Disease-associated-microglia (DAM) represent transcriptionally-distinct and neurodegeneration-specific microglial profiles with unclear significance in Alzheimer's disease (AD). An understanding of ...heterogeneity within DAM and their key regulators may guide pre-clinical experimentation and drug discovery.
Weighted co-expression network analysis (WGCNA) was applied to existing microglial transcriptomic datasets from neuroinflammatory and neurodegenerative disease mouse models to identify modules of highly co-expressed genes. These modules were contrasted with known signatures of homeostatic microglia and DAM to reveal novel molecular heterogeneity within DAM. Flow cytometric validation studies were performed to confirm existence of distinct DAM sub-populations in AD mouse models predicted by WGCNA. Gene ontology analyses coupled with bioinformatics approaches revealed drug targets and transcriptional regulators of microglial modules predicted to favorably modulate neuroinflammation in AD. These guided in-vivo and in-vitro studies in mouse models of neuroinflammation and neurodegeneration (5xFAD) to determine whether inhibition of pro-inflammatory gene expression and promotion of amyloid clearance was feasible. We determined the human relevance of these findings by integrating our results with AD genome-wide association studies and human AD and non-disease post-mortem brain proteomes.
WGCNA applied to microglial gene expression data revealed a transcriptomic framework of microglial activation that predicted distinct pro-inflammatory and anti-inflammatory phenotypes within DAM, which we confirmed in AD and aging models by flow cytometry. Pro-inflammatory DAM emerged earlier in mouse models of AD and were characterized by pro-inflammatory genes (Tlr2, Ptgs2, Il12b, Il1b), surface marker CD44, potassium channel Kv1.3 and regulators (NFkb, Stat1, RelA) while anti-inflammatory DAM expressed phagocytic genes (Igf1, Apoe, Myo1e), surface marker CXCR4 with distinct regulators (LXRα/β, Atf1). As neuro-immunomodulatory strategies, we validated LXRα/β agonism and Kv1.3 blockade by ShK-223 peptide that promoted anti-inflammatory DAM, inhibited pro-inflammatory DAM and augmented Aβ clearance in AD models. Human AD-risk genes were highly represented within homeostatic microglia suggesting causal roles for early microglial dysregulation in AD. Pro-inflammatory DAM proteins were positively associated with neuropathology and preceded cognitive decline confirming the therapeutic relevance of inhibiting pro-inflammatory DAM in AD.
We provide a predictive transcriptomic framework of microglial activation in neurodegeneration that can guide pre-clinical studies to characterize and therapeutically modulate neuroinflammation in AD.
In advanced age, some individuals maintain a stable cognitive trajectory while others experience a rapid decline. Such variation in cognitive trajectory is only partially explained by traditional ...neurodegenerative pathologies. Hence, to identify new processes underlying variation in cognitive trajectory, we perform an unbiased proteome-wide association study of cognitive trajectory in a discovery (n = 104) and replication cohort (n = 39) of initially cognitively unimpaired, longitudinally assessed older-adult brain donors. We find 579 proteins associated with cognitive trajectory after meta-analysis. Notably, we present evidence for increased neuronal mitochondrial activities in cognitive stability regardless of the burden of traditional neuropathologies. Furthermore, we provide additional evidence for increased synaptic abundance and decreased inflammation and apoptosis in cognitive stability. Importantly, we nominate proteins associated with cognitive trajectory, particularly the 38 proteins that act independently of neuropathologies and are also hub proteins of protein co-expression networks, as promising targets for future mechanistic studies of cognitive trajectory.
The complicated cellular and biochemical changes that occur in brain during Alzheimer's disease are poorly understood. In a previous study we used an unbiased label-free quantitative mass ...spectrometry-based proteomic approach to analyze these changes at a systems level in post-mortem cortical tissue from patients with Alzheimer's disease (AD), asymptomatic Alzheimer's disease (AsymAD), and controls. We found modules of co-expressed proteins that correlated with AD phenotypes, some of which were enriched in proteins identified as risk factors for AD by genetic studies.
