Lavis LD. ACS Chem. Bio. (2018)
"Phosphorylated EGFR dimers are not sufficient to activate Ras" Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon T-Y, von Zastrow M, Jura N, Gartner ZJ. Cell Reports (2018) [pdf]
"An Oil-Free Picodrop Bioassay Platform for Synthetic Biology" Siltanen CA, Cole RH, Poust S, Chao L, Tyerman J, Kauffman-Malaga B, Ubersax J, Gartner ZJ, Abate A. Sci Rep (2018) [pdf]
"Characterizing cellular mechanical phenotypes with mechano-node-pore sensing" Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MM, LaBarge MA, Sohn LL. Microsys Nanoeng (2018) [pdf]
"Engineered tissue folding by mechanical compaction of the mesenchyme" Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrusova Z, Schneider RA, Klein OD, Gartner ZJ. Developmental Cell (2018) [pdf]
"Quantius: a tool for rapid, flexible, crowd-based annotation of images" Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ. Nat. Meth. (2018)
"Unravelng cell-to-cell signaling networks with chemical biology" *Gartner ZJ, *Prescher JA, *Lavis LD. Nat. Chem. Biol.(2017)
Groups of mesenchymal cells dispersed in a loose and fibruous ECM compact to form condensates. We use this fundamental cell behavior to engineer tissues that fold up along specific trajectories, in a manner analagous to self-folding origami.
*co-corresponding authors
"Opportunities for organoids as new models of aging" Hu JH, Todhunter ME, *Labarge MA, *Gartner ZJ. J Cell Bio (2017) [pdf]
*co-corresponding authors
"Printed Droplet Microfluidics for on demand dispensing of picoliter droplets and cells" Cole R, Tang S, Siltanen C, Shahi P, Zhang J, Poust S, *Gartner ZJ, *Abate AR. Proc. Nat. Acad. Sci. USA (2017)
*co-corresponding authors
"A DNA-Based T Cell Receptor Reveals a Role for Receptor Clustering in Ligand Discrimination" Taylor MJ, Husain, K, Gartner ZJ, Mayor S, Vale RD. Cell (2017)
"Non-autonomous cell proliferation in the mammary gland and cancer." Weber RJ, Desai TA, Gartner ZJ. Curr Opin Cell Biol (2017)
"Dissecting the stem cell niche with organoid models: an engineering-based approach." Murrow LM, Weber RJ, Gartner ZJ. Development (2017)
"Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding" Shahi P, Kim SC, Haliburton JR, Gartner ZJ, Abate AR. Sci Rep. (2017)
"Effects of cell type and configuration on anabolic and catabolic activity in 3D coculture of mesenchymal stem cells and nucleus pulposus cells" Ouyang A, Cerchiari AE, Tang X, Liebenberg E, Alliston T, Gartner ZJ, Lotz JC. J Orthop Res (2016)
"Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC)" Todhunter ME, Weber RJ, Farlow J, Jee NY, Cerchiari AE, Gartner ZJ. Curr Protoc Chem Biol (2016)
"Probing the luminal microenvironment of reconstituted epithelial microtissues" Cerchiari AE, Samy KE, Todhunter ME, Schlesinger E, Henise J, Rieken C, Gartner ZJ, Desai TA. Sci Rep (2016)
"Mysteries in a Minimal Genome" Coyle M, Hu J, Gartner ZJ. ACS Cent Sci (2016)
"Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers" Cole RH, Gartner ZJ, Abate AR. J Vis Res (2016)
"A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time." Seo D**, Southard KM**, Kim JW, Farlow J, Lee JU, Litt DB, Haas T, Cheon J, Alivisatos PA, Gartner ZJ*, Jun YW*. Cell (2016) [pdf]
We describe a technology that enables deterministic printing of tailored groups of cells and reagents to arrays exceeding 10,000 features. In this image we printed exactly one green cell and one red cell to each feature in an array.
