Biology subjects

Lah, J. J.

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

At least 19 recordsLinked to original sources

bioRxiv2025

Multiplex Proteomics of Lewy Body Dementia Reveals Cerebrospinal Fluid Biomarkers of Disease Pathology and Progression

Lewy body dementia (LBD), which encompasses Parkinsons disease dementia (PDD) and Dementia with Lewy bodies (DLB), lacks established biofluid markers of its complex clinical and neuropathological heterogeneity. Multiplex proteomic tools, such as the recently developed NUcleic acid Linked ImmunoSandwich Assay (NULISATM), can assess a diverse array of neurodegenerative targets and address these biomarker gaps. We used this platform to analyze 852 baseline and longitudinal cerebrospinal fluid (CSF) samples from control, PD, and DLB subjects from the Parkinsons Disease Biomarker Program (PDBP). We then examined LBD protein signatures across different clinical diagnoses, patterns of cognitive progression, and underlying neuropathologies. Of the 124 markers analyzed, 54 were significantly altered in PD with cognitive impairment and/or DLB compared to controls, many serving as informative clinical classifiers in machine learning models. We also identified 15 proteins with significant baseline and/or longitudinal changes linked to cognitive progression. To identify neuropathological signatures, we stratified 209 cases by the presence of underlying synuclein and amyloid-beta (A{beta}) pathology using CSF alpha-synuclein seed amplification assay (Syn-SAA) results and NULISA pTau-217 levels, respectively. Select synaptic markers were decreased relative to synucleinopathy but increased relative to A{beta} accumulation, complicating their interpretation in cases with co-pathology. These neuropathological analyses were replicated in an independent cohort of 917 cases from the Alzheimers Disease Neuroimaging Initiative (ADNI). Overall, these results highlight the utility of multiplex proteomic analysis in the identification of candidate CSF biomarkers of disease heterogeneity in LBD. One Sentence SummaryThis multiplex proteomic analysis using the recently released NULISA platform revealed unique targets of Lewy body dementia progression and neuropathology.

systems biology↗

bioRxiv2025

Proteomic Subtyping of Alzheimer's Disease CSF links Blood-Brain Barrier Dysfunction to Reduced levels of Tau and Synaptic Biomarkers

Alzheimers disease (AD) is characterized by significant clinical and molecular heterogeneity, influenced by genetic and demographic factors. Using an unbiased, network-driven approach, we analyzed the cerebrospinal fluid (CSF) proteome from 431 individuals (483 samples), including 111 African American participants, to identify core protein modules associated with AD, race, sex, and age. Our analysis revealed ten co-expression modules linked to distinct biological pathways and cell types, many of which correlated with established AD biomarkers such as {beta}-amyloid, tau, and phosphorylated tau. To further resolve disease heterogeneity, we applied a proteomic subtyping approach, identifying six distinct CSF subtypes spanning the clinical and pathological spectrum. These subtypes were validated across independent cohorts, with many aligning with previously defined AD subtypes, including those linked to neuronal hyperplasticity, immune activation, and blood-brain barrier (BBB) integrity. Notably, the BBB subtype, enriched with African Americans and men, was characterized by low CSF tau, high CSF/serum albumin ratios, and reduced synaptic protein levels. This subtype also exhibited increased levels of proteolytic enzymes, including thrombin and matrix metalloproteases, that cleave tau. Plasma dilution into the neuronal hyperplastic AD subtype CSF led to reduced tau and synaptic protein module levels, indicating that plasma protease activity contributes to tau and synaptic protein depletion independent of underlying brain pathology. These findings highlight the impact of BBB integrity on CSF tau levels, particularly in men and African Americans, and underscore the need for diversity-informed AD biomarker strategies to improve diagnostics and therapeutic targeting across populations.

neuroscience↗

bioRxiv2024

Large- Scale Deep Proteomic Analysis in Alzheimer's Disease Brain Regions Across Race and Ethnicity

