Differential Expression and the Mouse Gut-Brain Axis

Overview

This module introduces students to differential expression analyses using the R programming language. Previous programming experience is helpful but not necessary. Students will work with real data from a mouse RNA-seq study to explore how the gut-brain axis might impact symptoms in Autism Spectrum Disorder.

This module is a companion and expansion to the C-MOOR RNA-seq miniCURE. It can be used as a stand-alone activity or as part of a broader miniCURE experience. Students do not have to have completed the miniCURE in order to use the stand-alone guide. If you are using the RNA-seq miniCURE in your class, this module adds an additional RNA-seq dataset that is suitable for an independent research project.

You can find out more about the RNA-seq miniCURE and other C-MOOR activities at the C-MOOR website. An online guide to the miniCURE is here.

Duration:

Learning Objectives

1. Explore differential expression data in mice.

2. Identify genes that are differentially expressed in an RNA-seq dataset.

3. (Optional) Formulate and test a hypothesis about differential expression of genes as a result of the gut-brain axis.

Materials and Setup

• Students will need either:

  • An internet connection for this activity as written (using Posit Cloud)
  • A local installation of R or RStudio (with data downloaded and tidyverse package installed ahead of time)

• Required R package: tidyverse

• Data hosting:

  • Comparing gene expression between ASD and control mice, both brain regions
  • Comparing gene expression between ASD and control mice, prefrontal cortex only
  • Comparing gene expression between ASD and control mice, striatum only
  • Comparing gene expression between prefrontal cortex and striatum, all mice
  • Comparing gene expression between prefrontal cortex and striatum, only ASD mice
  • Comparing gene expression between prefrontal cortex and striatum, only control mice

• If you are using this as a stand-alone activity: download the R student activity as:

  • Web page
  • Quarto (qmd)
  • Word (docx)
  • Google Doc - coming soon!

• If you are using this as an extension of the C-MOOR miniCURE: download the R student activity as:

  • Web page
  • Quarto (qmd)
  • Word (docx)
  • Google Doc - coming soon!

• Google Slides presentation available for borrowing images here.

• Answer key available here.

Scientific Topics

The activity uses data from a published research study “Human Gut Microbiota from Autism Spectrum Disorder Induces Behavioral Deficits in Mice.” Students will gain exposure to the following:

• Differential expression: the process where different cells within an organism, even those with the same DNA, express different genes, with some genes being expressed or “turned on”, while others are “turned off”

• Gut-brain axis: the proposed connection between the gut microbiome and gene expression in the brain

• Autism Spectrum Disorder: a neurological disorder that affects behavioral and social interactions

• Prefrontal cortex: the part of the brain that is primarily in charge of decision making, reasoning, personality, maintaining social appropriateness, and other complex behaviors that fall under the umbrella of executive functions

• Striatum: the part of the brain involved in motor control and cognitive tasks like reward processing, decision-making, and social interactions

Outline for Stand-Alone Activity

• Part 1: Background and Setup

• Part 2: Exploring Differential Expression Data

• Part 3: Exploring Differential Expression of Individual Genes

Outline for RNA-seq miniCURE Extension

• Background and Setup

• Exploring Differential Expression Data

• Creating Lists of Differentially Expressed Genes

• Cluster Analysis of Gene Lists