2021 Annual Meeting Report: An Introduction to High-Throughput Single Cell Assays for Toxicology

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By Sarah Carratt posted 03-25-2021 12:14

  

In an era of rapidly advancing technology, the learning curve required to incorporate new techniques into your research can be intimidating. The terminology alone can be a barrier to entry as you work through new protocols and read up on the available literature. Even as someone who uses single cell RNAseq and ATAC-seq in my research, it can be difficult to follow along with talks introducing new single cell technology.

The Workshop Session “The Methodological Road toward Single Cell High-Throughput Transcriptomics” during the Virtual SOT Annual Meeting introduced new technology and described advantages of emerging single cell systems. With my research in the field of cancer therapeutics and carcinogenesis, I came into this session with a particular interest in the second presentation, by Dr. José McFaline-Figueroa, who spoke on the subject of drug-induced molecular landscapes.

One of the advantages of using single cell technologies in drug screening is that you are able to capture the heterogeneity of patient responses to therapy—both between different patients and within tumors. Using high-throughput screens increases the amount of information you can achieve with a single experiment. In his talk, Dr. McFaline-Figueroa discussed sci-Plex multiplexing technology and demonstrated how you can use single cell technology to identify drug-induced transcriptional signatures. Incredibly, he was able to use his high-throughput screen to analyze 4,608 conditions (3 cell lines x 188 compounds x 4 doses x 2 replicates) in ONE experiment.

I encourage anyone who is unfamiliar with single cell technologies to give this talk a try. Dr. McFaline-Figueroa does a good job of walking us through his data and defining terms as he goes. In this blog, I’ve included key definitions for reference as you listen to his presentation. A disclaimer: this technology is still very new to me and I welcome anyone with more expertise to comment with clarifications, additional definitions, or further discussion.

Definitions to Help Follow Along with This Talk

Single Cell

Transcriptomics

The study of RNA transcripts that are produced by the genome under specific circumstances or in a specific cell using high-throughput methods.

Combinatorial indexing

Cells are uniquely labeled using barcodes so that samples can be pooled and parsed out during analysis.

Multiplexing

The pooling of samples that received individual barcodes.

UMAP (Uniform Manifold Approximation and Projection)

A method of visualizing large, high-dimensional datasets.

Consensus trajectory

When analyzing UMAPs, the plots will not automatically align to compare conditions. A consensus plot allows for the multi-dimensional data to be plotted along the same trajectories and overlaid on the same graph.

Transcriptional EC50

The amount of drug needed to get to halfway through the consensus trajectory, or halfway through the transcriptional response.

Differential expression analysis

Analysis that allows for the quantification of changes in expression levels between experimental groups.

Sci-Plex

A high-throughput screen used to quantify global transcriptional responses to thousands of independent perturbations at single cell resolution.

Epigenetics

Histones

A family of basic proteins that associate with DNA in the nucleus and help condense it into chromatin.

Histone acetylation

Acetylation of histones alters accessibility of chromatin and allows DNA binding proteins to interact with exposed sites to activate gene transcription and downstream cellular functions.

Closed chromatin (euchromatin)

Conformation of chromatin that is compact and does not allow transcription factors to bind DNA.

Open chromatin (heterochromatin)

Conformation of chromatin that is permissible for transcription.

Cell Lines

K562

A human erythroleukemic cell line.

A549

An adenocarcinomic human alveolar basal epithelial cell line.

MCF7

A mammary gland breast cancer cell line.

Therapeutics

Trametinib

A MEK inhibitor.

Epothilon A/B

Inhibitors of microtubule function.

Rigosertib

Inhibitor of the PI3K/Akt pathway and activator of oxidative stress.

UNC0379

Inhibitor of N-lysine methyltransferase SETD8.

HDAC (histone deacetylase) inhibitors

Remove the acetyl groups from the lysine residues, leading to the formation of a condensed and transcriptionally silenced chromatin.

Pracinostat

An HDAC inhibitor.

Temozolomide

An alkylating agent.


This blog was prepared by an SOT Reporter and represents the views of the author. SOT Reporters are SOT members who volunteer to write about sessions and events in which they participate during the SOT Annual Meeting and ToxExpo. SOT does not propose or endorse any position by posting this article. If you are interested in participating in the SOT Reporter program in the future, please email Giuliana Macaluso.

Sessions delivered during the 2021 SOT Annual Meeting and ToxExpo will be available on the Virtual Meeting Platform on demand to registrants through May 31, 2021.


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