Biology subjects

Yin, L.

Publications and source records attributed to Yin, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

LINC00599 Promotes Pulmonary Hypertension via LLPS with G3BP1 and MYH9

BACKGROUNDPulmonary hypertension (PH) represents a significant cardiovascular disorder marked by both functional and structural alterations within the pulmonary vasculature. Long non-coding RNAs (lncRNAs) have been closely associated with the pathogenesis and progression of PH. Nonetheless, the precise mechanisms by which lncRNAs interact with its downstream target molecules to modulate the disease remain inadequately elucidated. METHODSThe expression levels of LINC00599 were quantified in the lung tissues of mice and pulmonary arterial smooth muscle cells (PASMCs) under hypoxic conditions. The involvement of LINC00599 in the progression of PH and vascular remodeling was evaluated through in vivo studies. To investigate the mechanisms by which LINC00599 influences the proliferation of human PASMCs, small interfering RNA and overexpression plasmids were employed. RESUITSThe expression of LINC00599 is upregulated in the medial layer of pulmonary arteries in experimental models of PH and in hypoxic PASMCs. Administration of a single dose of lentivirus-mediated shRNA targeting LINC00599 effectively reverses hypoxic PH in murine models. LINC00599 plays a critical role in PASMC proliferation by modulating stress granule formation through N6-methyladenosine (m6A) modification and promoting proliferation via liquid-liquid phase separation with myosin heavy chain 9. Furthermore, the expression of LINC00599 is regulated by a super-enhancer, which is mediated by the transcription factor ZNF263. CONCLUSIONSThese findings demonstrate for the first time that LINC00599, involved in liquid-liquid phase separation, facilitates the progression of pulmonary hypertension by enhancing the proliferation of pulmonary artery smooth muscle cells. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/629439v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@7ac192org.highwire.dtl.DTLVardef@13a88b3org.highwire.dtl.DTLVardef@1e4c761org.highwire.dtl.DTLVardef@ddd105_HPS_FORMAT_FIGEXP M_FIG C_FIG What Is New?This study identified LINC00599 as a critical regulator of liquid-liquid phase separation through m6A modification and as a pivotal target in promoting the progression of PH. What Is Relevant?LncRNAs are intricately associated with the pathogenesis and progression of PH through the modulation of downstream target molecules. However, it remains unclear whether lncRNAs contribute to PH by forming specific subcellular structures with these target molecules. Furthermore, some studies have suggested that the increased presence of stress granules in PASMCs is implicated in the pathogenesis of pulmonary arterial hypertension. In this study, we provide evidence that LINC00599 promotes the development of PH by forming stress granules with its target proteins. Our findings indicate that the binding of LINC00599, modified with m6A, to G3BP1 and MYH9 in PASMCs suggests that the regulation of liquid-liquid phase separation by lncRNA m6A modification may represent a significant pathological mechanism underlying PH. What Are the Pathophysiological Implications?We found that LINC00599 levels were elevated in hypoxic PASMCs and experimental PH models. Knockout LINC00599 effectively prevented PH, indicating its potential as both a bomarker and therapeutic target for PH.

physiology↗

bioRxiv2024

I2SIM: Boosting High-Fidelity Isotropic Super-Resolution with Image Interference and Spatial-Spectrum Optimization

Spatial resolution is crucial for imaging subcellular structures. The advent of three-dimensional structured illumination microscopy (3D-SIM) greatly benefits the biology community, providing a powerful tool for imaging organelles with a two-fold resolution enhancement in all three dimensions. However, the axial resolution of 3D-SIM is limited to around 300 nm, which is inferior to its lateral resolution. Here, a novel method called image interference SIM (I2SIM) is reported, which utilizes two oppositely positioned objectives to detect fluorescence emission interference under three-beam excitation. By incorporating spectral modulation and spatial domain Frobenius-Hessian optimization, I2SIM achieves an axial resolution approximately twice that of 3D-SIM, reaching around 130 nm. Furthermore, the potential of I2SIM for imaging subcellular structures is demonstrated on various biological samples, including microtubules, actin filaments, and mitochondrial outer membranes. The enhanced optical sectioning capability can be utilized to resolve axial structures that are challenging to discern using ordinary 3D-SIM.

