Sepideh Kiani Shabestari

All Publications

• Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease. bioRxiv : the preprint server for biology Miyoshi, E., Morabito, S., Henningfield, C. M., Rahimzadeh, N., Kiani Shabestari, S., Das, S., Michael, N., Reese, F., Shi, Z., Cao, Z., Scarfone, V., Arreola, M. A., Lu, J., Wright, S., Silva, J., Leavy, K., Lott, I. T., Doran, E., Yong, W. H., Shahin, S., Perez-Rosendahl, M., Head, E., Green, K. N., Swarup, V. 2023

  Abstract

  The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with remarkable differences evident between individuals at the molecular level. Here we present a transcriptomic survey of AD using spatial transcriptomics (ST) and single-nucleus RNA-seq in cortical samples from early-stage AD, late-stage AD, and AD in Down Syndrome (AD in DS) donors. Studying AD in DS provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. Our analysis revealed spatial and cell-type specific changes in disease, with broad similarities in these changes between sAD and AD in DS. We performed additional ST experiments in a disease timecourse of 5xFAD and wildtype mice to facilitate cross-species comparisons. Finally, amyloid plaque and fibril imaging in the same tissue samples used for ST enabled us to directly link changes in gene expression with accumulation and spread of pathology.

  View details for DOI 10.1101/2023.07.24.550282

  View details for PubMedID 37546983

  View details for PubMedCentralID PMC10402031

• Author Correction: Gene expression and functional deficits underlie TREM2-knockout microglia responses in human models of Alzheimer's disease. Nature communications McQuade, A., Kang, Y. J., Hasselmann, J., Jairaman, A., Sotelo, A., Coburn, M., Shabestari, S. K., Chadarevian, J. P., Fote, G., Tu, C. H., Danhash, E., Silva, J., Martinez, E., Cotman, C., Prieto, G. A., Thompson, L. M., Steffan, J. S., Smith, I., Davtyan, H., Cahalan, M., Cho, H., Blurton-Jones, M. 2023; 14 (1): 1194

  View details for DOI 10.1038/s41467-023-36930-1

  View details for PubMedID 36864071

  View details for PubMedCentralID PMC9981556

• The P522R protective variant of PLCG2 promotes the expression of antigen presentation genes by human microglia in an Alzheimer's disease mouse model. Alzheimer's & dementia : the journal of the Alzheimer's Association Claes, C., England, W. E., Danhash, E. P., Kiani Shabestari, S., Jairaman, A., Chadarevian, J. P., Hasselmann, J., Tsai, A. P., Coburn, M. A., Sanchez, J., Lim, T. E., Hidalgo, J. L., Tu, C., Cahalan, M. D., Lamb, B. T., Landreth, G. E., Spitale, R. C., Blurton-Jones, M., Davtyan, H. 2022; 18 (10): 1765-1778

  Abstract

  The P522R variant of PLCG2, expressed by microglia, is associated with reduced risk of Alzheimer's disease (AD). Yet, the impact of this protective mutation on microglial responses to AD pathology remains unknown. Chimeric AD and wild-type mice were generated by transplanting PLCG2-P522R or isogenic wild-type human induced pluripotent stem cell microglia. At 7 months of age, single-cell and bulk RNA sequencing, and histological analyses were performed. The PLCG2-P522R variant induced a significant increase in microglial human leukocyte antigen (HLA) expression and the induction of antigen presentation, chemokine signaling, and T cell proliferation pathways. Examination of immune-intact AD mice further demonstrated that the PLCG2-P522R variant promotes the recruitment of CD8+ T cells to the brain. These data provide the first evidence that the PLCG2-P522R variant increases the capacity of microglia to recruit T cells and present antigens, promoting a microglial transcriptional state that has recently been shown to be reduced in AD patient brains.

