Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity

Stanislav S. Terekhov, Ivan V. Smirnov, Anastasiya V. Stepanova, Tatyana V. Bobik, Yuliana A. Mokrushina, Natalia A. Ponomarenko, Alexey A. Belogurov, Maria P. Rubtsova, Olga V. Kartseva, Marina O. Gomzikova, Alexey A. Moskovtsev, Anton S. Bukatin, Michael V. Dubina, Elena S. Kostryukova, Vladislav V. Babenko, Maria T. Vakhitova, Alexander I. Manolov, Maja V. Malakhova, Maria A. Kornienko, Alexander V. Tyakht & 5 others Anna A. Vanyushkina, Elena N. Ilina, Patrick Masson, Alexander G. Gabibov, Sidney Altman

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus, and predicted which genera were associated with inhibitory activity.

Original languageEnglish (US)
Pages (from-to)2550-2555
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
Issue number10
DOIs
StatePublished - Mar 7 2017
Externally publishedYes

Fingerprint

Microfluidics
Biodiversity
Paraoxon
Butyrylcholinesterase
Forensic Anthropology
Water
Genetic Selection
Microbiota
Emulsions
Cell Communication
Liquid Chromatography
Staphylococcus aureus
Mass Spectrometry
Oils
Yeasts
Genotype
Bacteria
Phenotype
Enzymes
Growth

Keywords

  • Butyrylcholinesterase
  • Cell-cell interactions
  • Microfluidic encapsulation
  • Staphylococcus aureus
  • Ultrahigh-throughput screening

ASJC Scopus subject areas

  • General

Cite this

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity. / Terekhov, Stanislav S.; Smirnov, Ivan V.; Stepanova, Anastasiya V.; Bobik, Tatyana V.; Mokrushina, Yuliana A.; Ponomarenko, Natalia A.; Belogurov, Alexey A.; Rubtsova, Maria P.; Kartseva, Olga V.; Gomzikova, Marina O.; Moskovtsev, Alexey A.; Bukatin, Anton S.; Dubina, Michael V.; Kostryukova, Elena S.; Babenko, Vladislav V.; Vakhitova, Maria T.; Manolov, Alexander I.; Malakhova, Maja V.; Kornienko, Maria A.; Tyakht, Alexander V.; Vanyushkina, Anna A.; Ilina, Elena N.; Masson, Patrick; Gabibov, Alexander G.; Altman, Sidney.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 114, No. 10, 07.03.2017, p. 2550-2555.

Research output: Contribution to journalArticle

Terekhov, SS, Smirnov, IV, Stepanova, AV, Bobik, TV, Mokrushina, YA, Ponomarenko, NA, Belogurov, AA, Rubtsova, MP, Kartseva, OV, Gomzikova, MO, Moskovtsev, AA, Bukatin, AS, Dubina, MV, Kostryukova, ES, Babenko, VV, Vakhitova, MT, Manolov, AI, Malakhova, MV, Kornienko, MA, Tyakht, AV, Vanyushkina, AA, Ilina, EN, Masson, P, Gabibov, AG & Altman, S 2017, 'Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity' Proceedings of the National Academy of Sciences of the United States of America, vol. 114, no. 10, pp. 2550-2555. https://doi.org/10.1073/pnas.1621226114
Terekhov, Stanislav S. ; Smirnov, Ivan V. ; Stepanova, Anastasiya V. ; Bobik, Tatyana V. ; Mokrushina, Yuliana A. ; Ponomarenko, Natalia A. ; Belogurov, Alexey A. ; Rubtsova, Maria P. ; Kartseva, Olga V. ; Gomzikova, Marina O. ; Moskovtsev, Alexey A. ; Bukatin, Anton S. ; Dubina, Michael V. ; Kostryukova, Elena S. ; Babenko, Vladislav V. ; Vakhitova, Maria T. ; Manolov, Alexander I. ; Malakhova, Maja V. ; Kornienko, Maria A. ; Tyakht, Alexander V. ; Vanyushkina, Anna A. ; Ilina, Elena N. ; Masson, Patrick ; Gabibov, Alexander G. ; Altman, Sidney. / Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity. In: Proceedings of the National Academy of Sciences of the United States of America. 2017 ; Vol. 114, No. 10. pp. 2550-2555.
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AU - Ponomarenko, Natalia A.

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