AbstractO_ST_ABSIntroductionC_ST_ABSAlzheimers disease (AD) is the most prevalent neurodegenerative disease, yet our comprehension predominantly relies on studies within the non-Hispanic White (NHW) population. Here we aimed to provide comprehensive insights into the proteomic landscape of AD across diverse racial and ethnic groups. MethodsDorsolateral prefrontal cortex (DLPFC) and superior temporal gyrus (STG) brain tissues were donated from multiple centers (Mayo Clinic, Emory University, Rush University, Mt. Sinai School of Medicine) and were harmonized through neuropathological evaluation, specifically adhering to the Braak staging and CERAD criteria. Among 1105 DLPFC tissue samples (998 unique individuals), 333 were from African American donors, 223 from Latino Americans, 529 from NHW donors, and the rest were from a mixed or unknown racial background. Among 280 STG tissue samples (244 unique individuals), 86 were African American, 76 Latino American, 116 NHW and the rest were mixed or unknown ethnicity. All tissues were uniformly homogenized and analyzed by tandem mass tag mass spectrometry (TMT-MS). ResultsAs a Quality control (QC) measure, proteins with more than 50% missing values were removed and iterative principal component analysis was conducted to remove outliers within brain regions. After QC, 9,180 and 9,734 proteins remained in the DLPC and STG proteome, respectively, of which approximately 9,000 proteins were shared between regions. Protein levels of microtubule-associated protein tau (MAPT) and amyloid-precursor protein (APP) demonstrated AD-related elevations in DLPFC tissues with a strong association with CERAD and Braak across racial groups. APOE4 protein levels in brain were highly concordant with APOE genotype of the individuals. DiscussionThis comprehensive region resolved large-scale proteomic dataset provides a resource for the understanding of ethnoracial-specific protein differences in AD brain.

neuroscience↗

bioRxiv2024

Bridging the Gap: Multi-Omics Profiling of Brain Tissue in Alzheimer's Disease and Older Controls in Multi-Ethnic Populations

INTRODUCTIONMulti-omics studies in Alzheimers disease (AD) revealed many potential disease pathways and therapeutic targets. Despite their promise of precision medicine, these studies lacked African Americans (AA) and Latin Americans (LA), who are disproportionately affected by AD. METHODSTo bridge this gap, Accelerating Medicines Partnership in AD (AMP-AD) expanded brain multi-omics profiling to multi-ethnic donors. RESULTSWe generated multi-omics data and curated and harmonized phenotypic data from AA (n=306), LA (n=326), or AA and LA (n=4) brain donors plus Non-Hispanic White (n=252) and other (n=20) ethnic groups, to establish a foundational dataset enriched for AA and LA participants. This study describes the data available to the research community, including transcriptome from three brain regions, whole genome sequence, and proteome measures. DISCUSSIONInclusion of traditionally underrepresented groups in multi-omics studies is essential to discover the full spectrum of precision medicine targets that will be pertinent to all populations affected with AD.

neuroscience↗

bioRxiv2024

Network Analysis of the Cerebrospinal Fluid Proteome Reveals Shared and Unique Differences Between Sporadic and Familial Forms of Amyotrophic Lateral Sclerosis