  View details for DOI 10.1002/alz.12577

  View details for PubMedID 35142046

  View details for PubMedCentralID PMC9360195

• Absence of microglia promotes diverse pathologies and early lethality in Alzheimer's disease mice. Cell reports Kiani Shabestari, S., Morabito, S., Danhash, E. P., McQuade, A., Sanchez, J. R., Miyoshi, E., Chadarevian, J. P., Claes, C., Coburn, M. A., Hasselmann, J., Hidalgo, J., Tran, K. N., Martini, A. C., Chang Rothermich, W., Pascual, J., Head, E., Hume, D. A., Pridans, C., Davtyan, H., Swarup, V., Blurton-Jones, M. 2022; 39 (11): 110961

  Abstract

  Microglia are strongly implicated in the development and progression of Alzheimer's disease (AD), yet their impact on pathology and lifespan remains unclear. Here we utilize a CSF1R hypomorphic mouse to generate a model of AD that genetically lacks microglia. The resulting microglial-deficient mice exhibit a profound shift from parenchymal amyloid plaques to cerebral amyloid angiopathy (CAA), which is accompanied by numerous transcriptional changes, greatly increased brain calcification and hemorrhages, and premature lethality. Remarkably, a single injection of wild-type microglia into adult mice repopulates the microglial niche and prevents each of these pathological changes. Taken together, these results indicate the protective functions of microglia in reducing CAA, blood-brain barrier dysfunction, and brain calcification. To further understand the clinical implications of these findings, human AD tissue and iPSC-microglia were examined, providing evidence that microglia phagocytose calcium crystals, and this process is impaired by loss of the AD risk gene, TREM2.

  View details for DOI 10.1016/j.celrep.2022.110961

  View details for PubMedID 35705056

  View details for PubMedCentralID PMC9285116

• Using Advanced Diffusion-Weighted Imaging to Predict Cell Counts in Gray Matter: Potential and Pitfalls. Frontiers in neuroscience Radhakrishnan, H., Shabestari, S. K., Blurton-Jones, M., Obenaus, A., Stark, C. E. 2022; 16: 881713

  Abstract

  Recent advances in diffusion imaging have given it the potential to non-invasively detect explicit neurobiological properties, beyond what was previously possible with conventional structural imaging. However, there is very little known about what cytoarchitectural properties these metrics, especially those derived from newer multi-shell models like Neurite Orientation Dispersion and Density Imaging (NODDI) correspond to. While these diffusion metrics do not promise any inherent cell type specificity, different brain cells have varying morphologies, which could influence the diffusion signal in distinct ways. This relationship is currently not well-characterized. Understanding the possible cytoarchitectural signatures of diffusion measures could allow them to estimate important neurobiological properties like cell counts, potentially resulting in a powerful clinical diagnostic tool. Here, using advanced diffusion imaging (NODDI) in the mouse brain, we demonstrate that different regions have unique relationships between cell counts and diffusion metrics. We take advantage of this exclusivity to introduce a framework to predict cell counts of different types of cells from the diffusion metrics alone, in a region-specific manner. We also outline the challenges of reliably developing such a model and discuss the precautions the field must take when trying to tie together medical imaging modalities and histology.

  View details for DOI 10.3389/fnins.2022.881713

  View details for PubMedID 35720733

  View details for PubMedCentralID PMC9204138

• Immunogenicity of MultiTEP-Platform-Based Recombinant Protein Vaccine, PV-1950R, Targeting Three B-Cell Antigenic Determinants of Pathological α-Synuclein. International journal of molecular sciences Zagorski, K., Chailyan, G., Hovakimyan, A., Antonyan, T., Kiani Shabestari, S., Petrushina, I., Davtyan, H., Cribbs, D. H., Blurton-Jones, M., Masliah, E., Agadjanyan, M. G., Ghochikyan, A. 2022; 23 (11)

