Brain organoids without immune cells may miss the real story of neurodegeneration

Brain organoids have become one of the most celebrated tools in modern neuroscience. Grown from human induced pluripotent stem cells, these miniature, three-dimensional assemblies of neural tissue allow researchers to study human brain development and neurodevelopmental disorders in a dish, capturing cellular diversity and tissue-level interactions that flat, two-dimensional cultures simply cannot reproduce. Yet according to a new Perspective published in PLOS Biology by Shiying Liu and Shi-Yan Ng of the Genome Institute of Singapore at A*STAR, the field is making a systematic mistake when it applies the same technology to neurodegenerative diseases such as Alzheimer’s disease and amyotrophic lateral sclerosis. The authors argue that most current organoid models of neurodegeneration are built around a reductionist formula: introduce a disease-associated mutation, generate neurons, and measure neuronal survival or function. That formula, they contend, leaves out the very cells that may drive the disease in the first place.

The core of the argument is that neurodegeneration is fundamentally different from neurodevelopment. Many neurodevelopmental disorders arise from intrinsic defects in neural stem cells or early neurons, so neuron-focused organoids can be genuinely informative. Neurodegenerative diseases, by contrast, unfold over decades of aging and emerge from a combination of intrinsic neuronal defects and dynamic, changing interactions among neurons, glia, vascular cells, immune cells, and their surrounding microenvironment. Neuroinflammation and vascular dysfunction are hallmarks of most neurodegenerative diseases, and Liu and Ng insist that immune and vascular cells should therefore be treated as fundamental components of organoids intended to model neurodegeneration, not as optional extras bolted on for realism.

A growing body of evidence supports this broader view. Although specific subtypes of neurons are the cells that ultimately die, neuronal death is unlikely to mark the beginning of the disease process. Studies cited in the Perspective show that astrocytes, oligodendrocytes, microglia, and endothelial cells all undergo disease-associated changes before overt neurodegeneration becomes visible. In mouse models of juvenile neuronal ceroid lipofuscinosis, low-level glial activation precedes late-onset neurodegeneration; in mice carrying a frontotemporal dementia-causing CHMP2B mutation, early microgliosis appears before neuronal loss and behavioral impairment. Genetic analyses of complex brain traits have also pointed to oligodendrocyte involvement in Parkinson’s disease etiology, while blood-brain barrier breakdown and endothelial dysfunction have been documented in Alzheimer’s disease and related disorders.

This reframing carries a profound implication for drug development. Neurodegeneration is increasingly understood as the consequence of both cell-autonomous and non-cell-autonomous processes, in which pathological changes in one cell type can initiate or amplify dysfunction in another. If that is true, it may help explain why therapeutic strategies focused primarily on protecting neurons have yielded limited clinical success despite decades of intensive research. Protecting neurons in isolation may be insufficient if the disease is initiated or sustained by interactions between multiple cell types. The authors argue that nonneuronal cells and pathological cell-cell interactions should be considered legitimate therapeutic targets in their own right, rather than background noise in a neuron-centric narrative.

Among the nonneuronal cells implicated in neurodegeneration, microglia receive particular attention in the Perspective. Microglia are the resident immune cells of the central nervous system, responding to changes in the extracellular environment by adopting a continuum of phenotypes that ranges from pro-inflammatory to anti-inflammatory. They are highly heterogeneous, displaying diverse molecular and functional states that emerge in response to disease, injury, or shifts in the local microenvironment. For many years, microglia were regarded primarily as responders to neuronal injury, with activated microglia considered a consequence of neurodegeneration rather than a primary contributor. That view, the authors note, has changed substantially, and the change has been driven largely by human genetics.

The genetic evidence is compelling. Mutations in TREM2 were first identified as genetic risk factors for Alzheimer’s disease in 2012. Within the brain, TREM2 is expressed primarily in microglia, where it functions as a cell surface receptor that senses cellular damage and drives phagocytosis. Studies have now convincingly shown that replacing Trem2-mutant microglia with Trem2 wild-type microglia reduces disease phenotypes in a mouse model of Alzheimer’s disease, a result that suggests microglial dysfunction actively influences the initiation and progression of neuronal disease phenotypes. The logical conclusion is stark: if microglial dysfunction can shape neurodegenerative disease progression, then an organoid that excludes microglia cannot replicate a key cellular process it is supposed to model.