*co-corresponding authors
**equal contributions
"Multicolor fluorescence detection for droplet microfluidics using optical fibers." Cole RH, Gartner ZJ, Abate AR. Journal of Visualized Experiments (2016)
"Interrogating Stem Cell Fate Decisions with High-Throughput Arrays of Cellular Communities." Chen S, Na YS, Todhunter M, Hsiao S, Scheideler OJ, Bremer AW, Bomdica P, Maharbiz MM, Gartner ZJ*, Schaffer DV*. Nature Communication (2016) [pdf]
We describe monovalent nanoparticles that can be used to independently localize or deliver quantitative mechanical loads to single cell surface receptors.
*co-corresponding authors
"Compact and modular multicolor fluorescence detector for droplet microfluidics" Cole RH, de Lange N, Gartner ZJ, Abate AR. Lab Chip (2015) [pdf]
"Coupling between apical tension and basal adhesion allow epithelia to sense and respond to substrate topography over long distances." Broaders KE, Cerchiari AE, Gartner ZJ Integrative Biology (2015) [pdf]
"Programmed Synthesis of Three-Dimensional Tissues." Todhunter ME*, Jee NY*, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ. Nature Methods (2015) [pdf]
*equal contributions
"Formation of spatially and geometrically controlled 3D tissues in soft gels via sacrificial micro molding." Cerchiari A, Garbe JC, Todhunter ME, Jee NY, LaBarge MA, Desai T*, Gartner ZJ. Tiss. Eng. Part C (2015) [pdf]
Three-dimensional image of a tissue constructed using DNA-programmed assembly of cells (DPAC). We aimed to synthesize a tissue with a structure similar to the Terminal Ductal Lobular Unit (TDLU) of the breast.
*co-corresponding authors
"A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity." Cerchiari A, Garbe JC, Todhunter ME, Jee NY, Broaders K, Peehl D, LaBarge MA, Desai T, Thomson M, Gartner ZJ. Proc. Natl. Acad. Sci. USA (2015) [pdf]
"Efficient targeting of fatty-acid modified oligonucleotides to live cell membranes through step-wise assembly." Weber RJ, Liang SI, Selden NS, Desai TA, Gartner ZJ. BioMacroMolecules (2014) [pdf]
"Production & Targeting of Monovalent Quantum Dots." Seo D, Farlow J, Southard K , Jun YW* Gartner ZJ*. J. Vis. Exp. (2014)
We investigate how the mammary gland maintains a single three-dimensional structure through a robust program of self-organization. In the movie, luminal (green) and myoepithelial (red) cells self-organize correctly in extracellular matrix (left), but into an inverted structure in non-adhesive microenvironments such as agarose (right).
*co-corresponding authors
“A Modular Approach for Assembling Aldehyde-Tagged Proteins on DNA Scaffolds.” Liang SI, McFarland J, Rabuka D, Gartner ZJ. J. Am. Chem. Soc. (2014) [pdf]
"Cells: Shaping tissues and organs." Rosenblatt J, Gartner ZJ. Mol. Bio. Cell (2014)
“Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging.” Sogi KM, Gartner ZJ, Breidenbach MA, Appel MJ, Schelle MW, Bertozzi CR. PLOS One (2013)
"Formation of targeted monovalent quantum dot by steric exclusion.” Farlow J, Seo D, Broaders KE, Taylor M, Gartner ZJ*, Jun YW*. Nature Methods (2013) [pdf]
A simple method for generating site-specific DNA-protein conjugates is presented. This method provides a means of assembling antibody fragments on DNA scaffolds in precisely defined nanoscale geometries. These constructs will find utility as nanoscale probes of receptor organization at the cell surface.
*co-corresponding authors
“Programmed Cell-to-Cell Variability in Ras Activity Triggers Emergent Behaviors during Mammary Epithelial Morphogenesis.” Liu J; Farlow J; Paulson AK; Labarge MA; Gartner ZJ Cell Reports (2012) (pdf)
“Directing the assembly of multiple cell types into spatially organized tissues.” Liu, J.; Gartner, Z. J. Trends in Cell Biology (2012) (pdf)
“Cellular Microfabrication: Observing Intercellular Interactions Using Lithographically-Defined DNA Capture Sequences.” Onoe, H.; Hsiao, S. C.; Douglas, E. S.; Gartner, Z. J.; Bertozzi, C. R.; Francis, M. B.; Mathies, R. A. Langmuir. (2012)
“Chemically Programmed Cell Adhesion with Membrane-Anchored Oligonucleotides.” Selden, N. S.; Todhunter, M. E.; Jee, N. Y.; Liu J. S.; Broaders, K. E.; Gartner, Z. J. J. Am. Chem. Soc. (2011)
"Programmed assembly of three-dimensional microtissues with defined cellular connectivity.” Gartner, Z. J.; Bertozzi, C. R. Proc. Natl. Acad. Sci. USA 106, 4606-4610 (2009).