BackgroundAmyotrophic Lateral Sclerosis (ALS), a neurodegenerative disease involving loss of motor neurons, typically results in death within 3-5 years of disease onset. Although roughly 10 % of cases can be linked to a specific inherited mutation (e.g., C9orf72 hexanucleotide repeat expansion or SOD1 mutation), the cause of the majority of cases is unknown. Consequently, there is a critical need for biomarkers that reflect disease onset and progression across ALS subgroups. MethodsWe employed tandem mass tag mass spectrometry (TMT-MS) based proteomics on cerebrospinal fluid (CSF) to identify and quantify 2105 proteins from ALS patients with sporadic disease (n=35), C9orf72 ALS (n=10), and SOD1 ALS (n=6), as well as age-matched healthy controls (n=44) and asymptomatic C9orf72 carriers (n=6). We used differential protein abundance and network analyses to determine how protein profiles vary across disease types in ALS CSF. ResultsIntegrated differential and co-expression network analysis identified proteomic differences between ALS and control, and differentially abundant proteins between sporadic, C9orf72 and SOD1 ALS. Groups of proteins also differentiated asymptomatic C9orf72 mutation carriers from those with C9orf72 ALS, marking a pre-symptomatic proteomic signature of C9orf72 ALS. Similarly, additional proteins differentiated asymptomatic from controls. Leveraging additional publicly available ALS and AD proteomic datasets, we validated our ALS CSF network and identified ALS-specific proteins within Module 5 (M5)-Extracellular matrix (e.g., IGF2, RARRES2, LGALS3, GALNT15, and LYZ) and shared biomarkers across neurodegenerative diseases linked to Module 10 (M10)-Ubiquitination/Gluconeogenesis (e.g., NEFL, NEFM, CHIT1, and CHI3L1). ConclusionsThis study represents a comprehensive analysis of the CSF proteome across sporadic and genetic causes of ALS that resolves differences among these disease subgroups and points to varying pathogenic pathways that result in disease.

neuroscience↗

bioRxiv2024

An interim exploratory biomarker analysis of a Phase 2 clinical trial to assess the impact of CT1812 in Alzheimers disease

CT1812 is a novel, brain penetrant small molecule modulator of the sigma-2 receptor (S2R) that is currently in clinical development for the treatment of Alzheimers disease (AD). Preclinical and early clinical data show that, through S2R, CT1812 selectively prevents and displaces binding of amyloid beta (A{beta}) oligomers from neuronal synapses and improves cognitive function in animal models of AD. SHINE is an ongoing Phase 2 randomized, double-blind, placebo-controlled clinical trial (COG0201) in patients with mild to moderate AD, designed to assess the safety and efficacy of 6 months of CT1812 treatment. To elucidate the mechanism of action in AD patients and pharmacodynamic biomarkers of CT1812, the present study reports exploratory cerebrospinal fluid (CSF) biomarker data from an interim analysis of the first set of patients in SHINE (part A). Untargeted mass spectrometry-based discovery proteomics can detect more than 2,000 proteins in patient CSF and has documented utility in accelerating the identification of novel AD biomarkers reflective of diverse pathophysiologies beyond amyloid and tau and enabling identification of pharmacodynamic biomarkers in longitudinal interventional trials. We leveraged this technique to analyze CSF samples taken at baseline and after 6 months of CT1812 treatment. Proteome-wide protein levels were detected using tandem mass tag-mass spectrometry (TMT-MS), change from baseline was calculated for each participant, and differential abundance analysis by treatment group was performed. This analysis revealed a set of proteins significantly impacted by CT1812, including pathway engagement biomarkers (i.e., biomarkers tied to S2R biology) and disease modification biomarkers (i.e., biomarkers with altered levels in AD vs. healthy control CSF but normalized by CT1812, and biomarkers correlated with favorable trends in ADAS-Cog11 scores). Brain network mapping, Gene Ontology, and pathway analyses revealed an impact of CT1812 on synapses, lipoprotein and amyloid beta biology, and neuroinflammation. Collectively, the findings highlight the utility of this method in pharmacodynamic biomarker identification and providing mechanistic insights for CT1812, which may facilitate the clinical development of CT1812 and enable appropriate pre-specification of biomarkers in upcoming clinical trials of CT1812. HIGHLIGHTSO_LIEffects of CT1812 on AD patients were investigated in a randomized Phase 2 clinical trial C_LIO_LIPharmacodynamic biomarkers of CT1812 were identified through unbiased analysis of proteomics quantitation data acquired using TMT Mass Spectrometry (TMT-MS) C_LIO_LICT1812 normalized a set of biomarkers altered in AD C_LIO_LIFindings provide proof of mechanism that CT1812 impacts synapse, inflammation, amyloid-related processes C_LI

neuroscience↗

bioRxiv2024

Network Proteomics of the Lewy Body Dementia Brain Reveals Presynaptic Signatures Distinct from Alzheimer's Disease