biophysics↗

bioRxiv2024

Machine Learning Identifies Genes Linked to Neurological Disorders Induced by Equine Encephalitis viruses (EEV), Traumatic Brain Injuries (TBI), and Organophosphorus nerve agents (OPNA)

Venezuelan, eastern, and western equine encephalitis viruses (collectively referred to as equine encephalitis viruses---EEV) cause serious neurological diseases and are a significant threat to the civilian population and the warfighter. Likewise, organophosphorus nerve agents (OPNA) are highly toxic chemicals that pose serious health threats of neurological deficits to both military and civilian personnel around the world. Consequently, only a select few approved research groups are permitted to study these dangerous chemical and biological warfare agents. This has created a significant gap in our scientific understanding of the mechanisms underlying neurological diseases. Valuable insights may be gleaned by drawing parallels to other extensively researched neuropathologies, such as traumatic brain injuries (TBI). By examining combined gene expression profiles, common and unique molecular characteristics may be discovered, providing new insights into medical countermeasures (MCMs) for TBI, EEV infection and OPNA neuropathologies and sequelae. In this study, we collected transcriptomic datasets for neurological disorders caused by TBI, EEV, and OPNA injury, and implemented a framework to normalize and integrate gene expression datasets derived from various platforms. Effective machine learning approaches were developed to identify critical genes that are associated, either shared among the three neuropathologies or to either TBI, EEV, and OPNA. With the aid of deep neural networks, we were able to extract important association signals for accurate prediction of different neurological disorders by using integrated gene expression datasets of VEEV, OPNA, and TBI samples. Gene ontology and pathway analyses further identified neuropathologic features with specific gene product attributes and functions, shedding light on the fundamental biology of these neurological disorders. Collectively, we highlight a workflow to analyze published transcriptomic data using machine learning, which can be used for both identification of gene biomarkers that are unique to specific neurological conditions, as well as genes shared across multiple neuropathologies. These shared genes could serve as potential neuroprotective drug targets for conditions like EEV, TBI, and OPNA.

neuroscience↗

bioRxiv2024

Elevated EGR1 Binding at Enhancers in Excitatory Neurons Correlates with Neuronal Subtype-Specific Epigenetic Regulation

Brain development and neuronal cell specification are accompanied with epigenetic changes to achieve diverse gene expression regulation. Interacting with cell-type specific epigenetic marks, transcription factors bind to different sets of cis-regulatory elements in different types of cells. Currently, it remains largely unclear how cell-type specific gene regulation is achieved for neurons. In this study, we generated epigenetic maps to perform comparative histone modification analysis between excitatory and inhibitory neurons. We found that neuronal cell-type specific histone modifications are enriched in super enhancer regions containing abundant EGR1 motifs. Further CUT&RUN data validated that more EGR1 binding sites can be detected in excitatory neurons and primarily located in enhancers. Integrative analysis revealed that EGR1 binding is strongly correlated with various epigenetic markers for open chromatin regions and associated with distinct gene pathways with neuronal subtype-specific functions. In inhibitory neurons, the majority of genomic regions hosting EGR1 binding sites become accessible at early embryonic stages. In contrast, the super enhancers in excitatory neurons hosting EGR1 binding sites gained their accessibility during postnatal stages. This study highlights the significance of transcription factor binding to enhancer regions, which may play a crucial role in establishing cell-type specific gene regulation in neurons.

neuroscience↗

bioRxiv2024

Sample-specific network analysis identifies gene coexpression patterns of immunotherapy response in advanced kidney cancer

Immunotherapies have recently emerged as a standard of care for advanced cancers, offering remarkable improvements in patient prognosis. However, only a small proportion of patients respond to the treatment, and no definitive molecular hallmark has been identified for clinical use in predicting treatment outcomes. Here, we propose a sample-specific weighted gene network approach to investigate the heterogeneity of patient clinical outcomes by leveraging multiscale network features derived from gene expression data. Our results show that patients exhibiting similar clinical benefits share comparable gene coexpression patterns. Increased gene connectivity and stronger negative gene-gene associations are also pivotal factors in patients with poor prognoses. Moreover, integrating pathway genes with topological measures enables the identification of the perturbed regulation of biological pathways associated with treatment responses. Additionally, sample-level network features enhance the prediction performance of gene expression values-based machine learning models. Collectively, our approach provides valuable guidance on the use of gene network information to stratify cancer patients and to optimize treatment strategies.

