Biology subjects

Lah, J. J.

Publications and source records attributed to Lah, J. J..

25 records · Page 2Linked to original sources

bioRxiv2019

Cerebral atherosclerosis contributes to Alzheimer’s dementia independently of its hallmark amyloid and tau pathologies

Cerebral atherosclerosis is a leading cause of stroke and an important contributor to dementia. However, little is known about its molecular effects on the human brain and how these alterations may contribute to dementia. Here, we investigated these questions using large-scale quantification of over 8300 proteins from 438 post-mortem brains from a discovery and replication cohort. A proteome-wide association study and protein network analysis of cerebral atherosclerosis found 114 proteins and 5 protein co-expression modules associated with cerebral atherosclerosis. Enrichment analysis of these proteins and modules revealed that cerebral atherosclerosis was associated with reductions in synaptic signaling and RNA splicing and increases in oligodendrocyte development and myelination. A subset of these proteins (n=23) and protein modules (n=2) were also associated with Alzheimers disease (AD) dementia, implicating a shared mechanism with AD through decreased synaptic signaling and regulation and increased myelination. Notably, neurofilament light (NEFL) and medium (NEFM) chain proteins were among these 23 proteins, and our data suggest they contribute to AD dementia through cerebral atherosclerosis. Together, our findings offer insights into effects of cerebral atherosclerosis on the human brain proteome, and how cerebral atherosclerosis contributes to dementia risk.

neuroscience↗

bioRxiv2019

A Consensus Proteomic Analysis of Alzheimer’s Disease Brain and Cerebrospinal Fluid Reveals Early Changes in Energy Metabolism Associated with Microglia and Astrocyte Activation

Our understanding of the biological changes in the brain associated with Alzheimers disease (AD) pathology and cognitive impairment remains incomplete. To increase our understanding of these changes, we analyzed dorsolateral prefrontal cortex of control, asymptomatic AD, and AD brains from four different centers by label-free quantitative mass spectrometry and weighted protein co-expression analysis to obtain a consensus protein co-expression network of AD brain. This network consisted of 13 protein co-expression modules. Six of these modules correlated with amyloid-{beta} plaque burden, tau neurofibrillary tangle burden, cognitive function, and clinical functional status, and were altered in asymptomatic AD, AD, or in both disease states. These six modules reflected synaptic, mitochondrial, sugar metabolism, extracellular matrix, cytoskeletal, and RNA binding/splicing biological functions. The identified protein network modules were preserved in a community-based cohort analyzed by a different quantitative mass spectrometry approach. They were also preserved in temporal lobe and precuneus brain regions. Some of the modules were influenced by aging, and showed changes in other neurodegenerative diseases such as frontotemporal dementia and corticobasal degeneration. The module most strongly associated with AD pathology and cognitive impairment was the sugar metabolism module. This module was enriched in AD genetic risk factors, and was also highly enriched in microglia and astrocyte protein markers associated with an anti-inflammatory state, suggesting that the biological functions it represents serve a protective role in AD. Proteins from the sugar metabolism module were increased in cerebrospinal fluid from asymptomatic AD and AD cases, highlighting their potential as biomarkers of the altered brain network. In this study of >2000 brains and nearly 400 cerebrospinal fluid samples by quantitative proteomics, we identify proteins and biological processes in AD brain that may serve as therapeutic targets and fluid biomarkers for the disease.

systems biology↗

bioRxiv2019

Microglial ERK activation is a critical regulator of pro-inflammatory immune responses in Alzheimer’s disease