Lewy body dementia (LBD), a class of disorders comprising Parkinsons disease dementia (PDD) and dementia with Lewy bodies (DLB), features substantial clinical and pathological overlap with Alzheimers disease (AD). The identification of biomarkers unique to LBD pathophysiology could meaningfully advance its diagnosis, monitoring, and treatment. Using quantitative mass spectrometry (MS), we measured over 9,000 proteins across 138 dorsolateral prefrontal cortex (DLPFC) tissues from a University of Pennsylvania autopsy collection comprising control, Parkinsons disease (PD), PDD, and DLB diagnoses. We then analyzed co-expression network protein alterations in those with LBD, validated these disease signatures in two independent LBD datasets, and compared these findings to those observed in network analyses of AD cases. The LBD network revealed numerous groups or "modules" of co-expressed proteins significantly altered in PDD and DLB, representing synaptic, metabolic, and inflammatory pathophysiology. A comparison of validated LBD signatures to those of AD identified distinct differences between the two diseases. Notably, synuclein-associated presynaptic modules were elevated in LBD but decreased in AD relative to controls. We also found that glial-associated matrisome signatures consistently elevated in AD were more variably altered in LBD, ultimately stratifying those LBD cases with low versus high burdens of concurrent beta-amyloid deposition. In conclusion, unbiased network proteomic analysis revealed diverse pathophysiological changes in the LBD frontal cortex distinct from alterations in AD. These results highlight the LBD brain network proteome as a promising source of biomarkers that could enhance clinical recognition and management.

systems biology↗

bioRxiv2023

Global analysis of the heparin-enriched plasma proteome captures matrisome-associated proteins in Alzheimer's disease

Matrisome-associated heparin binding proteins (HBPs) with roles in extracellular matrix assembly are strongly correlated to {beta}-amyloid (A{beta}) and tau pathology in Alzheimers disease (AD) brain and cerebrospinal fluid (CSF). However, it remains challenging to detect these proteins in plasma using standard mass spectrometry (MS)-based proteomic approaches. Here we utilized heparin affinity chromatography for the capture and enrichment of HBPs in plasma from healthy control and individuals with AD. This method was highly reproducible and effectively enriched well-known HBPs like APOE and thrombin, while also efficiently depleting high-abundance proteins such as albumin. To increase the depth of our analysis of the heparin-enriched plasma proteome and compare differences in disease we applied off-line fractionation and tandem mass tag mass spectrometry (TMT-MS) to compare the proteomic profiles between AD and control individuals across two datasets (n = 121 total samples). This led to the identification of 2865 proteins, spanning 10 orders of magnitude in protein abundance within the plasma. Notably, HBPs were some of the most increased proteins in AD plasma compared to controls. This included members of the matrisome-associated module in brain, SMOC1, SMOC2, SPON1, MDK, OLFML3, FRZB, GPNMB and the {varepsilon}4 isoform of APOE. Heparin-enriched plasma proteins also exhibited strong correlations to conventional AD biomarkers including CSF A{beta}, total tau (tTau), and phosphorylated tau (pTau) as well as plasma pTau supporting their role as potential surrogate markers of underlying brain pathology. Utilizing a consensus AD brain protein co-expression network, we assessed relationship between the plasma and brain proteomes and observed that specific plasma proteins exhibited consistent direction of change in both brain and plasma, whereas others displayed divergent changes, further highlighting the complex interplay between the two compartments. In summary, these findings provide support for the integration of a heparin enrichment method with MS-based proteomics for identifying a wide spectrum of plasma biomarkers that mirror pathological changes in the AD brain.