  Abstract

  Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are characterized by the aberrant accumulation of intracytoplasmic misfolded and aggregated α-synuclein (α-Syn), resulting in neurodegeneration associated with inflammation. The propagation of α-Syn aggregates from cell to cell is implicated in the spreading of pathological α-Syn in the brain and disease progression. We and others demonstrated that antibodies generated after active and passive vaccinations could inhibit the propagation of pathological α-Syn in the extracellular space and prevent/inhibit disease/s in the relevant animal models. We recently tested the immunogenicity and efficacy of four DNA vaccines on the basis of the universal MultiTEP platform technology in the DLB/PD mouse model. The antibodies generated by these vaccines efficiently reduced/inhibited the accumulation of pathological α-Syn in the different brain regions and improved the motor deficit of immunized female mice. The most immunogenic and preclinically effective vaccine, PV-1950D, targeting three B-cell epitopes of pathological α-Syn simultaneously, has been selected for future IND-enabling studies. However, to ensure therapeutically potent concentrations of α-Syn antibodies in the periphery of the vaccinated elderly, we developed a recombinant protein-based MultiTEP vaccine, PV-1950R/A, and tested its immunogenicity in young and aged D-line mice. Antibody responses induced by immunizations with the PV-1950R/A vaccine and its homologous DNA counterpart, PV-1950D, in a mouse model of PD/DLB have been compared.

  View details for DOI 10.3390/ijms23116080

  View details for PubMedID 35682759

  View details for PubMedCentralID PMC9181659

• A kinase-dead Csf1r mutation associated with adult-onset leukoencephalopathy has a dominant inhibitory impact on CSF1R signalling. Development (Cambridge, England) Stables, J., Green, E. K., Sehgal, A., Patkar, O. L., Keshvari, S., Taylor, I., Ashcroft, M. E., Grabert, K., Wollscheid-Lengeling, E., Szymkowiak, S., McColl, B. W., Adamson, A., Humphreys, N. E., Mueller, W., Starobova, H., Vetter, I., Shabestari, S. K., Blurton-Jones, M. M., Summers, K. M., Irvine, K. M., Pridans, C., Hume, D. A. 2022; 149 (8)

  Abstract

  Amino acid substitutions in the kinase domain of the human CSF1R gene are associated with autosomal dominant adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). To model the human disease, we created a disease-associated mutation (pGlu631Lys; E631K) in the mouse Csf1r locus. Homozygous mutation (Csf1rE631K/E631K) phenocopied the Csf1r knockout, with prenatal mortality or severe postnatal growth retardation and hydrocephalus. Heterozygous mutation delayed the postnatal expansion of tissue macrophage populations in most organs. Bone marrow cells from Csf1rE631K/+mice were resistant to CSF1 stimulation in vitro, and Csf1rE631K/+ mice were unresponsive to administration of a CSF1-Fc fusion protein, which expanded tissue macrophage populations in controls. In the brain, microglial cell numbers and dendritic arborisation were reduced in Csf1rE631K/+ mice, as in patients with ALSP. The microglial phenotype is the opposite of microgliosis observed in Csf1r+/- mice. However, we found no evidence of brain pathology or impacts on motor function in aged Csf1rE631K/+ mice. We conclude that heterozygous disease-associated CSF1R mutations compromise CSF1R signalling. We speculate that leukoencephalopathy associated with dominant human CSF1R mutations requires an environmental trigger and/or epistatic interaction with common neurodegenerative disease-associated alleles.

  View details for DOI 10.1242/dev.200237

  View details for PubMedID 35333324

  View details for PubMedCentralID PMC9002114

• Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer's disease. Molecular neurodegeneration Claes, C., Danhash, E. P., Hasselmann, J., Chadarevian, J. P., Shabestari, S. K., England, W. E., Lim, T. E., Hidalgo, J. L., Spitale, R. C., Davtyan, H., Blurton-Jones, M. 2021; 16 (1): 50