The amount of information that can be obtained from such systems-level proteomic analyses is critically dependent upon the number of proteins that can be quantified across a cohort. We report here a new proteomic systems-level analysis of AD brain based on 6,533 proteins measured across AD, AsymAD, and controls using an analysis pipeline consisting of isobaric tandem mass tag (TMT) mass spectrometry and offline prefractionation.
Our new TMT pipeline allowed us to more than double the depth of brain proteome coverage. This increased depth of coverage greatly expanded the brain protein network to reveal new protein modules that correlated with disease and were unrelated to those identified in our previous network. Differential protein abundance analysis identified 350 proteins that had altered levels between AsymAD and AD not caused by changes in specific cell type abundance, potentially reflecting biochemical changes that are associated with cognitive decline in AD. RNA binding proteins emerged as a class of proteins altered between AsymAD and AD, and were enriched in network modules that correlated with AD pathology. We developed a proteogenomic approach to investigate RNA splicing events that may be altered by RNA binding protein changes in AD. The increased proteome depth afforded by our TMT pipeline allowed us to identify and quantify a large number of alternatively spliced protein isoforms in brain, including AD risk factors such as BIN1, PICALM, PTK2B, and FERMT2. Many of the new AD protein network modules were enriched in alternatively spliced proteins and correlated with molecular markers of AD pathology and cognition.
Further analysis of the AD brain proteome will continue to yield new insights into the biological basis of AD.
Depression is a common condition, but current treatments are only effective in a subset of individuals. To identify new treatment targets, we integrated depression genome-wide association study ...(GWAS) results (N = 500,199) with human brain proteomes (N = 376) to perform a proteome-wide association study of depression followed by Mendelian randomization. We identified 19 genes that were consistent with being causal in depression, acting via their respective cis-regulated brain protein abundance. We replicated nine of these genes using an independent depression GWAS (N = 307,353) and another human brain proteomic dataset (N = 152). Eleven of the 19 genes also had cis-regulated mRNA levels that were associated with depression, based on integration of the depression GWAS with human brain transcriptomes (N = 888). Meta-analysis of the discovery and replication proteome-wide association study analyses identified 25 brain proteins consistent with being causal in depression, 20 of which were not previously implicated in depression by GWAS. Together, these findings provide promising brain protein targets for further mechanistic and therapeutic studies.
Purpose
For quantitative susceptibility mapping (QSM), the lack of ground‐truth in clinical settings makes it challenging to determine suitable parameters for the dipole inversion. We propose a ...probabilistic Bayesian approach for QSM with built‐in parameter estimation, and incorporate the nonlinear formulation of the dipole inversion to achieve a robust recovery of the susceptibility maps.
Theory
From a Bayesian perspective, the image wavelet coefficients are approximately sparse and modeled by the Laplace distribution. The measurement noise is modeled by a Gaussian‐mixture distribution with two components, where the second component is used to model the noise outliers. Through probabilistic inference, the susceptibility map and distribution parameters can be jointly recovered using approximate message passing (AMP).
Methods
We compare our proposed AMP with built‐in parameter estimation (AMP‐PE) to the state‐of‐the‐art L1‐QSM, FANSI, and MEDI approaches on the simulated and in vivo datasets, and perform experiments to explore the optimal settings of AMP‐PE. Reproducible code is available at:
https://github.com/EmoryCN2L/QSM_AMP_PE.
Results
On the simulated Sim2Snr1 dataset, AMP‐PE achieved the lowest NRMSE, deviation from calcification moment and the highest SSIM, while MEDI achieved the lowest high‐frequency error norm. On the in vivo datasets, AMP‐PE is robust and successfully recovers the susceptibility maps using the estimated parameters, whereas L1‐QSM, FANSI and MEDI typically require additional visual fine‐tuning to select or double‐check working parameters.
