Periodic Reporting for period 4 - CELLPHASE_AD (Genetics to understand cellular components of Alzheimer Disease pathogenesis)
Okres sprawozdawczy: 2024-05-01 do 2025-10-31
AD affects millions, placing a heavy burden on health care systems and economies. Societal impact depends on developing treatments that are biologically grounded, stage appropriate, and more likely to succeed in humans. Although many genetic risk factors have been identified for Alzheimer disease (AD), their roles in the progression of AD remain unclear. Moreover, many risk genes act in microglia and astroglia, cell types that have been historically understudied. Finally, commonly used experimental models do not reproduce key aspects of the human disease: human stem cell models are often overly simplified, and mouse models frequently do not translate to effective human therapies.
CELLPHASE_AD aimed to accelerate the translation of AD genetic risk into mechanistic insight by focusing on cellular states and cell interactions in vivo. The objectives were:
- Map how microglia and astroglia transition from homeostatic to disease states.
- Determine how genetic risk shifts these cellular transitions, using patient-derived and engineered stem cell lines.
- Establish mouse-human xenotransplantation platforms to link genetics, cell states, pathology, and therapeutic response.
Conclusions of the action
The project met its core objectives. It established human microglia and astrocyte xenotransplantation models, generated large single cell and spatial datasets, produced mechanistic insights into how genetic risk shapes disease cell states, and how these influence pathology. The work clarified microglial stage dependent roles in amyloid pathology, showed amyloid induced tau pathology and neuronal loss in human neuron xenografts, identified a targetable neuronal death pathway, and defined microglial programs engaged by anti-amyloid therapy. The project also produced transferable platforms with translational value and contributed to the founding of a company.
CELLPHASE_AD aimed to accelerate the translation of AD genetic risk into mechanistic insight by focusing on cellular states and cell interactions in vivo. The objectives were:
- Map how microglia and astroglia transition from homeostatic to disease states.
- Determine how genetic risk shifts these cellular transitions, using patient-derived and engineered stem cell lines.
- Establish mouse-human xenotransplantation platforms to link genetics, cell states, pathology, and therapeutic response.
Conclusions of the action
The project met its core objectives. It established human microglia and astrocyte xenotransplantation models, generated large single cell and spatial datasets, produced mechanistic insights into how genetic risk shapes disease cell states, and how these influence pathology. The work clarified microglial stage dependent roles in amyloid pathology, showed amyloid induced tau pathology and neuronal loss in human neuron xenografts, identified a targetable neuronal death pathway, and defined microglial programs engaged by anti-amyloid therapy. The project also produced transferable platforms with translational value and contributed to the founding of a company.
Work performed:
Completed polygenic risk score analyses and generated > 20 iPSC lines from donors with high or low AD polygenic risk.
Developed and applied isogenic lines to isolate genetic effects.
Established CRISPR Cas9 capacity and generated loss of function lines for key risk genes.
Established and validated human microglial and astrocyte xenograft models.
Implemented single cell transcriptomic profiling of transplanted cells across disease contexts.
Developed a pooled xenotransplantation or village approach enabling analysis of multiple donor lines in the same brain and computational donor assignment.
Data generation and computational analysis:
Generated and analysed > 300,000 human microglial and > 50,000 astrocyte single cell transcriptomes.
Developed robust pipelines for single-cell/nucleus analysis, cellular state identification, transition mapping, pathway analysis, and polygenic risk stratification.
Applied spatial transcriptomics to map gene programs within pathological niches and to infer cell-cell interaction networks.
Therapeutic and mechanistic testing:
Tested microglial effector programs for antibody-mediated amyloid clearance using lecanemab.
Established human neuron xenograft workflows to assess amyloid-induced tau pathology, biomarker release, and neuronal loss.
Identified and tested a pharmacologically targetable neuronal death pathway linked to tau pathology.
Roles of microglia and astrocytes:
Demonstrated that APOE isoforms shape transcriptional and epigenomic programs in human microglia exposed to amyloid pathology in vivo.
