RNA velocity of single cells

Gioele La Manno et al. 2018

Seminar by

Muhammad Hamid

14 Sep 2021
 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 2

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 3

 Outline

Bulk vs. single cell analogy

Photo by Element5 Digital on Unsplash

RNA velocity of single cells Muhammad Hamid 4

 What is single cell RNA sequencing?

Single cell data can identify cell subtypes

Zheng et al. 2016

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 What is single cell RNA sequencing?

Ehud Shapiro et al. 2013

RNA velocity of single cells Muhammad Hamid 6

 What is single cell RNA sequencing?

Valentine Svensson et al. 2018

RNA velocity of single cells Muhammad Hamid 7

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 8

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 9

 Motivation

RNA velocity of single cells Muhammad Hamid 10

 From static to dynamic

SIB Bioinformatics Awards 2019: RNA Velocity and the Velocyto tool

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 Motivation

https://scvelo.readthedocs.io/DynamicalModeling/

RNA velocity of single cells Muhammad Hamid 12

 Motivation

https://scvelo.readthedocs.io/DynamicalModeling/

RNA velocity of single cells Muhammad Hamid 13

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 14

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 15

 RNA Velocity from RNA metabolism

RNA velocity of single cells Muhammad Hamid 16

 RNA Velocity

u - unspliced/intronic/unprocessed/pre-
mRNA abundance
s- spliced/exonic/processed/mature
mRNA abundance

La manno et al 2018, Bergen et al 2019, Ziesel et al 2011

RNA velocity of single cells Muhammad Hamid 17

 RNA Velocity

transcription (state-
dependent) splicing

u - unspliced/intronic/unprocessed/pre-
mRNA abundance
s- spliced/exonic/processed/mature
mRNA abundance

degradation

La manno et al 2018, Bergen et al 2019, Ziesel et al 2011

RNA velocity of single cells Muhammad Hamid 18

 RNA Velocity as a vector in high-dimensional gene expression space

RNA velocity of single cells Muhammad Hamid 19

 RNA Velocity as a vector in high-dimensional gene expression space

RNA velocity of single cells Muhammad Hamid 20

 Branching lineages: hippocampus development (10x Chromium)

Unspliced
Unspliced

Spliced

RNA velocity of single cells Muhammad Hamid 21

RNA velocity of single cells Muhammad Hamid 22
RNA velocity of single cells Muhammad Hamid 23
RNA velocity of single cells Muhammad Hamid 24
RNA velocity of single cells Muhammad Hamid 25
RNA velocity of single cells Muhammad Hamid 26
 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 27

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 28

 Velocyto

 Computational framework for robust inference of

RNA velocity

 Implemented two pipelines:

Velocyto.r Velocyto.py

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 Velocyto

• Available at http://velocyto.org

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 Velocyto

RNA velocity of single cells Muhammad Hamid 31

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 32

 Outline

1 What is single cell RNA sequencing?

2 Motivation
3 RNA Velocity
4 Velocyto
5 Summary

RNA velocity of single cells Muhammad Hamid 33

 Summary

 Measures first derivative of RNA abundance

 Uses only standard scRNA-seq data
 Any organism, including human
 Scalable to whole organisms, including human
 Powerful computational properties
 Reveals the complete manifold without genetic
labeling

RNA velocity of single cells Muhammad Hamid 34

Thank you!
 Why this would work at all?

• There was a bit of a mystery of why this would work at all

because it's all based on distinguishing unspliced from an
spliced RNA.
• All these methods use oligodT priming
• Detect polyadenylated RNA always spliced
• It turns out all of these protocols that are used for scRNA
honesty have a prominent artifact where there is a lot of
internal priming on intronic sequences.
• That's why we can detect it and actually it's a happy
coincidence that kind of technological limitation of standard
single cell on a secret protocols actually made possible and a
really interesting new way of studying cell behavior.
-Author: Sten Linnarsson

RNA velocity of single cells Muhammad Hamid 36

 Appendix

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 Appendix

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 Appendix

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 Appendix

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 References

1. Zheng, G., Terry, J., Belgrader, P. et al. Massively parallel digital transcriptional profiling of
single cells. Nat Commun 8, 14049 (2017). https://doi.org/10.1038/ncomms14049
2. Shapiro E, Biezuner T, Linnarsson S. Single-cell sequencing-based technologies will
revolutionize whole-organism science. Nat Rev Genet. 2013 Sep;14(9):618-30. doi:
10.1038/nrg3542. Epub 2013 Jul 30. PMID: 23897237.
3. Svensson, V., Vento-Tormo, R. & Teichmann, S. Exponential scaling of single-cell RNA-seq in
the past decade. Nat Protoc 13, 599–604 (2018). https://doi.org/10.1038/nprot.2017.149
4. La Manno, G., Soldatov, R., Zeisel, A. et al. RNA velocity of single cells. Nature 560, 494–498
(2018). https://doi.org/10.1038/s41586-018-0414-6
5. Bergen, V., Lange, M., Peidli, S. et al. Generalizing RNA velocity to transient cell states through
dynamical modeling. Nat Biotechnol 38, 1408–1414 (2020). https://doi.org/10.1038/s41587-
020-0591-3
6. Zeisel A, Köstler WJ, Molotski N, Tsai JM, Krauthgamer R, Jacob-Hirsch J, Rechavi G, Soen Y,
Jung S, Yarden Y, Domany E. Coupled pre-mRNA and mRNA dynamics unveil operational
strategies underlying transcriptional responses to stimuli. Mol Syst Biol. 2011 Sep 13;7:529.
doi: 10.1038/msb.2011.62. PMID: 21915116; PMCID: PMC3202801.
7. Dynamical Modeling - https://scvelo.readthedocs.io/DynamicalModeling/

RNA velocity of single cells Muhammad Hamid 41