Publications
Selected recent highlights
Preprints
Engineered bacteria launch and control an oncolytic virus
Singer, Z.S.*, Pabón, J.*, Huang, H., Rice, C.M., Danino, T.
bioRxiv 559873 (2023)
Publications
Probiotic neoantigen delivery vectors for precision cancer immunotherapy
Redenti, A.*, Im, J.*, Redenti, B,, Li, F., Rouanne, M., Sheng, Z., Sun, W., Gubatri, C.R., Huang, S., Komaranchath, M., Jang, Y., Hahn, J., Ballister, E., Vincent, R.L., Vardoshivilli, A., Danino, T.*, Arpaia, N*.
Nature (2024) https://doi.org/10.1038/s41586-024-08033-4
• Columbia University Irving Medical Center News: Hacking bacteria to attack cancer
Dynamic gene expression mitigates mutational escape in lysis-driven bacteria cancer therapy
Liguori, F., Pellicciotta, N., Milanetti, E., Windemuth, S.X., Ruocco, G., Di Leonardo, R., Danino, T.
Biodesign Research 6:0049 (2024)
Colorectal cancer detection and treatment with engineered probiotics
Gurbatri, C.R.*, Radford, G.*, Vrbanac, L., Coker, C., Im, J., Taylor, S.R., Jang, Y., Sivan, A., Rhee, K., Saleh, A.A., Chien, T., Zandkarimi, F., Lia, I., Lannagan, T.R., Wang, T., Wright, J.A., Thomas, E., Kobayashi, H., Ng, J.Q., Lawrence, M., Sammour, T., Thomas, M., Lewis, M., Papanicolas, L., Perry, J., Fitzsimmons, T., Kaazan, P., Lim, A., Marker, J., Ostroff, C., Rogers, G., Arpaia, N., Worthley, D.L., Woods, S.L.*, Danino, T.*
Nature Communications 15:646 (2024)
Probiotic-guided CAR-T cells for solid tumor targeting
Vincent, R.L.*, Gurbatri, C.R.*, Li, F., Vardoshvili, A., Coker, C., Im, J., Ballister, E.R., Rouanne, M., Savage, T., de los Santos-Alexis, K., Redenti, A., Brockmann, L., Komaranchath, M., Arpaia, N., Danino, T.
Science 382(6667), 211-218 (2023)
• Nature Reviews Drug Discovery: Bacteria tag tumours for CAR-T cell attack
• Nature Biotechnology Research Highlights: A bacterial assist for CAR-T cells
• ScienceAdviser: Engineered bacteria + CAR-T cells: A dynamic duo to crush cancer?
• Science Perspectives: Engineered bacteria guide T cells to tumors
• Columbia News: Engineered Bacteria Paint Targets on Tumors for Cancer-killing T Cells to See
Bacterial therapies at the interface of synthetic biology and nanomedicine
Hahn, J., Ding, S., Im, J., Harimoto, T., Leong, K.W., Danino, T.
Nature Reviews Bioengineering (2023). doi 10.1038/s44222-023-00119-4
Engineered bacterial swarm patterns as spatial records of environmental inputs
Doshi, A., Shaw, M., Tonea, R., Moon, S., Minyety, R., Doshi, A., Laine, A., Guo, J., Danino, T.
Nature Chemical Biology 19(7), 878–886 (2023)
Engineered bacteria for short-chain-fatty-acid-repressed expression of biotherapeutic molecules
Serebrinsky-Duek, K., Barra, M., Danino, T., Garrido, D.
Microbiology Spectrum 11(2), (2023)
Chemokines expressed by engineered bacteria recruit and orchestrate antitumor immunity
Savage, T.M., Vincent, R.L., Rae, S.S., Huang, L.H., Ahn, A., Pu, K., Li, F., de Los Santos-Alexis, K., Coker, C., Danino, T., Arpaia, N.
Science Advances 9(10), (2023)
Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer
Deb, D., Wu, Y., Coker, C., Harimoto, T., Huang, R., Danino, T.
Scientific Reports 12:21551 (2022)
Engineering bacteria as interactive cancer therapies
Gurbatri, C.R., Arpaia, N., Danino, T.
Science 378(6622), 858-864 (2022)
Assessing chemotherapy dosing strategies in a spatial cell culture model
Deb, D.*, Zhu, S.*, Leblanc, M.J., Danino, T.
Frontiers in Oncology 12:980770 (2022)
Segmentation with residual attention U-Net and an edge-enhancement approach preserves cell shape features
Zhu, N.*, Liu, C.*, Forsyth, B., Singer, Z., Laine, A., Danino, T., Guo, J.
IEEE Engineering in Medicine & Biology Society (EMBC) 2115-2118 (2022)
A rapid screening platform to coculture bacteria within tumor spheroids
Harimoto, T., Deb, D., Danino, T.