Identified effects of PICALM loss on microglial identity and microglia-amyloid interactions.
Showed that microglia contribute to plaque seeding in early states, while compacting them and limiting neuritic damage in later states.
Demonstrated that astrocytic APOE can restore amyloid pathology and trigger microglial responses in Apoe-deficient mice.
Established that antibody-mediated amyloid clearance requires an intact Fc, functional microglia, and a microglial effector program.
Mapped microglia–astroglia networks around plaques via spatial transcriptomics, supporting a cellular AD phase.
Human neuron vulnerability and neuronal death:
Demonstrated that human neurons xenografted into amyloid bearing mouse brains develop tau pathology, release p-tau into the blood, and undergo neuronal loss.
Identified a granulovacuolar degeneration-associated necroptosis program as a driver of neuronal loss and showed pharmacological rescue.
Exploitation and dissemination:
Disseminated results through high-impact publications such as Cell, Nat Neurosc, Nat Comm, EMBO Mol Med, and Science Transl Med, and an invited Science review.
Released and shared methodologies, including xenograft protocols and computational pipelines, adopted by multiple laboratories.
Contributed to Tech Transfer and exploitation through company formation: results led to the creation of K5, now part of Muna Therapeutics, to translate spatially resolved molecular insights into therapeutic strategies.
Provided training and knowledge transfer through the development of researchers who progressed to independent positions and through collaborations with academic and industry partners.
Completed polygenic risk score analyses and generated > 20 iPSC lines from donors with high or low AD polygenic risk.
Developed and applied isogenic lines to isolate genetic effects.
Established CRISPR Cas9 capacity and generated loss of function lines for key risk genes.
Established and validated human microglial and astrocyte xenograft models.
Implemented single cell transcriptomic profiling of transplanted cells across disease contexts.
Developed a pooled xenotransplantation or village approach enabling analysis of multiple donor lines in the same brain and computational donor assignment.
Data generation and computational analysis:
Generated and analysed > 300,000 human microglial and > 50,000 astrocyte single cell transcriptomes.
Developed robust pipelines for single-cell/nucleus analysis, cellular state identification, transition mapping, pathway analysis, and polygenic risk stratification.
Applied spatial transcriptomics to map gene programs within pathological niches and to infer cell-cell interaction networks.
Therapeutic and mechanistic testing:
Tested microglial effector programs for antibody-mediated amyloid clearance using lecanemab.
Established human neuron xenograft workflows to assess amyloid-induced tau pathology, biomarker release, and neuronal loss.
Identified and tested a pharmacologically targetable neuronal death pathway linked to tau pathology.
Roles of microglia and astrocytes:
Demonstrated that APOE isoforms shape transcriptional and epigenomic programs in human microglia exposed to amyloid pathology in vivo.
Identified effects of PICALM loss on microglial identity and microglia-amyloid interactions.
Showed that microglia contribute to plaque seeding in early states, while compacting them and limiting neuritic damage in later states.
Demonstrated that astrocytic APOE can restore amyloid pathology and trigger microglial responses in Apoe-deficient mice.
Established that antibody-mediated amyloid clearance requires an intact Fc, functional microglia, and a microglial effector program.
Mapped microglia–astroglia networks around plaques via spatial transcriptomics, supporting a cellular AD phase.
Human neuron vulnerability and neuronal death:
Demonstrated that human neurons xenografted into amyloid bearing mouse brains develop tau pathology, release p-tau into the blood, and undergo neuronal loss.
Identified a granulovacuolar degeneration-associated necroptosis program as a driver of neuronal loss and showed pharmacological rescue.
Exploitation and dissemination:
Disseminated results through high-impact publications such as Cell, Nat Neurosc, Nat Comm, EMBO Mol Med, and Science Transl Med, and an invited Science review.
Released and shared methodologies, including xenograft protocols and computational pipelines, adopted by multiple laboratories.
