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A new tool allows researchers to simultaneously study the physical, genetic and electrical properties of individual neurons. The multipurpose tool, dubbed Patch-seq, could help autism researchers more efficiently classify neurons implicated in autism.
Scientists can sort neurons into types by separately analyzing their gene expression profiles, physical appearance and electrical firing patterns. But previous attempts to simultaneously probe all three features damaged the cells’ genetic material or characterized only a short list of genes.
Patch-seq, described in two papers from different labs on 21 December in Nature Biotechnology, sidesteps these pitfalls by protecting the cells’ RNA from damage up front, allowing researchers to relate a cell’s gene expression profile to its form and function1,2.
The method builds on a decades-old tool known as patch clamping. In this technique, researchers stimulate a cell and record the ions that pour out as it fires, using an electrode-containing pipette stuck to the cell surface. Neurons can be sorted into distinct cell types based on their signature firing patterns, offering clues to a cell’s role in the brain.
In the first paper, researchers isolated and cultured two types of sensory neurons from the mouse brain: elongated neurogliaform cells (eNGCs) and single bouquet cells (SBCs).
They bathed each individual cell in a solution that protects its genetic material from degrading during electrical stimulation. They then stimulated the cell for about two minutes before suctioning out its contents through the pipette. Next, they isolated and sequenced the cell’s RNA, picking up about 7,000 genes per cell.
A newly developed computer program identified each cell as an eNGC or an SBC by matching the Patch-seq gene expression data and recordings of neural activity to what is known about each cell type.
An analysis of 58 cells revealed that eNGCs and SBCs differ in their shape, firing patterns and gene expression profiles. For example, SBCs express many copies of an autism-linked gene called DPP6 and two others — NPAS1 and NPAS3 — in a class of gene regulators tied to cognitive disabilities in people with autism. The eNGCs express these molecules at much lower levels. These results finger SBCs, which integrate different types of sensory information, as possible contributors to autism.
In the second paper, researchers recorded from neurons in the mouse somatosensory cortex that express the chemical messenger cholecystokinin. These neurons may play a role in anxiety, mood disorders and schizophrenia.
In this case, the researchers protected the cells’ RNA by limiting the duration and intensity of the stimulation. Over 20 minutes, they alternated 5-millisecond pulses with pauses of the same duration.
They identified about 2,000 genes per cell, including genetic markers for ion channels and cell surface receptors. By comparing the list of genes each cell expressed with those in a published library of cell types, the researchers were able to sort the neurons into subtypes.