Nature Protocols 17(10), 2216-2239 (2022)
A programmable encapsulation system improves delivery of therapeutic bacteria in mice
Harimoto, T., Hahn, J., Chen, Y., Im, J., Zhang, J., Hou, N., Coker, C., Gray, K., Harr, N., Chowdhury, C., Pu, K., Nimura, C., Arpaia, N., Leong, K.*, Danino, T.*
Nature Biotechnology 40, 1259-1269 (2022)
• Nature Reviews Drug Discovery: Bacteria deliver the goods
• Columbia News: Engineering an “Invisible Cloak” for Bacteria to Deliver Cancer Drugs
Reimagining cancer research with art
Deb, D., Shoreibah, S., Danino, T.
Nature Reviews Cancer 22, 191 (2022)
Bacterial couriers as cancer vaccines
Redenti, A., Hahn, J., Danino, T.
Nature Biomedical Engineering News & Views 6, 3-5 (2022)
A deep learning pipeline for segmentation of Proteus mirabilis colony patterns
Doshi, A.*, Shaw, M.*, Tonea, R., Minyety, R., Moon, S., Laine, A., Guo, J.*, Danino, T.*
IEEE International Symposium on Biomedical Imaging (ISBI) 1-5 (2022)
CAR-T cells SEAK help from enzymes
Vincent, R., Danino, T.
Nature Chemical Biology News & Views 18, 122-123 (2022)
The Origin and Contribution of Cancer-Associated Fibroblasts in Colorectal Carcinogenesis Gastroenterology
Kobayashi H*, Gieniec KA*, Lannagan TRM*, Wang T, Asai N, Mizutani Y, Iida T, Ando R, Thomas EM, Sakai A, Suzuki N, Ichinose M, Wright JA, Vrbanac L, Ng JQ, Goyne J, Radford G, Lawrence MJ, Sammour T, Hayakawa Y, Klebe S, Shin AE, Asfaha S, Bettington ML, Rieder F, Arpaia N, Danino T, Butler LM, Burt AD, Leedham SJ, Rustgi AK, Mukherjee S, Takahashi M, Wang TC, Enomoto A, Woods SL, Worthley DL.
Gastroenterology 162(3), 890-906 (2022)
Enhancing the tropism of bacteria via genetically programmed biosensors
Chien, T.*, Harimoto, T.*, Kepecs, B., Gray, K., Coker, C., Hou, N., Pu, K., Azad, T., Nolasco, A., Pavlicova, M., Danino, T.
Nature Biomedical Engineering 6, 94-104 (2021)
• Columbia News: Genetic Circuit Could Help Engineered Bacteria Hunt Down Tumors
Quantitative measurements of early alphaviral replication dynamics in single cells reveals the basis for superinfection exclusion
Singer, Z.S., Ambrose, P.M., Danino, T.*, Rice, C.M.*
Cell Systems 12(3), 210-219 (2021)
Engineered Bacterial Production of Volatile Methyl Salicylate
Chien, T., Jones, D.R. , and Danino, T.
ACS Synthetic Biology 10(1), 204-208 (2020)
Engineered Probiotics for Detection and Treatment of Inflammatory Intestinal Diseases
Barra, M., Danino, T., Garrido, D.
Frontiers in bioengineering and biotechnology, 8, 265 (2020)
Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies
Gurbatri, C., Iona, L., Vincent, R., Coker, C., Castro, S., Treuting, P., Hinchliffe, T.E., Arpaia, N., Danino, T.
Science Translational Medicine 12(530):eaax0876 (2020)
• Nature Medicine Research Highlights: Delivering immunotherapy with bacteria
• Columbia News: Designer Probiotic Treatment for Cancer Immunotherapy
• C&EN: Bacteria producing checkpoint inhibitors shrink tumors in mice
• GEN: Engineered Probiotic Bacteria Deliver Anticancer Nanobodies to Regress Tumors in Mice
• BBC Science Focus: Seek and destroy: beneficial bacteria programmed to fight cancer
Engineering Bacteria For Cancer Therapy
Harimoto, T., Danino, T.
Emerging Topics In Life Science 3(5), 623-629 (2019)
Programmable bacteria induce durable tumor regression and systemic antitumor immunity
Chowdhury, S., Castro, S., Coker, C., Hinchliffe, T.E., Arpaia, N.*, Danino, T.*
Nature Medicine 25(7), 1057–1063 (2019)
• Nature Medicine News & Views: Programmable bacteria as cancer therapy
• New York Times: New Weapons Against Cancer: Millions of Bacteria Programmed to Kill
• F1000 Recommendation
Rapid screening of engineered microbial therapies in a 3-D multicellular model
Harimoto, T., Singer, Z.S., Velazquez, O.S., Zhang, J., Castro, S., Hinchliffe, T.E., Mather, W., Danino, T.