neuroscience↗

bioRxiv2022

Quantitative proteomics of cerebrospinal fluid from African Americans and Caucasians reveals shared and divergent changes in Alzheimer's disease

Despite being twice as likely to get Alzheimers disease (AD), African Americans have been grossly underrepresented in AD research. While emerging evidence indicates that African Americans with AD have lower cerebrospinal fluid (CSF) levels of Tau compared to Caucasians, other differences in AD CSF biomarkers have not been fully elucidated. Here, we performed unbiased proteomic profiling of CSF from African Americans and Caucasians with and without AD to identify both common and divergent AD CSF biomarkers. Multiplex tandem mass tag-based mass spectrometry (TMT-MS) quantified 1,840 proteins from 105 control and 98 AD patients of which 100 identified as Caucasian while 103 identified as African American. Consistent with previous findings, the increase of Tau levels in AD was greater in Caucasians than in African Americans by both immunoassay and TMT-MS measurements. Network analysis organized the CSF proteome into 14 modules associated with brain cell-types and biological pathways. CSF modules which included 14-3-3 proteins (YWHAZ and YWHAG), demonstrated equivalent disease-related elevations in both African Americans and Caucasians with AD, whereas other modules demonstrated more profound disease changes within race. Modules enriched with proteins involved with glycolysis and neuronal/cytoskeletal proteins, including Tau, were more increased in Caucasians than in African Americans with AD. In contrast, a module enriched with synaptic proteins including VGF, SCG2, and NPTX2 was significantly lower in African Americans than Caucasians with AD. Using a targeted proteomic approach (selected reaction monitoring) followed by a receiver operating characteristic curve (ROC) analysis we measured levels of VGF, SCG2, and NPTX2, which were significantly better at classifying African Americans than Caucasians with AD. Collectively, our findings provide insight into additional protein biomarkers and pathways reflecting underlying brain pathology that are shared or differ by race.

neuroscience↗

bioRxiv2022

Unbiased Classification of the Human Brain Proteome Resolves Distinct Clinical and Pathophysiological Subtypes of Cognitive Impairment

The hallmark amyloid-{beta} and tau deposition of Alzheimers disease (AD) represents only a fraction of its diverse pathophysiology. Molecular subtyping using large-scale -omic strategies can help resolve this biological heterogeneity. Using quantitative mass spectrometry, we measured ~8,000 proteins across >600 dorsolateral prefrontal cortex tissues from Religious Orders Study and Rush Memory and Aging Project participants with clinical diagnoses of no cognitive impairment, mild cognitive impairment (MCI), and AD dementia. Unbiased classification of MCI and AD cases based on individual proteomic profiles resolved three classes with expression differences across numerous cell types and biological ontologies. Two classes displayed molecular signatures atypical of those previously observed in AD neurodegeneration, such as elevated synaptic and decreased inflammatory markers. In one class, these atypical proteomic features were associated with clinical and pathological hallmarks of cognitive resilience. These results promise to better define disease heterogeneity within AD and meaningfully impact its diagnostic and therapeutic precision.

neuroscience↗

bioRxiv2022

Multi-Platform Proteomic Analysis of Alzheimer s Disease Cerebrospinal Fluid and Plasma Reveals Network Biomarkers Associated with Proteostasis and the Matrisome

