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Illustration of a cerebral organoids in a cell culture dish derived from human brain cells

New Screening System Identifies Genetic Cause of Microcephaly

A new high-throughput screen has identified a genetic cause of a brain disorder associated with Zika virus

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Miriam Bergeret, MSc

Miriam Bergeret, MSc, is Today's Clinical Lab's managing editor.

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Published:Dec 31, 2020
|Updated:Jan 25, 2021
|2 min read

By developing a new high-throughput genetic screening method called CRISPR-LIneage tracing at Cellular resolution in Heterogenous Tissue (CRISPR-LICHT), researchers have identified a genetic cause of a developmental condition called microcephaly, where babies are born with a small head and brain, usually accompanied by intellectual disability. In recent years, microcephaly has been associated with Zika virus infection during the first trimester of pregnancy.

Recently published in Science, the results arose from a series of genetic screening experiments in 3D human brain organoids grown for 40 days, a period of time equivalent to the first trimester of pregnancy. By combining CRISPR-Cas9 and barcoded cellular lineage tracing, CRISPR-LICHT can be used to delete a selection of genes then track which deletions affect the organoids.

Of 172 microcephaly gene candidates included in the screen, 25 were found to be involved in cell proliferation, most of which play a role in cell division and the DNA damage response. 

To characterize other gene pathways that could be involved in microcephaly, the researchers then focused on Immediate Early Response 3 Interacting Protein 1 (IER3IP1), which encodes a small endoplasmic reticulum (ER) protein. Deletion of IER3IP1 led to smaller brain organoids compared to controls, and while reintroducing wildtype IER3IP1 restored normal function, introducing a mutated version of IER3IP1 found in microcephaly patients did not, demonstrating that this mutation is directly involved in the condition.

Organoids lacking IER3IP1 showed increased ER stress and decreased protein synthesis due to the unfolded protein response, interfering with neuronal development. The new research helps solidify the genetic link between microcephaly and the unfolded protein response, which is known to contribute to Zika virus-associated microcephaly.

According to Yale neuroscientists, with 600 genes listed in the Developmental Brain Disorder Gene Database, CRISPR-LICHT could be used to study other neurodevelopmental conditions, as well as to conduct high-throughput genetic screens in other 3D organoid systems.