New Gene Expression Technologies Improve Understanding of ALS

Post by Flora Moujaes

What's the science?

Amyotrophic lateral sclerosis (ALS) is a type of motor neuron disease. Motor neuron diseases are caused by the gradual deterioration of motor neurons found in the brain and spinal cord. As the motor neurons die, they can no longer control voluntary movement and the muscles begin to atrophy. The cause of the disease and the mechanisms that underlie ALS are still poorly understood, though previous work has indicated genetic factors play a role. This week in Science, Maniatis and colleagues combined new technologies for mapping gene expression that take into account spatial location (where the genes are expressed), and computational modelling, to provide new insights into the mechanisms that contribute to ALS.

How did they do it?

Researchers can determine whether a gene is activated or ‘expressed’ in a cell by examining messenger RNA (mRNA). mRNA is essentially a template for DNA: it is a set of molecules copied from the DNA code that tells the cell how to behave. There are thousands of RNA molecules per cell, and together they make up the mRNA, or ‘transcriptome’. Thus, the transcriptome reflects the genes that are being actively expressed in a cell at any given time. Standard methods to examine mRNA involve extracting all the RNA molecules from a tissue biopsy, and analysing them together. This results in an average representation of all the genes expressed in that tissue, however, spatial information of where the particular genes are expressed within the tissue is lost. Spatial transcriptomics enables you to capture the mRNA in the tissue while retaining the information about where in the tissue this mRNA is expressed. The method involves placing tissue samples on a glass slide covered in tiny spots. These tiny spots contain DNA strands with built in address labels that 1) capture and copy the mRNA and 2) encode a unique ‘barcode’ in the copy that corresponds to the spatial location of the spot on the slide.

The researchers used spatial transcriptomics to examine gene expression in 1) 56 ALS mice, 2) 11 control mice, and 3) post-mortem spinal cord tissue from seven deceased ALS patients. They collected over 76,000 spatial gene expression measurements (or ‘spots’) from 1,165 mouse tissue sections, and over 60,000 spatial gene expression measurements from 80 human tissue sections. The mice were examined at three disease time points: onset, symptomatic, and end-stage, which enabled the researchers to track gene expression over time. The human samples were collected from either end of the spine, which allowed the researchers to examine how ALS pathology spreads, as ALS symptoms usually appear in one part of the body before going on to cause widespread paralysis. The researchers then used computational methods to combine the spatial location and gene expression information.

What did they find?

The researchers produced a multidimensional gene expression atlas which they made available through an interactive data exploration portal at https://als-st.nygenome.org/ .

One of the main hypotheses explored in this study was that even though motor neurons are the most vulnerable in ALS, neighbouring cells such as microglial cells play a key role in the disease. Microglial cells are of particular interest to ALS as they are involved in removing damaged neurons. This study indicated that microglia dysfunction occurs well before the onset of ALS symptoms. This is important as it helps us understand how mutations may disrupt the function of both neuronal and non-neuronal cells, and how the impaired interactions between the different cell types in the nervous system may then lead to motor neuron loss in ALS. To further explore the spatiotemporal dynamics of microglial activation, the researchers examined two genes that had previously been indicated in ALS: TREM2 and TYROBP. They found that TREM2 and TYROBP were both expressed at higher levels by microglial cells; in particular spinal cord regions of mice with ALS symptoms. Thus, they were able to refine our understanding of such gene expressions, showing TREM2- and TYROBP-mediated signalling is an early step in disease-relevant changes in microglial gene expression.

What's the impact?

This is the largest study to examine spatial transcriptomics in mice and humans with ALS. This study highlights the value of examining gene expression in individual cell types in relation to their wider spatial context. The vast dataset generated by this study may aid with the development of therapeutic interventions for ALS and earlier diagnostic markers. This is especially important given that ALS currently affects over 200,000 patients worldwide and results in a life expectancy of up to 5 years following diagnosis.  In addition, the methods used in this study could be extended to examine other neurodegenerative diseases including Alzheimer’s, Parkinson’s, and Huntington’s disease.

Maniatis et al. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science (2019). Access the original scientific publication here.