  Abstract

  Disease-associated microglia (DAMs), that surround beta-amyloid plaques, represent a transcriptionally-distinct microglial profile in Alzheimer's disease (AD). Activation of DAMs is dependent on triggering receptor expressed on myeloid cells 2 (TREM2) in mouse models and the AD TREM2-R47H risk variant reduces microglial activation and plaque association in human carriers. Interestingly, TREM2 has also been identified as a microglial lipid-sensor, and recent data indicates lipid droplet accumulation in aged microglia, that is in turn associated with a dysfunctional proinflammatory phenotype. However, whether lipid droplets (LDs) are present in human microglia in AD and how the R47H mutation affects this remains unknown.To determine the impact of the TREM2 R47H mutation on human microglial function in vivo, we transplanted wild-type and isogenic TREM2-R47H iPSC-derived microglial progenitors into our recently developed chimeric Alzheimer mouse model. At 7 months of age scRNA-seq and histological analyses were performed.Here we report that the transcriptome of human wild-type TREM2 and isogenic TREM2-R47H DAM xenografted microglia (xMGs), isolated from chimeric AD mice, closely resembles that of human atherosclerotic foam cells. In addition, much like foam cells, plaque-bound xMGs are highly enriched in lipid droplets. Somewhat surprisingly and in contrast to a recent in vitro study, TREM2-R47H mutant xMGs exhibit an overall reduction in the accumulation of lipid droplets in vivo. Notably, TREM2-R47H xMGs also show overall reduced reactivity to plaques, including diminished plaque-proximity, reduced CD9 expression, and lower secretion of plaque-associated APOE.Altogether, these results indicate lipid droplet accumulation occurs in human DAM xMGs in AD, but is reduced in TREM2-R47H DAM xMGs, as it occurs secondary to TREM2-mediated changes in plaque proximity and reactivity.

  View details for DOI 10.1186/s13024-021-00473-0

  View details for PubMedID 34301296

  View details for PubMedCentralID PMC8305935

• Gene expression and functional deficits underlie TREM2-knockout microglia responses in human models of Alzheimer's disease. Nature communications McQuade, A., Kang, Y. J., Hasselmann, J., Jairaman, A., Sotelo, A., Coburn, M., Shabestari, S. K., Chadarevian, J. P., Fote, G., Tu, C. H., Danhash, E., Silva, J., Martinez, E., Cotman, C., Prieto, G. A., Thompson, L. M., Steffan, J. S., Smith, I., Davtyan, H., Cahalan, M., Cho, H., Blurton-Jones, M. 2020; 11 (1): 5370

  Abstract

  The discovery of TREM2 as a myeloid-specific Alzheimer's disease (AD) risk gene has accelerated research into the role of microglia in AD. While TREM2 mouse models have provided critical insight, the normal and disease-associated functions of TREM2 in human microglia remain unclear. To examine this question, we profile microglia differentiated from isogenic, CRISPR-modified TREM2-knockout induced pluripotent stem cell (iPSC) lines. By combining transcriptomic and functional analyses with a chimeric AD mouse model, we find that TREM2 deletion reduces microglial survival, impairs phagocytosis of key substrates including APOE, and inhibits SDF-1α/CXCR4-mediated chemotaxis, culminating in an impaired response to beta-amyloid plaques in vivo. Single-cell sequencing of xenotransplanted human microglia further highlights a loss of disease-associated microglial (DAM) responses in human TREM2 knockout microglia that we validate by flow cytometry and immunohistochemistry. Taken together, these studies reveal both conserved and novel aspects of human TREM2 biology that likely play critical roles in the development and progression of AD.

