Deep Learning‐Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard‐to‐Transfect Cells

Mukherjee, Prithvijit; Patino, Cesar A.; Pathak, Nibir; Lemaitre, Vincent; Espinosa, Horacio D.

doi:10.1002/smll.202107795

Title: Deep Learning‐Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard‐to‐Transfect Cells

Journal Article · Mon Mar 21 00:00:00 EDT 2022 · Small

DOI:https://doi.org/10.1002/smll.202107795· OSTI ID:1856281

Mukherjee, Prithvijit ^[1]; Patino, Cesar A. ^[2]; Pathak, Nibir ^[3]; Lemaitre, Vincent ^[4];

^[1]

Department of Mechanical Engineering Northwestern University Evanston IL 60208 USA, Theoretical and Applied Mechanics Program Northwestern University Evanston IL 60208 USA, iNfinitesimal LLC Skokie IL 60077 USA
Department of Mechanical Engineering Northwestern University Evanston IL 60208 USA, iNfinitesimal LLC Skokie IL 60077 USA
Department of Mechanical Engineering Northwestern University Evanston IL 60208 USA, Theoretical and Applied Mechanics Program Northwestern University Evanston IL 60208 USA
iNfinitesimal LLC Skokie IL 60077 USA

Abstract Genome engineering of cells using CRISPR/Cas systems has opened new avenues for pharmacological screening and investigating the molecular mechanisms of disease. A critical step in many such studies is the intracellular delivery of the gene editing machinery and the subsequent manipulation of cells. However, these workflows often involve processes such as bulk electroporation for intracellular delivery and fluorescence activated cell sorting for cell isolation that can be harsh to sensitive cell types such as human‐induced pluripotent stem cells (hiPSCs). This often leads to poor viability and low overall efficacy, requiring the use of large starting samples. In this work, a fully automated version of the nanofountain probe electroporation (NFP‐E) system, a nanopipette‐based single‐cell electroporation method is presented that provides superior cell viability and efficiency compared to traditional methods. The automated system utilizes a deep convolutional network to identify cell locations and a cell‐nanopipette contact algorithm to position the nanopipette over each cell for the application of electroporation pulses. The automated NFP‐E is combined with microconfinement arrays for cell isolation to demonstrate a workflow that can be used for CRISPR/Cas9 gene editing and cell tracking with potential applications in screening studies and isogenic cell line generation.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Center for Nanoscale Materials (CNM)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1856281

Alternate ID(s):: OSTI ID: 1860987; OSTI ID: 1981442

Journal Information:: Small, Journal Name: Small Vol. 18 Journal Issue: 20; ISSN 1613-6810

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: Germany

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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human-induced pluripotent stem cells (hiPSCs)
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Title: Deep Learning‐Assisted Automated Single Cell Electroporation Platform for Effective Genetic Manipulation of Hard‐to‐Transfect Cells

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