Robust and accessible biomarkers that can capture the heterogeneity of Alzheimers disease and its diverse pathological processes are urgently needed. Here, we undertook an investigation of Alzheimers disease cerebrospinal fluid (CSF) and plasma from the same subjects using three different proteomic platforms--SomaLogic SomaScan, Olink proximity extension assay, and tandem mass tag-based mass spectrometry--to assess which protein markers in these two biofluids may serve as reliable biomarkers of AD pathophysiology observed from unbiased brain proteomics studies. Median correlation of overlapping protein measurements across platforms in CSF (r[~]0.7) and plasma (r[~]0.6) was good, with more variability in plasma. The SomaScan technology provided the most measurements in plasma. Surprisingly, many proteins altered in AD CSF were found to be altered in the opposite direction in plasma, including important members of AD brain co-expression modules. An exception was SMOC1, a key member of the brain matrisome module associated with amyloid-{beta} deposition in AD, which was found to be elevated in both CSF and plasma. Protein co-expression analysis on greater than 7000 protein measurements in CSF and 9500 protein measurements in plasma across all proteomic platforms revealed strong changes in modules related to autophagy, ubiquitination, and sugar metabolism in CSF, and endocytosis and the matrisome in plasma. Cross-platform and cross-biofluid proteomics represents a promising approach for AD biomarker development.

systems biology↗

bioRxiv2021

Large-Scale Deep Multi-Layer Analysis of Alzheimer's Disease Brain Reveals Strong Proteomic Disease-Related Changes Not Observed at the RNA Level

The biological processes that are disrupted in the Alzheimers disease (AD) brain remain incompletely understood. We recently performed a proteomic analysis of >2000 brains to better understand these changes, which highlighted alterations in astrocytes and microglia as likely key drivers of disease. Here, we extend this analysis by analyzing >1000 brain tissues using a tandem mass tag mass spectrometry (TMT-MS) pipeline, which allowed us to nearly triple the number of quantified proteins across cases. A consensus protein co-expression network analysis of this deeper dataset revealed new co-expression modules that were highly preserved across cohorts and brain regions, and strongly altered in AD. 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. Analysis of paired genomic and proteomic data within subjects showed that expression level of the matrisome module was influenced by the APOE {varepsilon}4 allele, but was not related to the rate of cognitive decline after adjustment for neuropathology. In 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.

systems biology↗

bioRxiv2020

TBK1 interacts with tau and enhances neurodegeneration in tauopathy

One of the defining pathological features of Alzheimers Disease (AD) is the deposition of neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau in the brain. Aberrant activation of kinases in AD has been suggested to enhance phosphorylation and toxicity of tau, making the responsible tau-directed kinases attractive therapeutic targets. The full complement of tau interacting kinases in AD brain and their activity in disease remains incompletely defined. Here, immunoaffinity enrichment coupled with mass spectrometry (MS) identified TANK-binding kinase 1 (TBK1) as a tau-interacting partner in human AD cortical brain tissues. We validated this interaction in both human AD and familial frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) caused by mutations in MAPT (R406W) postmortem brain tissues as well as human cell lines. Further, we document increased TBK1 activity in both AD and FTDP-17 and map the predominant TBK1 phosphorylation sites on tau based on in vitro kinase assays coupled to MS. Lastly, in a Drosophila tauopathy model, activating expression of a conserved TBK1 ortholog triggers tau hyperphosphorylation and enhanced neurodegeneration, whereas knockdown had the reciprocal effect, suppressing tau toxicity. Collectively, our findings suggest that increased TBK1 activity may promote tau hyperphosphorylation and neuronal loss in AD and related tauopathies.

neuroscience↗

bioRxiv2020

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease

Alzheimers disease (AD) is characterized by an early, asymptomatic phase (AsymAD) in which individuals exhibit amyloid-beta (A{beta}) plaque accumulation in the absence of clinically detectable cognitive decline. Here we report an unbiased multiplex quantitative proteomic and phosphoproteomic analysis using tandem mass tag (TMT) isobaric labeling of human post-mortem cortex (n=27) across pathology-free controls, AsymAD and symptomatic AD individuals. With off-line high-pH fractionation and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on an Orbitrap Lumos mass spectrometer, we identified 11,378 protein groups across three TMT 11-plex batches. Immobilized metal affinity chromatography (IMAC) was used to enrich for phosphopeptides from the same TMT-labeled cases and 51,736 phosphopeptides were identified. Of these, 48,992 were quantified by TMT reporter ions representing 33,652 unique phosphosites. Two reference standards in each TMT 11-plex were included to assess intra- and inter-batch variance at the protein and peptide level. This comprehensive human brain proteome and phosphoproteome dataset will serve as a valuable resource for the identification of biochemical, cellular and signaling pathways altered during AD progression.

