Reliable multiplex generation of pooled induced pluripotent stem cells

Molly Smullen; Meagan N Olson; Julia M Reichert; Pepper Dawes; Liam F Murray; Christina E Baer; Qi Wang; Benjamin Readhead; George M Church; Elaine T Lim; Yingleong Chan

doi:10.1016/j.crmeth.2023.100570

Reliable multiplex generation of pooled induced pluripotent stem cells

Cell Rep Methods. 2023 Sep 25;3(9):100570. doi: 10.1016/j.crmeth.2023.100570. Epub 2023 Aug 31.

Authors

Affiliations

¹ Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
² Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
³ Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
⁴ ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA.
⁵ Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
⁶ Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA. Electronic address: rigel.chan@umassmed.edu.

Abstract

Reprogramming somatic cells into pluripotent stem cells (iPSCs) enables the study of systems in vitro. To increase the throughput of reprogramming, we present induction of pluripotency from pooled cells (iPPC)-an efficient, scalable, and reliable reprogramming procedure. Using our deconvolution algorithm that employs pooled sequencing of single-nucleotide polymorphisms (SNPs), we accurately estimated individual donor proportions of the pooled iPSCs. With iPPC, we concurrently reprogrammed over one hundred donor lymphoblastoid cell lines (LCLs) into iPSCs and found strong correlations of individual donors' reprogramming ability across multiple experiments. Individual donors' reprogramming ability remains consistent across both same-day replicates and multiple experimental runs, and the expression of certain immunoglobulin precursor genes may impact reprogramming ability. The pooled iPSCs were also able to differentiate into cerebral organoids. Our procedure enables a multiplex framework of using pooled libraries of donor iPSCs for downstream research and investigation of in vitro phenotypes.

Keywords: CP: Stem cell; bioinformatics; deconvolution; differentiation; flow cytometry; genomics; iPSCs; multiplex; organoids; reprogramming; sequencing.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Algorithms
Cell Line
Genes, Immunoglobulin
Induced Pluripotent Stem Cells*
Pluripotent Stem Cells*

Abstract

Publication types

MeSH terms

Grants and funding