bioinformatics↗

bioRxiv2024

TET2-mediated epigenetic modification promotes stress senescence of pancreatic β cells in type 2 diabetes mellitus

Epigenetic modification plays a key role in {beta} cell senescence. In the regulation of gene expression, there is a complex and close relationship between DNA methylation and histone modification. In order to explore its specific mechanism in T2DM {beta} cell senescence, we used postbisulfite aptamer labeling of genome-wide bisulfite-SEQ, chromatin immunocoprecipitation-SEQ, RNA-SEQ, CRISPR/Cas9 TETs knockout, RNA interference, TET2 inhibitors, lentiviral overexpression, and gene knockout mouse models. Our study found that demethylase TET2 was localized in the islets of mice, and the expression level increased with age. TET2 knockout in pancreatic {beta} cells can hypermethylate PTEN, up-regulate MOF and enrich H4K16ac, and reduce the level of aging markers. This study confirmed that TET2-mediated PTEN DNA methylation can promote a new mechanism of {beta} cell senescence by regulating H4K16ac, providing a new molecular mechanism and therapeutic target for T2DM {beta} cell senescence therapy.

cell biology↗

bioRxiv2024

Brainstem neurons coordinate the bladder and urethra sphincter for urination

Urination, a vital and conserved process of emptying urine from the urinary bladder in mammals, requires precise coordination between the bladder and external urethral sphincter (EUS) that is tightly controlled by a complex neural network. However, the specific subpopulation of neurons that accounts for such coordination remains unidentified, limiting the development of target-specific therapies for certain urination disorders, e.g., detrusor-sphincter dyssynergia. Here, we find that cells expressing estrogen receptor 1 (ESR1+) in the pontine micturition center (PMC) initiate voiding when activated and suspend ongoing voiding when suppressed, each at 100% reliability. Transection of the pelvic nerve does not impair PMCESR1+ neurons control of the EUS via the pudendal nerve, whereas transection of the pudendal nerve does not impair their control of the bladder via the pelvic nerve. Anatomically, PMCESR1+ neurons consist of three distinct spinal-projection-based subpopulations: one targeting the sacral parasympathetic nucleus (SPN), one innervating the dorsal gray commissure (DGC), and a third that projects to both regions, thereby enforcing the coordination of bladder contraction and sphincter relaxation in a rigid temporal sequence. Thus, we identify a cell type in the brainstem that controls the bladder-urethra coordination for urination.

neuroscience↗

bioRxiv2024

Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA

DNA deaminase toxins are involved in interbacterial antagonism and the generation of genetic diversity in surviving bacterial populations. These enzymes have also been adopted as genome engineering tools. The single-stranded (ss)DNA deaminase SsdA represents the bacterial deaminase toxin family-2 (BaDTF2) and it deaminates ssDNA cytosines with little sequence context dependence, which contrasts with the AID/APOBEC family of sequence-selective ssDNA cytosine deaminases. Here we report the crystal structure of SsdA in complex with a ssDNA substrate. The structure reveals a unique mode of substrate binding, in which a cluster of aromatic residues of SsdA engages ssDNA in a V-shaped conformation sharply bent across the target cytosine. The bases 5 or 3 to the target cytosine are stacked linearly and make few sequence-specific protein contacts, thus explaining the broad substrate selectivity of SsdA. Unexpectedly, SsdA contains a {beta}-amino acid isoaspartate, which is important for enzymatic activity and may contribute to the stability of SsdA as a toxin. Structure- function studies helped to design SsdA mutants active in human cells, which could lead to future applications in genome engineering.

biochemistry↗

bioRxiv2024

A biodegradable and restorative peripheral neural interface for the interrogation of neuropathic injuries