  View details for DOI 10.1038/s41467-020-19227-5

  View details for PubMedID 33097708

  View details for PubMedCentralID PMC7584603

• Controlled Release of Stem Cell Secretome Attenuates Inflammatory Response against Implanted Biomaterials. Advanced healthcare materials Mohammadi, M., Luong, J. C., Rodriguez, S. M., Cao, R., Wheeler, A. E., Lau, H., Li, S., Shabestari, S. K., Chadarevian, J. P., Alexander, M., de Vos, P., Zhao, W., Lakey, J. R. 2020; 9 (12): e1901874

  Abstract

  Inflammatory response against implanted biomaterials impairs their functional integration and induces medical complications in the host's body. To suppress such immune responses, one approach is the administration of multiple drugs to halt inflammatory pathways. This challenges patient's adherence and can cause additional complications such as infection. Alternatively, biologics that regulate multiple inflammatory pathways are attractive agents in addressing the implants immune complications. Secretome of mesenchymal stromal cells (MSCs) is a multipotent biologic, regulating the homeostasis of lymphocytes and leukocytes. Here, it is reported that alginate microcapsules loaded with processed conditioned media (pCM-Alg) reduces the infiltration and/or expression of CD68+ macrophages likely through the controlled release of pCM. In vitro cultures revealed that alginate can dose dependently induce macrophages to secrete TNFα, IL-6, IL-1β, and GM-CSF. Addition of pCM to the cultures attenuates the secretion of TNFα (p = 0.023) and IL-6 (p < 0.0001) by alginate or lipopolysaccharide (LPS) stimulations. Mechanistically, pCM suppressed the NfκB pathway activation of macrophages in response to LPS (p < 0.0001) in vitro and cathepsin activity (p = 0.005) in response to alginate in vivo. These observations suggest the efficacy of using MSC-derived secretome to prevent or delay the host rejection of implants.

  View details for DOI 10.1002/adhm.201901874

  View details for PubMedID 32419390

• Testing a MultiTEP-based combination vaccine to reduce Aβ and tau pathology in Tau22/5xFAD bigenic mice. Alzheimer's research & therapy Davtyan, H., Hovakimyan, A., Kiani Shabestari, S., Antonyan, T., Coburn, M. A., Zagorski, K., Chailyan, G., Petrushina, I., Svystun, O., Danhash, E., Petrovsky, N., Cribbs, D. H., Agadjanyan, M. G., Blurton-Jones, M., Ghochikyan, A. 2019; 11 (1): 107

  Abstract

  Alzheimer disease (AD) is characterized by the accumulation of beta-amyloid (Aβ) plaques and neurofibrillary tangles composed of hyperphosphorylated tau, which together lead to neurodegeneration and cognitive decline. Current therapeutic approaches have primarily aimed to reduce pathological aggregates of either Aβ or tau, yet phase 3 clinical trials of these approaches have thus far failed to delay disease progression in humans. Strong preclinical evidence indicates that these two abnormally aggregated proteins interact synergistically to drive downstream neurodegeneration. Therefore, combinatorial therapies that concurrently target both Aβ and tau might be needed for effective disease modification.A combinatorial vaccination approach was designed to concurrently target both Aβ and tau pathologies. Tau22/5xFAD (T5x) bigenic mice that develop both pathological Aβ and tau aggregates were injected intramuscularly with a mixture of two MultiTEP epitope vaccines: AV-1959R and AV-1980R, targeting Aβ and tau, respectively, and formulated in AdvaxCpG, a potent polysaccharide adjuvant. Antibody responses of vaccinated animals were measured by ELISA, and neuropathological changes were determined in brain homogenates of vaccinated and control mice using ELISA and Meso Scale Discovery (MSD) multiplex assays.T5x mice immunized with a mixture of Aβ- and tau-targeting vaccines generated high Aβ- and tau-specific antibody titers that recognized senile plaques and neurofibrillary tangles/neuropil threads in human AD brain sections. Production of these antibodies in turn led to significant reductions in the levels of soluble and insoluble total tau, and hyperphosphorylated tau as well as insoluble Aβ42, within the brains of bigenic T5x mice.AV-1959R and AV-1980R formulated with AdvaxCpG adjuvant are immunogenic and therapeutically potent vaccines that in combination can effectively reduce both of the hallmark pathologies of AD in bigenic mice. Taken together, these findings warrant further development of this vaccine technology for ultimate testing in human AD.