Conclusion
AMP‐PE provides automatic and adaptive parameter estimation for QSM and avoids the subjectivity from the visual fine‐tuning step, making it an excellent choice for the clinical setting.
Microglia are innate immune cells of the brain that perform phagocytic and inflammatory functions in disease conditions. Transcriptomic studies of acutely-isolated microglia have provided novel ...insights into their molecular and functional diversity in homeostatic and neurodegenerative disease states. State-of-the-art mass spectrometry methods can comprehensively characterize proteomic alterations in microglia in neurodegenerative disorders, potentially providing novel functionally relevant molecular insights that are not provided by transcriptomics. However, comprehensive proteomic profiling of adult primary microglia in neurodegenerative disease conditions has not been performed.
We performed quantitative mass spectrometry based proteomic analyses of purified CD11b
acutely-isolated microglia from adult (6 mo) mice in normal, acute neuroinflammatory (LPS-treatment) and chronic neurodegenerative states (5xFAD model of Alzheimer's disease AD). Differential expression analyses were performed to characterize specific microglial proteomic changes in 5xFAD mice and identify overlap with LPS-induced pro-inflammatory changes. Our results were also contrasted with existing proteomic data from wild-type mouse microglia and from existing microglial transcriptomic data from wild-type and 5xFAD mice. Neuropathological validation studies of select proteins were performed in human AD and 5xFAD brains.
Of 4133 proteins identified, 187 microglial proteins were differentially expressed in the 5xFAD mouse model of AD pathology, including proteins with previously known (Apoe, Clu and Htra1) as well as previously unreported relevance to AD biology (Cotl1 and Hexb). Proteins upregulated in 5xFAD microglia shared significant overlap with pro-inflammatory changes observed in LPS-treated mice. Several proteins increased in human AD brain were also upregulated by 5xFAD microglia (Aβ peptide, Apoe, Htra1, Cotl1 and Clu). Cotl1 was identified as a novel microglia-specific marker with increased expression and strong association with AD neuropathology. Apoe protein was also detected within plaque-associated microglia in which Apoe and Aβ were highly co-localized, suggesting a role for Apoe in phagocytic clearance of Aβ.
We report a comprehensive proteomic study of adult mouse microglia derived from acute neuroinflammation and AD models, representing a valuable resource to the neuroscience research community. We highlight shared and unique microglial proteomic changes in acute neuroinflammation aging and AD mouse models and identify novel roles for microglial proteins in human neurodegeneration.
Differences in expressing facial emotions are broadly observed in people with cognitive impairment. However, these differences have been difficult to objectively quantify and systematically evaluate ...among people with cognitive impairment across disease etiologies and severity. Therefore, a computer vision-based deep learning model for facial emotion recognition trained on 400.000 faces was utilized to analyze facial emotions expressed during a passive viewing memory test. In addition, this study was conducted on a large number of individuals (n = 493), including healthy controls and individuals with cognitive impairment due to diverse underlying etiologies and across different disease stages. Diagnoses included subjective cognitive impairment, Mild Cognitive Impairment (MCI) due to AD, MCI due to other etiologies, dementia due to Alzheimer's diseases (AD), and dementia due to other etiologies (e.g., Vascular Dementia, Frontotemporal Dementia, Lewy Body Dementia, etc.). The Montreal Cognitive Assessment (MoCA) was used to evaluate cognitive performance across all participants. A participant with a score of less than or equal to 24 was considered cognitively impaired (CI). Compared to cognitively unimpaired (CU) participants, CI participants expressed significantly less positive emotions, more negative emotions, and higher facial expressiveness during the test. In addition, classification analysis revealed that facial emotions expressed during the test allowed effective differentiation of CI from CU participants, largely independent of sex, race, age, education level, mood, and eye movements (derived from an eye-tracking-based digital biomarker for cognitive impairment). No screening methods reliably differentiated the underlying etiology of the cognitive impairment. The findings provide quantitative and comprehensive evidence that the expression of facial emotions is significantly different in people with cognitive impairment, and suggests this may be a useful tool for passive screening of cognitive impairment.