BackgroundThe mitogen-activated protein kinase (MAPK) pathway is a central regulator of gene expression, pro-survival signaling, and inflammation. However, the importance of MAPK pathway signaling in regulating microglia-mediated neuroinflammation in Alzheimers Disease (AD) remains unclear. Here we examined the role of MAPK signaling in microglia using pre-clinical in-vitro and in-vivo models of AD pathology integrated with quantitative proteomics studies of post-mortem human brains.\n\nMethodsWe performed multiplexed immunoassay analyses of MAPK phosphoproteins, particularly ERK1/2, in acutely-isolated microglia and brain tissue from wild-type and 5xFAD mice. Neuropathological studies of mouse and human brain tissues were performed to quantify total and phosphorylated ERK protein in AD. The importance of ERK signaling in unstimulated and interferon {gamma} (IFN{gamma})-stimulated primary microglia cultures was investigated using NanoString transcriptomic profiling, coupled with functional assays of amyloid {beta} (A{beta}) and neuronal phagocytosis. Receptor tyrosine kinases (RTKs) likely responsible for ERK signaling in homeostatic microglia and disease-associated-microglia (DAM) states and ERK-regulated human AD risk genes were identified using gene expression data. Total and phosphorylated MAPKs in human post-mortem brain tissues were measured in quantitative proteomic datasets.\n\nResultsPhosphorylated ERK was the most strongly up-regulated signaling protein within the MAPK pathway in microglia acutely isolated from 5xFAD brains. Neuroinflammatory transcriptomic and phagocytic profiling of mouse microglia confirmed that ERK is a critical regulator of IFN{gamma}-mediated pro-inflammatory activation of microglia, although it was also important for constitutive microglial functions. Phospho-ERK was an upstream regulator of disease-associated microglia (DAM) gene expression (Trem2, Tyrobp), as well as of several human AD risk genes (Bin1, Cd33, Trem2, Cnn2). Among RTKs that signal via ERK, CSF1R and MERTK were primarily expressed by homeostatic microglia while AXL and FLT1 were likely regulators of ERK signaling in DAM. Within DAM, FLT4 and IGF1R were specifically expressed by pro- and anti-inflammatory DAM sub-profiles respectively. In quantitative proteomic analyses of post-mortem human brains from non-disease, asymptomatic and cognitively-impaired AD cases, ERK1 and ERK2 were the only MAPK pathway signaling proteins with increased protein expression and positive associations with neuropathological grade. Moreover, in a phospho-proteomic study of post-mortem human brains from controls, asymptomatic and symptomatic AD cases, we found evidence for a progressive increased flux through the ERK signaling pathway.\n\nConclusionsOur integrated analyses using pre-clinical models and human proteomic data strongly suggest that ERK phosphorylation in microglia is a critical regulator of pro-inflammatory immune response in AD pathogenesis and that modulation of ERK via upstream RTKs may reveal novel avenues for immunomodulation.

neuroscience↗

bioRxiv2019

Large-scale proteomic analysis of human prefrontal cortex identifies proteins associated with cognitive trajectory in advanced age

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 novel evidence for increased neuronal mitochondrial activities in cognitive stability regardless of the burden of traditional neuropathologies. Furthermore, we provide additional evidence for increased synaptic activities 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.

neuroscience↗

bioRxiv2019

Tau-mediated Disruption of the Spliceosome Triggers Cryptic RNA-splicing and Neurodegeneration in Alzheimer’s Disease

In Alzheimers 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 core components. In Drosophila models, pan-neuronal Tau expression triggers reductions in 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 pathologic burden. Our results implicate spliceosome disruption and perturbations of the neuronal transcriptome in Tau-mediated neurodegeneration in AD.

neuroscience↗

bioRxiv2018

Multiscale causal network models of Alzheimer’s disease identify VGF as a key regulator of disease

Though discovered over 100 years ago, the molecular foundation of sporadic Alzheimers disease (AD) remains elusive. To elucidate its complex nature, we constructed multiscale causal network models on a large human AD multi-omics dataset, integrating clinical features of AD, DNA variation, and gene and protein expression into probabilistic causal models that enabled detection and prioritization of high-confidence key drivers of AD, including the top predicted key driver VGF. Overexpression of neuropeptide precursor VGF in 5xFAD mice partially rescued beta-amyloid-mediated memory impairment and neuropathology. Molecular validation of network predictions downstream of VGF was achieved, with significant enrichment for homologous genes identified as differentially expressed in 5xFAD brains overexpressing VGF versus controls. Our findings support a causal and/or protective role for VGF in AD pathogenesis and progression.\n\nOne sentence summaryVGF protects against Alzheimers disease

genomics↗

bioRxiv2018

RNA-binding proteins with mixed charge domains self-assemble and aggregate in Alzheimer’s Disease

U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary Tau aggregates in Alzheimers disease (AD), yet understanding of the mechanisms that cause their aggregation is limited. Many RBPs that aggregate in neurodegenerative diseases self-assemble into RNA granules through intrinsically disordered low complexity (LC) domains. We report here that a LC domain within U1-70K of mixed charge, containing highly repetitive complementary repeats of basic (R/K) and acidic (D/E) residues, shares many of the same properties of the Q/N-rich LC domains found in the RBPs TDP-43 and FUS. These properties include the ability to self-assemble into oligomers, and to form nuclear granules. To analyze the functional roles of the U1-70K LC domains, we performed co-immunoprecipitation and quantitative mass spectrometry analysis of recombinant U1-70K and deletions lacking the C-terminal LC domain(s). A network-driven approach resolved functional classes of U1-70K interacting proteins that showed dependency on the U1-70K LC domain(s) for their interaction. This included structurally similar RBPs, such as LUC7L3 and RBM25, which require their respective mixed charge domains for reciprocal interactions with U1-70K and for participation in nuclear RNA granules. Strikingly, a significant proportion of RBPs with mixed charge domains have elevated insolubility in AD brain proteome compared to controls. Furthermore, we show that the mixed charge LC domain of U1-70K can interact with Tau from AD brain. These findings highlight mechanisms for mixed charge domains in stabilizing RBP interactions and in potentially mediating co-aggregation with pathological Tau isoforms in AD.

biochemistry↗