neuroscience↗

bioRxiv2019

Identification of conserved proteomic networks in neurodegenerative dementia

Data-driven analyses of human brain across neurodegenerative diseases possess the potential for identifying disease-specific and shared biological processes. We integrated functional genomics data from postmortem brain, including label-free quantitative proteomics and RNA-seq based transcriptomics in an unprecedented dataset of over 1000 individuals across 5 cohorts representing Alzheimers disease (AD), asymptomatic AD, Progressive Supranuclear Palsy (PSP), and control patients, as a core analysis of the Accelerating Medicines Project - Alzheimers Disease (AMP-AD) consortium. We identified conserved, high confidence proteomic changes during the progression of dementias that were absent in other neurodegenerative disorders. We defined early changes in asymptomatic AD cases that included microglial, astrocyte, and immune response modules and later changes related to synaptic processes and mitochondria, many, but not all of which were conserved at the transcriptomic level. This included a novel module C3, which is enriched in MAPK signaling, and only identified in proteomic networks. To understand the relationship of core molecular processes with causal genetic drivers, we identified glial, immune, and cell-cell interaction processes in modules C8 and C10, which were robustly preserved in multiple independent data sets, up-regulated early in the disease course, and enriched in AD common genetic risk. In contrast to AD, PSP genetic risk was enriched in module C1, which represented synaptic processes, clearly demonstrating that despite shared pathology such as synaptic loss and glial inflammatory changes, AD and PSP have distinct causal drivers. These conserved, high confidence proteomic changes enriched in genetic risk represent new targets for drug discovery.\n\nHighlightsO_LIWe distinguish robust early and late proteomic changes in AD in multiple cohorts.\nC_LIO_LIWe identify changes in dementias that are not preserved in other neurodegenerative diseases.\nC_LIO_LIAD genetic risk is enriched in early up-regulated glial-immune modules and PSP in synaptic modules.\nC_LIO_LIAlmost half of the variance in protein expression reflects gene expression, but an equal fraction is post-transcriptional or -translational.\nC_LI

neuroscience↗

bioRxiv2019

Genetic control of the human brain proteome

Alteration of protein abundance and conformation are widely believed to be the hallmark of neurodegenerative diseases. Yet relatively little is known about the genetic variation that controls protein abundance in the healthy human brain. The genetic control of protein abundance is generally thought to parallel that of RNA expression, but there is little direct evidence to support this view. Here, we performed a large-scale protein quantitative trait locus (pQTL) analysis using single nucleotide variants (SNVs) from whole-genome sequencing and tandem mass spectrometry-based proteomic quantification of 12,691 unique proteins (7,901 after quality control) from the dorsolateral prefrontal cortex (dPFC) in 144 cognitively normal individuals. We identified 28,211 pQTLs that were significantly associated with the abundance of 864 proteins. These pQTLs were compared to dPFC expression quantitative trait loci (eQTL) in cognitive normal individuals (n=169; 81 had protein data) and a meta-analysis of dPFC eQTLs (n=1,433). We found that strong pQTLs are generally only weak eQTLs, and that the majority of strong eQTLs are not detectable pQTLs. These results suggest that the genetic control of mRNA and protein abundance may be substantially distinct and suggests inference concerning protein abundance made from mRNA in human brain should be treated with caution.

genetics↗

bioRxiv2019

Quantitative multiplexed proteomics of mouse microglia by flow-cytometric sorting reveals a core set of highly-abundant microglial proteins