Contributed to Tech Transfer and exploitation through company formation: results led to the creation of K5, now part of Muna Therapeutics, to translate spatially resolved molecular insights into therapeutic strategies.
Provided training and knowledge transfer through the development of researchers who progressed to independent positions and through collaborations with academic and industry partners.
Human in vivo modelling at scale:
The project moved beyond conventional mouse models and simple stem cell systems by enabling human microglia, astrocytes, and neurons to be studied in vivo in a brain environment. A key innovation was the pooled xenotransplantation or village approach, allowing multiple donor genotypes to be analysed under identical conditions. This increased scalability, reduced inter-animal variability, and enabled direct comparisons of genetic backgrounds in the same disease context.
A cell state based, time resolved framework for AD progression:
By mapping cellular transitions across disease stages, the project revealed a state- and stage-dependent framework, showing that microglia and astrocytes shift through distinct programmes as pathology evolves. These shifts influence plaque dynamics and neuronal injury, helping to refine therapeutic windows and guide more targeted interventions.
Human specific mechanisms of pathology and neuronal death:
The project showed that human neurons xenografted into amyloid mouse brains develop core AD features, including tau pathology, biomarker release, and selective neuronal loss, highlighting human specific vulnerability absent from neighboring mouse neurons. We identified a necroptosis pathway downstream of tau pathology and showed that it is pharmacologically targetable.
Mechanistic clarity for immunotherapy:
The project provided mechanistic insight into anti-amyloid therapy, showing that amyloid clearance requires an intact Fc fragment and functional microglia, driven by a defined microglial effector programme. This clarified how microglia contribute to antibody efficacy and offers a framework for designing and evaluating next generation immunotherapies.
Delivered integration, validation, and translation:
Polygenic risk stratification was linked to microglial and astroglial state trajectories using large-scale datasets and in vivo platforms. Candidate pathways were tested using genetic perturbations and functional assays. Spatial transcriptomics was integrated with single cell state maps to refine cell interaction networks within pathological niches. Finally, the project supported technology transfer and exploitation through translation partnerships and company formation, aimed at advancing molecular insights toward therapeutics and biomarkers.
The project moved beyond conventional mouse models and simple stem cell systems by enabling human microglia, astrocytes, and neurons to be studied in vivo in a brain environment. A key innovation was the pooled xenotransplantation or village approach, allowing multiple donor genotypes to be analysed under identical conditions. This increased scalability, reduced inter-animal variability, and enabled direct comparisons of genetic backgrounds in the same disease context.
A cell state based, time resolved framework for AD progression:
By mapping cellular transitions across disease stages, the project revealed a state- and stage-dependent framework, showing that microglia and astrocytes shift through distinct programmes as pathology evolves. These shifts influence plaque dynamics and neuronal injury, helping to refine therapeutic windows and guide more targeted interventions.
Human specific mechanisms of pathology and neuronal death:
The project showed that human neurons xenografted into amyloid mouse brains develop core AD features, including tau pathology, biomarker release, and selective neuronal loss, highlighting human specific vulnerability absent from neighboring mouse neurons. We identified a necroptosis pathway downstream of tau pathology and showed that it is pharmacologically targetable.
Mechanistic clarity for immunotherapy:
The project provided mechanistic insight into anti-amyloid therapy, showing that amyloid clearance requires an intact Fc fragment and functional microglia, driven by a defined microglial effector programme. This clarified how microglia contribute to antibody efficacy and offers a framework for designing and evaluating next generation immunotherapies.
Delivered integration, validation, and translation:
Polygenic risk stratification was linked to microglial and astroglial state trajectories using large-scale datasets and in vivo platforms. Candidate pathways were tested using genetic perturbations and functional assays. Spatial transcriptomics was integrated with single cell state maps to refine cell interaction networks within pathological niches. Finally, the project supported technology transfer and exploitation through translation partnerships and company formation, aimed at advancing molecular insights toward therapeutics and biomarkers.