PNAS 116(18), 9002-9007 (2019)
• Columbia News: Bacterial Therapy in a Dish
Two new plasmid post-segregational killing mechanisms for the implementation of synthetic gene networks in E. coli
Fedorec, A J.H., Ozdemir, T., Doshi, A., Rosa, L., Velazquez, O., Danino, T., Barnes, C P.
iScience 14, 323-334 (2019)
Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity
Ozdemir, T., Fedorec, A J.H., Danino, T., Barnes, C P.
Cell Systems 7(1), 5-16 (2018)
Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine
Geller, L.*, Barzily-Rokni, M.*, Danino, T., Jonas, O.H., Shental, N., Nejman, D., Gavert, N., Zwang, Y., Cooper, Z., A., Shee, K., Thaiss, C., A., Reuben, A., Livny, J., Avraham, R., Frederick, D., T., Ligorio, M., Chatman, K., Johnston, S., E., Mosher, C., M., Brandis, A., Fuks, G., Gurbatri, C., Gopalakrishnan, V., Kim, M., Hurd, M., W., Katz, M., Fleming, J., Maitra, A., Smith, D., A., Skalak, M., Bu, J., Michaud, M., Trauger, S., A., Barshack, I., Golan, T., Sandbank, J., Flaherty, K., T., Mandinova, A., Garrett, W., S., Thayer, S., P., Ferrone, C., R., Huttenhower, C., Bhatia, S., N., Gevers, D., Wargo, J., A., Golub, T., R. Straussman, R.
Science 357(6356), 1156-1160 (2017)
Advances in bacterial cancer therapies using synthetic biology
Chien, T.*, Doshi, A.*, Danino, T.
Current Opinions in Systems Biology 5, 1-8 (2017)
Spatial Control of Bacteria Using Screen Printing
Moon, S.*, Fritz, I.*, Singer, Z.*, Danino, T.
3D Printing and Additive Manufacturing 3(4), 194-203 (2016)
Synchronized cycles of bacterial lysis for in vivo delivery
Din, O.*, Danino, T.*, Prindle, A., Skalak, M., Selimkhanov, J., Allen, K., Julio, E., Atolia, A., Tsimring, L., Bhatia, S., Hasty, J.
Nature 536(7614), 81-85 (2016)
Hepatitis C virus RNA functionally sequesters miR-122
Luna, J., Scheel, T., Danino, T., Shaw, K., Takacs, C., Mele, A., Fak, J., Nishiuchi, E., Cantanese, M., Rice, C., Darnell, R.
Cell 160(6), 1099–1110 (2015)
Programmable probiotics for detection of cancer in urine
Danino, T.*, Prindle, A.*, Kwong, G., Skalak, M., Li, H., Allen, K., Hasty, J., and Bhatia, S.
Science Translational Medicine 7, 289ra84 (2015)
Measuring growth and gene expression dynamics of tumor-targeted S. typhimurium bacteria
Danino, T.*, Prindle, A.*, Hasty, J., and Bhatia, S.
Journal of Visualized Experiments 77, e50540 (2013)
Genetic Circuits in Salmonella typhimurium
Prindle, A., Selimkhanov, J.S., Danino, T., Samayoa, P., Goldberg, A., Bhatia, S., and Hasty, J.
ACS Synthetic biology 1(10), 458-464 (2012)
In vivo gene expression dynamics from tumor-targeted bacteria
Danino, T., Lo, J., Prindle, A., Hasty, J., and Bhatia, S.
ACS Synthetic biology 1(10), 465-470 (2012)
Queueing up for enzymatic processing: Correlated signaling through coupled degradation
Cookson, N.A.*, Mather, W.H.*, Danino, T., Mondragón-Palomino, O., Williams, R. J., Tsimring, L. S., and Hasty, J.
Molecular Systems Biology 7:561, (2011)
A sensing array of radically coupled genetic ‘biopixels’
Prindle, A.*, Samayoa, P.*, Razinkov, I., Danino, T., Tsimring, L.S. and Hasty, J.
Nature 481, 39-44 (2011)
Entrainment of a population of synthetic genetic oscillators
Mondragon-Palomino, O., Danino, T., Selimkhanov, J., Tsimring, L.S., and Hasty, J.
Science 333(6047), 1315-1319 (2011)
Buckling instability in ordered bacterial colonies
Boyer, D., Mather, W., Mondragon-Palomino, O., Orozco-Fuentes, S., Danino, T., Hasty, J., and Tsimring, L. S.
Physical Biology 8, 026008 (2011)
In-silico pattern formation of vascular mesenchymal stem-cells in three-dimensions
Danino,T., Volfson, D., Bhatia, S., Tsimring, L., and Hasty, J.
PLoS ONE 6(5), e20182 (2011)
Streaming instability in growing cell populations
Mather, W., Mondragon-Palomino, O., Danino, T., Hasty, J., and Tsimring, L.S.
Physical Review Letters 104(20), 208101 (2010)
A synchronized quorum of genetic clocks
Danino, T.*, Mondragon-Palomino, O.*, Tsimring, L., and Hasty, J.
Nature 463, 326-330 (2010)