BackgroundProteomic characterization of microglia provides the most proximate assessment of functionally relevant molecular mechanisms of neuroinflammation. However, microglial proteomics studies have been limited by low cellular yield and contamination by non-microglial proteins using existing enrichment strategies. MethodsWe coupled magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) of microglia with tandem mass tag-mass spectrometry (TMT-MS) to obtain a highly-pure microglial proteome and identified a core set of highly-abundant microglial proteins in adult mouse brain. We interrogated existing human proteomic data for Alzheimers disease (AD) relevance of highly-abundant microglial proteins and performed immuno-histochemical and in-vitro validation studies. ResultsQuantitative multiplexed proteomics by TMT-MS of CD11b+ MACS-enriched (N = 5 mice) and FACS-isolated (N = 5 mice), from adult wild-type mice, identified 1,791 proteins. A total of 203 proteins were highly abundant in both datasets, representing a core-set of highly abundant microglial proteins. In addition, we found 953 differentially enriched proteins comparing MACS and FACS-based approaches, indicating significant differences between both strategies. The FACS-isolated microglia proteome was enriched with cytosolic, endoplasmic reticulum, and ribosomal proteins involved in protein metabolism and immune system functions, as well as an abundance of canonical microglial proteins. Conversely, the MACS-enriched microglia proteome was enriched with mitochondrial and synaptic proteins and higher abundance of neuronal, oligodendrocytic and astrocytic proteins. From the 203 consensus microglial proteins with high abundance in both datasets, we confirmed microglial expression of moesin (Msn) in wild-type and 5xFAD mouse brains as well as in human AD brains. Msn expression is nearly exclusively found in microglia that surround A{beta} plaques in 5xFAD brains. In in-vitro primary microglial studies, Msn silencing by siRNA decreased A{beta} phagocytosis and increased lipopolysaccharide-induced production of the pro-inflammatory cytokine, tumor necrosis factor (TNF). In network analysis of human brain proteomic data, Msn was a hub protein of an inflammatory co-expression module positively associated with AD neuropathological features and cognitive dysfunction. ConclusionsUsing FACS coupled with TMT-MS as the method of choice for microglial proteomics, we define a core set of highly-abundant adult microglial proteins. Among these, we validate Msn as highly-abundant in plaque-associated microglia with relevance to human AD.

neuroscience↗

bioRxiv2019

Integrated Proteomics Reveals Brain-Based Cerebrospinal Fluid Biomarkers in Asymptomatic and Symptomatic Alzheimer’s Disease

Alzheimers disease (AD) features a complex web of pathological processes beyond amyloid accumulation and tau-mediated neuronal death. To meaningfully advance AD therapeutics, there is an urgent need for novel biomarkers that comprehensively reflect these disease mechanisms. Here we applied an integrative proteomics approach to identify cerebrospinal fluid (CSF) biomarkers linked to a diverse set of pathophysiological processes in the diseased brain. Using multiplex proteomics, we identified >3,500 proteins across 40 CSF samples from control and AD patients and >12,000 proteins across 48 postmortem brain tissues from control, asymptomatic AD (AsymAD), AD, and other neurodegenerative cases. Co-expression network analysis of the brain tissues resolved 44 protein modules, nearly half of which significantly correlated with AD neuropathology. Fifteen modules robustly overlapped with proteins quantified in the CSF, including 271 CSF markers highly altered in AD. These 15 overlapping modules were collapsed into five panels of brain-linked fluid markers representing a variety of cortical functions. Neuron-enriched synaptic and metabolic panels demonstrated decreased levels in the AD brain but increased levels in diseased CSF. Conversely, glial-enriched myelination and immunity panels were highly increased in both the brain and CSF. Using high-throughput proteomic analysis, proteins from these panels were validated in an independent CSF cohort of control, AsymAD, and AD samples. Remarkably, several validated markers were significantly altered in AsymAD CSF and appeared to stratify subpopulations within this cohort. Overall, these brain-linked CSF biomarker panels represent a promising step toward a physiologically comprehensive tool that could meaningfully enhance the prognostic and therapeutic management of AD.

systems biology↗