Microglia and other related immune cells are increasingly recognized as essential in central nervous system function and almost all neurological diseases (Li and Barres. 2018. Nature Reviews Immunology). Recent advances in single-cell genomic technologies also have revealed heterogeneous states of microglia that may underlie their multifaceted roles in health and disease. On the other hand, human genetics studies have unambiguously linked microglia-associated genes and regulatory elements to neurodegenerative diseases. These exciting discoveries raise numerous questions regarding the regulation and function of microglia in various contexts.
The Li Lab researches neuroimmunology, specifically microglial biology, intending to leverage cutting-edge genomic technologies alongside novel molecular and genetic tools to investigate neuro-immune interactions that impact brain structure and disease.
Current projects involve:
- Models: rodents (mainly mice)
- Techniques: mouse genetics, histology, imaging, single cell transcriptomics, epigenetics, primary cell culture, transplantation, flow cytometry and cell sorting
- Research topics: development, aging, neurodegenerative diseases
- Research questions: origin, gene regulation, plasticity and function of heterogeneous microglial states (see below for details)
We hope our research will not only address fundamental questions on how specific microglial states are generated and change, but also provide mechanistic insights into their roles in disease, ultimately paving a new avenue for the development of precise microglia-based interventions to treat devastating neurological diseases.
Microglial heterogeneity
Microglia, as central nervous system (CNS) parenchymal macrophages, are involved in a plethora of developmental and pathological processes, such as modulating neurogenesis, sculpting neural circuits, fine-tuning neural activity, promoting myelination, and interacting with protein aggregates. A fundamental question in the field has been how heterogeneous microglia are and to what extent this heterogeneity can be translated to functional differences. The Li Lab is one of the earliest adopters to employ an unbiased single-cell transcriptomic profiling approach to systematically assess microglial heterogeneity in developing and healthy adult brains (Li et al. 2019. Neuron). This work reveals that microglia shift from more functional heterogeneous states early in life to a more homogenous one in the adult under normal conditions, which paves the way for understanding their phenotypic alterations in disease and injury. Specifically, we identify a distinct subpopulation of microglia, named PAM (proliferative-region-associated microglia), which are transiently enriched in the white matter and neurogenic regions of the early postnatal brain. PAM are amoeboid in morphology, metabolically active, and highly phagocytic, and they share a conserved gene signature with DAM (disease-associated microglia) enriched in aging and neurodegenerative diseases. Following up on this initial characterization of PAM, we are investigating the ontogeny and molecular mechanisms that generate PAM, as well as their functionality in brain development.
Parallel to our work in development, we also are part of the Tabula Muris Consortium, a large collaborative effort aiming to use single-cell genomics to dissect cellular heterogeneity in all major organs of mice across the animals’ lifespan (Tabula Muris Consortium. 2018. 2020. Nature). We have generated deep single-cell RNA sequencing datasets for microglia from different brain regions in aging and parabiosis conditions that allow us to identify changes in microglia that contribute to brain aging and young plasma-mediated rejuvenation.
Plasticity of microglial states
As a major sentinel of the brain, microglia can quickly respond to changes in the microenvironment by adopting various reactive states. PAM, DAM, and WAM (white matter-associated microglia, mainly found during aging) are prominent examples of reactive microglial states, enriched in developing, diseased, and aging brains, respectively. Interestingly, compared to homeostatic microglia in a healthy adult brain, these reactive microglia all share a common gene signature, including an immune receptor gene, Clec7a. A fundamental key question in the field is how plastic these microglial states are over time. Given their transcriptomic similarity, is it possible that they represent microglia from the same lineage and are just manifestations of state switches in response to similar environmental signals?
To address this question, we have generated a novel inducible driver line Clec7a-CreERT that allows us to specifically label, track, and manipulate these reactive microglial states in developing, aging, and disease (Barclay et al. 2024. Immunity). Particularly, we show for the first time that DAM — at least during white matter degeneration — are highly plastic by returning to homeostasis when the disease is resolved. In this same acute disease model, we also demonstrate that DAM are neuroprotective for myelin repair. With this new tool, we can now track dynamic changes of similar microglial states, such as PAM and DAM, in many other conditions to understand the functional implications of these changes in shaping brain structure and pathology.
Transcriptional and epigenetic regulation
ScRNA-seq has firmly established a shared transcriptomic signature of PAM and DAM compared to homeostatic microglia, which includes upregulation of Clec7a, Apoe, Trem2, Itgax, CD63, CD9, Lpl, and downregulation of Tmem119, P2ry12, and Cx3cr1 among other genes. Interestingly, they also display context-dependent gene expression changes (Barclay et al. 2024. Immunity), suggesting convergent and divergent regulatory mechanisms. Trem2 and Apoe, the two strongest genetic risk factors for late-onset Alzheimer’s disease, are required for establishing a DAM expression profile in Alzheimer’s. In contrast, they are not required for generating PAM, despite the similar upregulation of these two genes in PAM during early postnatal development (Li et al. 2019. Neuron). The molecular mechanisms that control these reactive microglia states remain largely unknown.
Like many other tissue-resident macrophages, the identity of microglia is determined by enhancer landscapes. However, the enhancer landscapes that regulate specific microglial states have not been defined. We are keen to understand the convergent and divergent cis-regulatory elements governing the formation of PAM and DAM. Once these enhancers are characterized, we also can investigate the plastic nature of them as microglia undergo a state switch. In addition, we are interested in dissecting key transcription factors that interact with these enhancers to regulate microglial states.
Origin and fate specification
Microglia and certain brain border-associated macrophages (BAM) are generated from yolk sac precursors during embryogenesis. However, the exact cellular origins of these cells are under debate. In addition, how microglia and macrophage diverge from ontogenically relevant precursors during development remain elusive. Combining unbiased single-cell profiling, genetic fate mapping, and tissue-level examination, we want to delineate the developmental trajectories of microglia and BAM. This study provides a rich resource to generate new hypotheses on the transcriptional and epigenetic regulation of microglial fate specification, which we are testing in the lab. Lastly, we also are interested in understanding how perturbation of microglia differentiation by environmental factors may lead to aberrant brain architecture and neurodevelopmental disorders.