"Boron Nitride Nanotubes Are Noncytotoxic and Can Be Functionalized for Interaction with Proteins and Cells." Chen, X; Wu, P; Rousseas, M; Okawa, D; Gartner, Z. J.; Zettl, A; Bertozzi, C. R. J. Am. Chem. Soc. 131, 890-891 (2009).
"Direct cell surface modification with DNA for the capture of primary cells and the investigation of myotube formation on defined patterns." Hsiao, H.C.; Shum, B.J.; Onoe, H; Douglas, E.S.; Gartner, Z.J.; Mathies, R.A.; Bertozzi, C.R.; Francis, M.B. Langmuir 25, 6985-6991 (2009).
“Evolutionary Approaches for the Discovery of Functional Synthetic Small Molecules.” Gartner, Z. J. Pure and Applied Chemistry 78[1] 1-14 (2006).
“DNA-Templated Organic Synthesis and Selection of a Library of Macrocycles.” Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. Science 305, 1601-1605 (2004).
“Directed Evolution of Ligand Dependence: Small Molecule-Activated Protein Splicing.” Buskirk, A. R.; Ong, Y.; Gartner, Z. J.; Liu, D. R. Proc. Natl. Acad. Sci. USA 101 , 10505-10510 (2004).
“Translation of DNA into Synthetic N-Acyloxazolidines.” Li, X.; Gartner, Z. J.; Tse, B. N.; Liu, D. R. J. Am. Chem. Soc. 126, 5090-5092 (2004).
“Two Enabling New Architectures for DNA-Templated Synthesis.” Gartner, Z. J.; Grubina, R.; Calderone, C. T.; Liu, D.R. Angew. Chem. Int. Ed. 42, 1370 (2002).
“Directing Otherwise Incompatible Reactions in a Single Solution Using DNA-Templated Organic Synthesis.” Calderone, C. T.; Puckett, J. W.; Gartner, Z. J.; Liu, D. R. Angew. Chem. Int. Ed. 41, 4104 (2002).
“Multistep Small-Molecule Synthesis Programmed by DNA Templates.” Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 124, 10304 (2002).
“Expanding the Reaction Scope of DNA-Templated Synthesis.” Gartner, Z, J.; Kanan, M. W.; Liu, D. R. Angew. Chem. Int. Ed., 41, 1796 (2002).
“The Generality of DNA-Templated Synthesis as a Basis for Evolving Non-Natural Small Molecules.” Gartner, Z. J. and Liu, D. R. J. Am. Chem. Soc. 123, 6961-6963 (2001).
Controlling the valency of targeting elements on nanoparticles is a major challenge. Here we describe a modular and scalable synthetic strategy to generate monovalent semiconductor quantum dots by steric exclusion. Phosphorothioate DNA is mixed with ZnS coated CdSe QDs to produce targetable and highly fluorescent nanoparticles of a single valency.
Variability in cell state can arise as a consequence of noisy gene expression, microenvironmental heterogeneity, or somatic mutations. Heterogeneity can become accentuated in tumors. In this paper, we find that tissues exhibiting heterogeneity in signaling through the Ras oncogene can drive the emergence of more invasive collective cell behaviors when compared to tissue with more homogeneous signaling through Ras.
This work was featured in MIT's Technology Review, a Science and Technology Concentrates in C and E news, and in the August 2009 issue of the HHMI Bulletin.
IL-3 producing cells (green, top), but not controls (green, bottom) rescue the growth of IL-3 dependent hematopoietic progenitors (Phase). This paracrine signaling network mimics certain aspects of immune system function.
A library of macrocyclic peptide fumaramides.