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Single-Cell RNA-Seq Analysis of Human iPSC-Derived Motor Neurons Resolves Early and Predictive ALS Signatures

79 Pages Posted: 14 May 2020 Sneak Peek Status: Under Review

See all articles by Ritchie Ho

Ritchie Ho

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute; Cedars Sinai Medical Center - Center for Neural Science and Medicine

Michael J. Workman

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Pranav Mathkar

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Kathryn Wu

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Kevin J. Kim

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Jacqueline G. O'Rourke

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Mariko Kellogg

Illumina, Inc.

Valerie Montel

Illumina, Inc.

Maria G. Banuelos

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Olubankole Aladesuyi

University of California, San Diego (UCSD) - Department of Neurosciences

Sandra Diaz Garcia

University of California, San Diego (UCSD) - Department of Neurosciences

Daniel Oheb

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Steven Huang

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

Irena Khrebtukova

Illumina, Inc.

Lisa Watson

Illumina, Inc.

John Ravits

University of California, San Diego (UCSD) - Department of Neurosciences

Kevin Taylor

Illumina, Inc.

Robert H. Baloh

Cedars Sinai Medical Center - Department of Neurology

Clive N. Svendsen

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

More...

Abstract

Induced pluripotent stem cell (iPSC) derived neural cultures from amyotrophic lateral sclerosis (ALS) patients can reflect disease phenotypes targetable by treatments. However, widely used differentiation protocols produce mixtures of progenitors, neurons, glia, and other cells at various developmental stages and rostrocaudal neural tube segments. Here we present a methodology using single-cell RNA sequencing analysis to distinguish cell type expression in C9orf72 ALS, sporadic ALS, control, and genome-edited cultures across multiple subjects, experiments, and commercial platforms. Combinations of HOX and developmental gene expression with global clustering classified rostrocaudal, progenitor, and mantle zone fates. This demonstrated that iPSC-differentiated cells recapitulate fetal hindbrain and spinal cord development and resolved early, reproducible, and motor neuron-specific signatures of familial and sporadic ALS. This includes downregulated ELAVL3 expression, which persists into disease endstages. Single-cell analysis thus yielded predictive ALS markers in other human and mouse models which were otherwise undiscovered through bulk omics assays.

Keywords: Single-cell RNA-seq, iPSC, ALS, ELAVL3

Suggested Citation

Ho, Ritchie and Workman, Michael J. and Mathkar, Pranav and Wu, Kathryn and Kim, Kevin J. and O'Rourke, Jacqueline G. and Kellogg, Mariko and Montel, Valerie and Banuelos, Maria G. and Aladesuyi, Olubankole and Garcia, Sandra Diaz and Oheb, Daniel and Huang, Steven and Khrebtukova, Irena and Watson, Lisa and Ravits, John and Taylor, Kevin and Baloh, Robert H. and Svendsen, Clive N., Single-Cell RNA-Seq Analysis of Human iPSC-Derived Motor Neurons Resolves Early and Predictive ALS Signatures. Available at SSRN: https://ssrn.com/abstract=3586565 or http://dx.doi.org/10.2139/ssrn.3586565
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Ritchie Ho (Contact Author)

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute ( email )

8700 Beverly Blvd.
Los Angeles, CA
United States

Cedars Sinai Medical Center - Center for Neural Science and Medicine ( email )

8700 Beverly Blvd.
Los Angeles, CA
United States

Michael J. Workman

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Pranav Mathkar

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute ( email )

8700 Beverly Blvd.
Los Angeles, CA
United States

Kathryn Wu

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Kevin J. Kim

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Jacqueline G. O'Rourke

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute ( email )

8700 Beverly Blvd.
Los Angeles, CA
United States

Mariko Kellogg

Illumina, Inc.

5200 illumina way
san diego, CA 92122
United States

Valerie Montel

Illumina, Inc.

5200 illumina way
san diego, CA 92122
United States

Maria G. Banuelos

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Olubankole Aladesuyi

University of California, San Diego (UCSD) - Department of Neurosciences

9500 Gilman Dr.
La Jolla, CA 92093
United States

Sandra Diaz Garcia

University of California, San Diego (UCSD) - Department of Neurosciences

9500 Gilman Dr.
La Jolla, CA 92093
United States

Daniel Oheb

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Steven Huang

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

Irena Khrebtukova

Illumina, Inc.

5200 illumina way
san diego, CA 92122
United States

Lisa Watson

Illumina, Inc.

5200 illumina way
san diego, CA 92122
United States

John Ravits

University of California, San Diego (UCSD) - Department of Neurosciences

9500 Gilman Dr.
La Jolla, CA 92093
United States

Kevin Taylor

Illumina, Inc.

5200 illumina way
san diego, CA 92122
United States

Robert H. Baloh

Cedars Sinai Medical Center - Department of Neurology

127 S. San Vicente Blvd.
Advanced Health Sciences Pavilion, Sixth Floor, A6
Los Angeles, CA 90048
United States

Clive N. Svendsen

Cedars Sinai Medical Center - Board of Governors Regenerative Medicine Institute

8700 Beverly Blvd.
Los Angeles, CA
United States

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