Monitoring the early-stage healing of severe traumatic nerve injuries is essential to gather physiological and pathological information for timely interventions and optimal clinical outcomes. While implantable peripheral nerve interfaces provide direct access to nerve fibers for precise interrogation and modulation, conventional non-degradable designs pose limited utilization in nerve injury rehabilitation. Here, we introduce a biodegradable and restorative neural interface for wireless real-time tracking and recovery of long-gap nerve injuries. Leveraging machine learning techniques, this electronic platform deciphers nerve recovery status and identifies traumatic neuroma formation at the early phase, enabling timely intervention and significantly improved therapeutic outcomes. The biodegradable nature of the device eliminates the need for retrieval procedures, reducing infection risks and secondary tissue damage. This research sheds light on bioresorbable multifunctional peripheral nerve interfaces for probing neuropathic injuries, offering vital information for early diagnosis and therapeutic intervention.

bioengineering↗

bioRxiv2024

Spatial Transcriptomics and Single-Nucleus Multi-omics Analysis Revealing the Impact of High Maternal Folic Acid Supplementation on Offspring Brain Development

Folate, an essential vitamin B9, is crucial for diverse biological processes including neurogenesis. Folic acid (FA) supplementation during pregnancy is a standard practice for preventing neural tube defects (NTDs). However, concerns are growing over the potential risks of excessive maternal FA intake. Here, we employed mouse model and spatial transcriptomics and single-nucleus multi-omics approaches to investigate the impact of high maternal FA supplementation during the periconceptional period on offspring brain development. Maternal high FA supplementation affected gene pathways linked to neurogenesis and neuronal axon myelination across multiple brain regions, as well as gene expression alterations related to learning and memory in thalamic and ventricular regions. Single-nucleus multi-omics analysis revealed that maturing excitatory neurons in the dentate gyrus (DG) are particularly vulnerable to high maternal FA intake, leading to aberrant gene expressions and chromatin accessibility in pathways governing ribosomal biogenesis critical for synaptic formation. Our findings provide new insights into specific brain regions, cell types, gene expressions and pathways that can be affected by maternal high FA supplementation.

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

Targeted NAD+ Delivery for Intimal Hyperplasia and Re-endothelialization: A Novel Anti-restenotic Therapy Approach

Endovascular interventions often fail due to restenosis, primarily caused by smooth muscle cell (SMC) proliferation, leading to intimal hyperplasia (IH). Current strategies to prevent restenosis are far from perfect and impose significant collateral damage on the fragile endothelial cell (EC), causing profound thrombotic risks. Nicotinamide adenine dinucleotide (NAD+) is a co-enzyme and signaling substrate implicated in redox and metabolic homeostasis, with a pleiotropic role in protecting against cardiovascular diseases. However, a functional link between NAD+ repletion and the delicate duo of IH and EC regeneration has yet to be established. NAD+ repletion has been historically challenging due to its poor cellular uptake and low bioavailability. We have recently invented the first nanocarrier that enables direct intracellular delivery of NAD+ in vivo. Combining the merits of this prototypic NAD+-loaded calcium phosphate (CaP) nanoparticle (NP) and biomimetic surface functionalization, we created a biomimetic P-NAD+-NP with platelet membrane coating, which enabled an injectable modality that targets IH with excellent biocompatibility. Using human cell primary culture, we demonstrated the benefits of NP-assisted NAD+ repletion in selectively inhibiting the excessive proliferation of aortic SMC, while differentially protecting aortic EC from apoptosis. Moreover, in a rat balloon angioplasty model, a single-dose treatment with intravenously injected P-NAD+-NP immediately post angioplasty not only mitigated IH, but also accelerated the regeneration of EC (re-endothelialization) in vivo in comparison to control groups (i.e., saline, free NAD+ solution, empty CaP-NP). Collectively, our current study provides proof-of-concept evidence supporting the role of targeted NAD+ repletion nanotherapy in managing restenosis and improving re-endothelialization.