  View details for DOI 10.1186/s13195-019-0556-2

  View details for PubMedID 31847886

  View details for PubMedCentralID PMC6918571

• A MultiTEP platform-based epitope vaccine targeting the phosphatase activating domain (PAD) of tau: therapeutic efficacy in PS19 mice. Scientific reports Hovakimyan, A., Antonyan, T., Shabestari, S. K., Svystun, O., Chailyan, G., Coburn, M. A., Carlen-Jones, W., Petrushina, I., Chadarevian, J. P., Zagorski, K., Petrovsky, N., Cribbs, D. H., Agadjanyan, M. G., Ghochikyan, A., Davtyan, H. 2019; 9 (1): 15455

  Abstract

  Pathological tau correlates well with cognitive impairments in Alzheimer's disease (AD) patients and therefore represents a promising target for immunotherapy. Targeting an appropriate B cell epitope in pathological tau could in theory produce an effective reduction of pathology without disrupting the function of normal native tau. Recent data demonstrate that the N-terminal region of tau (aa 2-18), termed the "phosphatase activation domain (PAD)", is hidden within native Tau in a 'paperclip'-like conformation. Conversely, PAD is exposed in pathological tau and plays an essential role in the inhibition of fast axonal transport and tau polymerization. Thus, we hypothesized that anti-tau2-18 antibodies may safely and specifically reduce pathological tau and prevent further aggregation, which in turn would neutralize tau toxicity. Therefore, we evaluated the immunogenicity and therapeutic efficacy of our MultiTEP platform-based vaccine targeting tau2-18 formulated with AdvaxCpG adjuvant (AV-1980R/A) in PS19 tau transgenic mice. The AV-1980R/A induced extremely high antibody responses and the resulting sera recognized neurofibrillary tangles and plaque-associated dystrophic neurites in AD brain sections. In addition, under non-denaturing conditions AV-1980R/A sera preferentially recognized AD-associated tau. Importantly, vaccination also prevented age-related motor and cognitive deficits in PS19 mice and significantly reduced insoluble total and phosphorylated tau species. Taken together, these findings suggest that predominantly targeting misfolded tau with AV-1980R/A could represent an effective strategy for AD immunotherapy.

  View details for DOI 10.1038/s41598-019-51809-2

  View details for PubMedID 31664089

  View details for PubMedCentralID PMC6820729

• Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo. Neuron Hasselmann, J., Coburn, M. A., England, W., Figueroa Velez, D. X., Kiani Shabestari, S., Tu, C. H., McQuade, A., Kolahdouzan, M., Echeverria, K., Claes, C., Nakayama, T., Azevedo, R., Coufal, N. G., Han, C. Z., Cummings, B. J., Davtyan, H., Glass, C. K., Healy, L. M., Gandhi, S. P., Spitale, R. C., Blurton-Jones, M. 2019; 103 (6): 1016-1033.e10

  Abstract

  iPSC-derived microglia offer a powerful tool to study microglial homeostasis and disease-associated inflammatory responses. Yet, microglia are highly sensitive to their environment, exhibiting transcriptomic deficiencies when kept in isolation from the brain. Furthermore, species-specific genetic variations demonstrate that rodent microglia fail to fully recapitulate the human condition. To address this, we developed an approach to study human microglia within a surrogate brain environment. Transplantation of iPSC-derived hematopoietic-progenitors into the postnatal brain of humanized, immune-deficient mice results in context-dependent differentiation into microglia and other CNS macrophages, acquisition of an ex vivo human microglial gene signature, and responsiveness to both acute and chronic insults. Most notably, transplanted microglia exhibit robust transcriptional responses to Aβ-plaques that only partially overlap with that of murine microglia, revealing new, human-specific Aβ-responsive genes. We therefore have demonstrated that this chimeric model provides a powerful new system to examine the in vivo function of patient-derived and genetically modified microglia.

  View details for DOI 10.1016/j.neuron.2019.07.002

  View details for PubMedID 31375314

  View details for PubMedCentralID PMC7138101