Culture Dish: Setting a Standard in Neuroscience Research

A new research resource makes it easier for scientists to model neurodegenerative diseases in a dish, catalyzing progress toward effective preventions and treatments. It consists of a collection of stem cell lines engineered with genetic mutations linked to neurodegenerative diseases. Researchers can use these cells to investigate how genetic changes lead to cell damage in Alzheimer’s, Parkinson’s and related disorders.

The resource is the result of a collaboration between the U.S. National Institutes of Health’s Center for Alzheimer’s and Related Dementias (CARD), the Jackson Laboratories (JAX), and researchers affiliated with the Chan Zuckerberg Initiative’s Neurodegeneration Challenge Network (NDCN).

The collaboration makes use of induced human pluripotent stem cells (iPSCs), which are stem cells reprogrammed from skin or blood samples. Creating stem cells this way allows scientists to study disease-relevant cell types in a petri dish. Like a caterpillar transforming into a butterfly, iPSCs can undergo a metamorphosis that changes their identity. Using a drug cocktail, researchers can coax the stem cells into becoming almost any cell type, including brain cells.

A collection of iPSC lines related to Alzheimer’s disease, Parkinson’s and Frontotemporal Degeneration launched this month at JAX. These cell lines were developed by researchers who are part of CARD’s iPSC Neurodegenerative Disease Initiative (iNDI). The collection will grow to more than 400, becoming the world’s largest iPSC genome engineering project, with cell lines containing mutations related to Amyotrophic Lateral Sclerosis (ALS), triplet repeat disorders like Huntington’s disease, and other neurodegenerative conditions.

Some scientists are already using iPSCs to model neurodegeneration in a dish. However, the neuroscience community has yet to coalesce around a reference cell line — a go-to standard that would promote reproducibility and collaboration in the field and ultimately accelerate biomedical research. iNDI aims to change that. iNDI researchers have selected a high-quality reference cell line and used it to generate disease-related iPSC lines that are now available to the worldwide scientific community at low cost via JAX Mice, Clinical & Research Services.

NDCN researchers assisted with iNDI’s development, as part of an effort to generate tools, data, resources, and approaches for neuroscience research that will benefit the whole research community. Continue reading to learn about our grantees and the research iNDI is making possible for them.

Sarah Cohen, University of North Carolina at Chapel Hill

Organelles moving within developing neurons. Labeled organelles are: nucleus, blue; lysosomes, cyan; mitochondria, green; Golgi, yellow; peroxisomes, orange; endoplasmic reticulum, red; lipid droplets, magenta. Photo courtesy of Maria Clara Zanellati.

Peering through a microscope in Sarah Cohen’s lab is like looking at a rainbow. Cohen uses a powerful imaging technique that can simultaneously capture different colors of light within live human cells. Cohen can label specialized structures called organelles, including the nucleus, energy-producing mitochondria, and lipid droplets, to emit different colors. Using her microscope, she can watch seven different organelles move and interact with each other, and measure their number, size, shape, and speed.

Tracking organelle dynamics is useful for understanding cells’ inner workings — especially human cells that are hard to access, such as neurons. It could also illuminate what goes wrong at the cellular level in neurodegenerative diseases. Evidence is mounting that the function and dynamics of organelles change in diseases such as Alzheimer’s, Parkinson’s, and ALS.

“We’re trying to detect differences in organelle morphology or communication in each type of neurodegeneration and also whether they have anything in common,” said Cohen, who is working on a NDCN Collaborative Pairs Pilot Project with Mohanish Deshmukh, an expert in modeling disease with iPSCs.

Cohen and Deshmukh are tapping into the iNDI collection to study how organelles change as immature cells develop into specialized cell types, such as neurons and astrocytes. They plan to conduct similar experiments using cells carrying genetic mutations associated with neurodegenerative diseases, including the APOE4 variant found in some people with Alzheimer’s.

What is vital about the iNDI collection is that all the cells have the same genetic background, said Cohen. This makes it much easier to interpret the results of experiments carried out in different cells.

“Traditionally, a lot of this research has used patient-derived iPSCs, so every cell line is unique, and it’s really hard to compare them. Now, we can directly compare the effects of different [disease-related] mutations because that’s the only thing changing,” she said.

Florian Merkle, University of Cambridge

Neurons differentiated from the KOLF2.1J cell line stained for DNA (blue) and various proteins, including the synaptic protein synapsin (green). Photo courtesy of Florian Merkle.

Florian Merkle helped lead the effort to select iNDI’s reference cell line, known as KOLF2.1J, which is being used to generate iPSCs for modeling neurodegenerative diseases. The cells are available to researchers worldwide, via Jackson Labs, breaking down barriers that usually limit access to such tools.

Merkle is the recipient of an NDCN Ben Barres Early Career Acceleration Award to unravel the connections between obesity, metabolism and neurodegeneration in mouse models and neurons, astrocytes, and microglia grown from iPSCs. KOLF2.1J has already become the “workhouse” cell line in his lab.

To identify the best cell line to serve as the foundation of the iNDI collection, Merkle and others studied a handful of cell lines and compared their characteristics, including survival, growth, gene expression, and how readily they could be edited. The goal was to identify a star performer.

The team posted the results of the selection process to the bioRxiv preprint server. “To our knowledge, this is the first study to broadly and deeply study the genomes and functional behavior of a collection of cell lines,” said Merkle, who believes it could provide a roadmap for other researchers who want to develop similar collections.

He said the iNDI team is building on its experience with KOLF2.1J to build out the catalog with cell lines that reflect human diversity, including lines from different sex chromosomes and genetic ancestries.

Coalescing around a single, high-quality cell line could be transformative, promoting reproducibility and collaboration, said Merkle. Specifically, the iNDI cell lines will allow studies to be replicated by other researchers and facilitate data sharing and integration across research groups, cell types, and disease models. In fact, Merkle said that is already happening.

Deborah Kronenberg-Versteeg, Hertie Institute for Clinical Brain Research, University of Tuebingen

KOLF2.1-derived microglia in mouse brain tissue. Photo courtesy of Deborah Kronenberg-Versteeg.

The immune system touches every part of the body, including the brain, which hosts immune cells called microglia. Naturally, those cells play a role in the brain’s response to infection. But it is increasingly clear that they are also involved in brain development and everyday function — as well as in neurodegenerative diseases like Alzheimer’s.

Deborah Kronenberg-Versteeg wants to understand the crosstalk between microglia and neurons, and how it plays out in aging and neurodegeneration.

Researchers have traditionally relied on animal models to study the brain, but they only approximate human biology. Instead, Kronenberg-Versteeg is taking advantage of new tools like the iNDI cell lines to create chimeras — part human brain tissue, part iPSCs. These chimeras are a powerful platform for studying how neurons and microglia interact, especially in Alzheimer’s disease.

The research team is differentiating cells from the iNDI collection into neurons and microglia as part of Kronenberg-Versteeg’s NDCN Collaborative Pairs Pilot Project with Henner Koch, a neuroscientist at RWTH Aachen University.

“More work is underway to investigate the Alzheimer’s disease-related variants in these chimeric human brain slice cultures,” said Kronenberg-Versteeg.

“The iNDI project is already emerging as a real game-changer for the scientific community,” she added. “It has opened up a whole plethora of questions that we can now start to investigate more closely, for example, whether there is a ‘dosage effect’ of having one or two copies of the respective genetic variant.”

Learn more about CZI’s Neurodegeneration Challenge Network.

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Chan Zuckerberg Initiative Science

Chan Zuckerberg Initiative Science

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.