pathology↗

bioRxiv2024

The kinematics and aerodynamics of hinged wing of honeybees during takeoff

In this study, we utilize a high-speed camera array to meticulously capture the intricate wing kinematics of honeybees during free voluntary takeoffs. This allows us to investigate the variation in kinematic parameters over time. According to the variation of Euler angles, the takeoff process can be categorized into three stages: initial, adjusting, and stable. Our analysis reveals that honeybees typically execute at least 15 wingbeats before taking off, with wing stroke amplitudes exceeding 100 degrees and wingbeat frequencies ranging from 180 to 260 Hz. Significantly, the hinged wing mechanism, connecting the forewing and hindwing via hamuli, undergoes considerable chordwise deformation during this process, with the angle between the fore- and hind-wings surpassing 50 degrees. Notably, the forewing and hindwing maintain a positive camber throughout the wingbeat cycle during takeoff, contributing to the enhanced thrust generation instead of lift, comparing to the flat wings. The positive camber can be passively formed at beginning and ending of each half stroke, but should be actively maintained around middle half-stroke.This study provides valuable insights for aeronautical engineers in the design of flapping wing micro air vehicles, specifically in the effective implementation of hinged wings inspired by the wing motion of honeybees.

biophysics↗

bioRxiv2024

Leptin Activated Hypothalamic BNC2 Neurons Acutely Suppress Food Intake

Leptin is an adipose tissue hormone that maintains homeostatic control of adipose tissue mass by regulating the activity of specific neural populations controlling appetite and metabolism1. Leptin regulates food intake by inhibiting orexigenic agouti-related protein (AGRP) neurons and activating anorexigenic pro-opiomelanocortin (POMC) neurons2. However, while AGRP neurons regulate food intake on a rapid time scale, acute activation of POMC neurons has only a minimal effect3-5. This has raised the possibility that there is a heretofore unidentified leptin-regulated neural population that suppresses appetite on a rapid time scale. Here, we report the discovery of a novel population of leptin-target neurons expressing basonuclin 2 (Bnc2) that acutely suppress appetite by directly inhibiting AGRP neurons. Opposite to the effect of AGRP activation, BNC2 neuronal activation elicited a place preference indicative of positive valence in hungry but not fed mice. The activity of BNC2 neurons is finely tuned by leptin, sensory food cues, and nutritional status. Finally, deleting leptin receptors in BNC2 neurons caused marked hyperphagia and obesity, similar to that observed in a leptin receptor knockout in AGRP neurons. These data indicate that BNC2-expressing neurons are a key component of the neural circuit that maintains energy balance, thus filling an important gap in our understanding of the regulation of food intake and leptin action.

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↗

bioRxiv2024

Plaat1l1 controls feeding induced NAPE biosynthesis and contributes to energy balance regulation in zebrafish.

Dysregulation of energy balance leading to obesity is a significant risk factor for cardiometabolic diseases such as diabetes, non-alcoholic fatty liver disease and atherosclerosis. In rodents and a number of other vertebrates, feeding has been shown to induce a rapid rise in the intestinal levels of N-acyl-ethanolamines (NAEs) and the chronic consumption of a high fat diet abolishes this rise. Administering NAEs to rodents consuming a high fat diet reduces their adiposity, in part by reducing food intake and enhancing fat oxidation, so that feeding-induced intestinal NAE biosynthesis appears to be critical to appropriate regulation of energy balance. However, the contribution of feeding-induced intestinal NAE biosynthesis to appropriate energy balance remains poorly understood because the specific enzymes responsible for feeding-induced NAE biosynthesis have not been identified. The rate-limiting step in the intestinal biosynthesis of NAEs is formation of their immediate precursors, the N-acyl-phosphatidylethanolamines (NAPEs), by phosphatidylethanolamine N-acyltransferases (NATs). At least six NATs are found in humans and multiple homologs of these NATs are found in most vertebrate species. In recent years, the fecundity and small size of zebrafish (Danio rerio), as well as their similarities in feeding behavior and energy balance regulation with mammals, have led to their use to model key features of cardiometabolic disease. We therefore searched the Danio rerio genome to identify all NAT homologs and found two additional NAT homologs besides the previously reported plaat1, rarres3, and rarres3l, and used CRISPR/cas9 to delete these two NAT homologs (plaat1l1 and plaat1l2). While wild-type fish markedly increased their intestinal NAPE and NAE levels in response to a meal after fasting, this response was completely ablated in plaat1l1-/- fish. Furthermore, plaat1l1-/-fish fed a standard flake diet had increased weight gain and glucose intolerance compared to wild-type fish. The results support a critical role for feeding-induced NAE biosynthesis in regulating energy balance and suggest that restoring this response in obese animals could potentially be used to treat obesity and cardiometabolic disease.

biochemistry↗

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↗