Purpose
Undersampling is used to reduce the scan time for high‐resolution three‐dimensional magnetic resonance imaging. In order to achieve better image quality and avoid manual parameter tuning, we ...propose a probabilistic Bayesian approach to recover R2∗$$ {R}_2^{\ast } $$ map and phase images for quantitative susceptibility mapping (QSM), while allowing automatic parameter estimation from undersampled data.
Theory
Sparse prior on the wavelet coefficients of images is interpreted from a Bayesian perspective as sparsity‐promoting distribution. A novel nonlinear approximate message passing (AMP) framework that incorporates a mono‐exponential decay model is proposed. The parameters are treated as unknown variables and jointly estimated with image wavelet coefficients.
Methods
Undersampling takes place in the y‐z plane of k‐space according to the Poisson‐disk pattern. Retrospective undersampling is performed to evaluate the performances of different reconstruction approaches, prospective undersampling is performed to demonstrate the feasibility of undersampling in practice.
Results
The proposed AMP with parameter estimation (AMP‐PE) approach successfully recovers R2∗$$ {R}_2^{\ast } $$ maps and phase images for QSM across various undersampling rates. It is more computationally efficient, and performs better than the state‐of‐the‐art l1$$ {l}_1 $$‐norm regularization (L1) approach in general, except a few cases where the L1 approach performs as well as AMP‐PE.
Conclusion
AMP‐PE achieves better performance by drawing information from both the sparse prior and the mono‐exponential decay model. It does not require parameter tuning, and works with a clinical, prospective undersampling scheme where parameter tuning is often impossible or difficult due to the lack of ground‐truth image.
In Alzheimer’s disease (AD), spliceosomal proteins with critical roles in RNA processing aberrantly aggregate and mislocalize to Tau neurofibrillary tangles. We test the hypothesis that ...Tau-spliceosome interactions disrupt pre-mRNA splicing in AD. In human postmortem brain with AD pathology, Tau coimmunoprecipitates with spliceosomal components. In Drosophila, pan-neuronal Tau expression triggers reductions in multiple core and U1-specific spliceosomal proteins, and genetic disruption of these factors, including SmB, U1-70K, and U1A, enhances Tau-mediated neurodegeneration. We further show that loss of function in SmB, encoding a core spliceosomal protein, causes decreased survival, progressive locomotor impairment, and neuronal loss, independent of Tau toxicity. Lastly, RNA sequencing reveals a similar profile of mRNA splicing errors in SmB mutant and Tau transgenic flies, including intron retention and non-annotated cryptic splice junctions. In human brains, we confirm cryptic splicing errors in association with neurofibrillary tangle burden. Our results implicate spliceosome disruption and the resulting transcriptome perturbation in Tau-mediated neurodegeneration in AD.
Display omitted
•Genetic manipulation of the spliceosome enhances Tau neurotoxicity in flies•Mutation of the core spliceosome factor, SmB, causes progressive neurodegeneration•The Tau and SmB transcriptomes share similar profiles of RNA-splicing errors•Alzheimer’s disease Tau pathology associates with cryptic splicing errors in human brains
Integrating studies of human postmortem brain tissue and Drosophila melanogaster models, Hsieh et al. show that Alzheimer’s disease Tau neurofibrillary tangle pathology disrupts spliceosome activity. RNA-splicing errors, including intron retention and non-annotated cryptic junctions, and resulting transcriptome perturbation are implicated in Tau-mediated neurodegenerative mechanisms.
The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain tissues to reveal ...new AD-related protein co-expression modules that were highly preserved across cohorts and brain regions. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism and a module related to the matrisome. The matrisome module was influenced by the APOE ε4 allele but was not related to the rate of cognitive decline after adjustment for neuropathology. By contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD.
PDF