These findings have direct consequences for therapeutic discovery pipelines. Most phenotypic screening in neurodegeneration currently relies on neuronal mono-cultures, with compounds evaluated against relatively simple endpoints such as neuronal survival, neurite morphology, or protein aggregation. Such assays are amenable to high-throughput screening, but they rest on the assumption that the therapeutic target resides within the neuron. What if it does not? A drug candidate that protects neurons in isolation may fail in vivo because it never corrects the pathological neural microenvironment. If diseases such as Alzheimer’s and motor neuron disease are driven at least in part by early dysfunction of nonneuronal cells like microglia, then screening paradigms built on neuronal mono-cultures may require fundamental re-evaluation, the authors warn.

The Perspective does not simply call for bigger, more complicated organoids. The next frontier, Liu and Ng argue, is not complexity for its own sake but disease relevance. If neuroinflammation is a fundamental component of pathogenesis, immune cells must be incorporated; if vascular dysfunction is central, endothelial cells should be too. The objective is not to recreate every component of the human brain but to reconstruct the cellular interactions necessary to model the disease process. To that end, the authors propose explicit benchmarks: at a minimum, organoids intended to model neurodegenerative diseases should contain relevant neuronal and astrocytic populations plus a functional neuroimmune component including microglia. Crucially, the mere presence of microglia should not be considered sufficient. These cells must exhibit appropriate maturation, spatial localization, and molecular states in response to the neural environment. Where vascular dysfunction is central to a particular disease, vascular components should similarly be included.

As organoid systems grow more sophisticated, the technologies needed to deconvolute multicellular interactions become equally important. Single-cell and spatial profiling can determine whether cellular states within organoids resemble those observed in human disease, while genetic and pharmacological perturbation can establish whether specific cell types or signaling pathways are causal rather than merely correlated with pathology. Whole-organoid imaging, automated phenotypic screening, and computational modeling can enable longitudinal interrogation of how disease-associated states emerge, interact, and propagate across the tissue. The authors envision scalable small-molecule or CRISPR perturbation screens coupled with spatial and single-cell multi-omics and whole-organoid imaging, identifying perturbations that reverse disease-associated phenotypes and uncovering therapeutic targets for prioritization and in vivo validation. Recent work on vascularized neuroimmune organoids, in which extracts from Alzheimer’s disease patient brains induced multiple pathologies, hints at what such platforms could achieve for disease modeling and drug discovery.

Ultimately, the authors conclude, the value of next-generation organoids will not be measured by how closely they resemble the human brain anatomically, but by whether they enable reconstruction of the cellular interactions that drive disease. For neurodegeneration, microglia are central to that equation. An organoid without microglia might still be a useful model for some questions, but for diseases in which neuro-immune dysfunction is integral to pathogenesis, it should no longer be considered a complete model of neurodegeneration. No disease model can fully recapitulate human disease, the authors acknowledge, and the benchmark should always be a clear definition of the biological questions a model is designed to address, together with honest acknowledgment of its limitations. But as the genetics, pathology, and therapeutic failures of neurodegeneration converge on the same message, the era of the neuron-only brain organoid may be drawing to a close, and with it, perhaps, a new chapter in the search for effective treatments.

Subject of Research: Cellular diversity requirements for human neural organoid models of neurodegenerative disease

Article Title: Cellular diversity in neural organoids is critical for neurodegenerative disease modeling

Article References: Liu, S., & Ng, S.-Y. (2026). Cellular diversity in neural organoids is critical for neurodegenerative disease modeling. PLOS Biology, 24(10), e3004074. https://doi.org/10.1371/journal.pbio.3004074

Image Credits: AI Generated

DOI: 10.1371/journal.pbio.3004074

Keywords: brain organoids, neurodegeneration, microglia, neuroinflammation, Alzheimer's disease, iPSC, TREM2, vascular dysfunction, drug screening, glial cells, PLOS Biology, disease modeling