Biology subjects

Zhu, K.

Publications and source records attributed to Zhu, K..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

An efficient method for visualizing the plaques of Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus preys upon other Gram-negative bacteria. This obligate predator is recognized as a living antibiotic to control the rising problem of antibiotic resistance. Plaque forming units (PFU) counting is commonly used to determine the viable numbers of B. bacteriovorus. However, nearly 3-days incubation is always necessary for getting the single, obvious plaques on the double layer agar plate. This time-consuming procedure greatly impedes the purification and enumeration efficiency of B. bacteriovorus. In this work, we evaluated the advantages of fluorescent prey on the plaque visualization of the predator. Our study reveals that plaques of the B. bacteriovorus have already formed before they could be monitored by eyes on the double layer agar plate. The regular single plaques are easily observed under the enhanced background of fluorescent prey lawn in 1.5 days, reducing nearly half of the time consumption in the purification and enumeration of B. bacteriovorus. In addition, it also provides some paradigms for modeling and testing the subtle predation process on the solid medium. IMPORTANCEThe viability of predator Bdellovibrio bacteriovorus is typically suggested by the lysis of the prey bacteria on the double layer agar plate. However, long period incubation is necessary to get single obvious plaques of B. bacteriovorus. Here, we found that plaques are already generated before it can be monitored by eyes. The plaques are obvious on the enhanced background of the double layer agar plate in the presence of fluorescent prey under UV light. We confirmed that the utilization of fluorescence labeled prey bacteria reduces the time spent on the isolation, purification, and enumeration of the predator B. bacteriovorus on the double layer agar plate.

microbiology↗

bioRxiv2024

Natural antibodies to polysaccharide capsules enable Kupffer cells to capture invading bacteria in the liver sinusoids

The interception of blood-borne bacteria in the liver defines the outcomes of invasive bacterial infections, but the mechanisms of this anti-bacterial immunity are largely speculative. This study shows that natural antibodies (nAbs) to capsules enable liver macrophage Kupffer cells (KCs) to rapidly capture and kill blood-borne encapsulated bacteria in mice. Affinity pulldown with serotype-10A capsular polysaccharides (CPS10A) of S. pneumoniae (Spn10A) led to the identification of CPS10A-binding nAbs in serum. The CPS10A-antibody interaction enabled KCs to capture Spn10A bacteria from the bloodstream, in part through complement receptors on KCs. The nAbs were found to recognize the {beta}1-6-linked galactose branch of CPS10A, and similar moieties of serotype-39 S. pneumoniae and serotype-K50 Klebsiella pneumoniae capsules. More importantly, the nAbs empowered KCs to capture serotype-39 S. pneumoniae and serotype-K50 K. pneumoniae in the liver. Collectively, our data have revealed a highly effective immune function of nAb against encapsulated bacteria, and provided a proof of concept for treating septic bacterial diseases with monoclonal antibodies. Short summaryRapid capture of potentially harmful bacteria in blood by liver macrophages are vital for the blood sterility and health. This work reports how naturally occurring antibodies in the plasma enable macrophages to capture and kill blood-borne bacteria in the liver.

microbiology↗

bioRxiv2024

Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L

Recent discoveries expanding the spectrum of ubiquitylation substrates to include non-proteinaceous molecules have broadened our understanding of this modification beyond conventional protein targets. However, the existence of additional types of substrates remains elusive. Here, we present evidence that nucleic acids can also be directly ubiquitylated. DTX3L, a member of the DELTEX family E3 ubiquitin ligases, ubiquitylates DNA and RNA in vitro and that this activity is not shared with another DELTEX family member DTX2. DTX3L shows preference for the 3-terminal adenosine over other nucleotides. In addition, we demonstrate that ubiquitylation of nucleic acids is reversible by DUBs such as USP2 and SARS-CoV-2 PLpro. Overall, our study provides evidence for reversible ubiquitylation of nucleic acids in vitro and discusses its potential functional implications.

biochemistry↗

bioRxiv2024

Rat primary cortical cell tri-culture to study effects of amyloid-beta on microglia function

IntroductionThe etiology and progression of sporadic Alzheimers Disease (AD) have been studied for decades. One proposed mechanism is that amyloid-beta (A{beta}) proteins induce neuroinflammation, synapse loss, and neuronal cell death. Microglia play an especially important role in A{beta} clearance, and alterations in microglial function due to aging or disease may result in A{beta} accumulation and deleterious effects on neuronal function. However, studying these complex factors in vivo, where numerous confounding processes exist, is challenging, and until recently, in vitro models have not allowed sustained culture of microglia, astrocytes and neurons in the same culture. Here, we employ a tri-culture model of rat primary neurons, astrocytes, and microglia and compare it to co-culture (neurons and astrocytes) and mono-culture enriched for microglia to study microglial function (i.e., motility and A{beta} clearance) and proteomic response to exogenous A{beta}. MethodsWe established cortical co-culture (neurons and astrocytes), tri-culture (neurons, astrocytes, and microglia), and mono-culture (microglia) from perinatal rat pups. On days in vitro (DIV) 7 - 14, the cultures were exposed to fluorescently-labeled A{beta} (FITC-A{beta}) particles for varying durations. Images were analyzed to determine the number of FITC-A{beta} particles after specific lengths of exposure. A group of cells were stained for {beta}III-tubulin, GFAP, and Iba1 for morphological analysis via quantitative fluorescence microscopy. Cytokine profiles from conditioned media were obtained. Live-cell imaging with images acquired every 5 minutes for 4 hours was employed to extract microglia motility parameters (e.g., Euclidean distance, migration speed, directionality ratio). Results and discussionFITC-A{beta} particles were more effectively cleared in the tri-culture compared to the co-culture. This was attributed to microglia engulfing FITC-A{beta} particles, as confirmed via epifluorescence and confocal microscopy. Adding FITC-A{beta} significantly increased the size of microglia, but had no significant effect on neuronal surface coverage or astrocyte size. Analysis of the cytokine profile upon FITC-A{beta} addition revealed a significant increase in proinflammatory cytokines (TNF-, IL-1, IL-1{beta}, IL-6) in tri-culture, but not co-culture. In addition, A{beta} addition altered microglia motility marked by swarming-like motion with decreased Euclidean distance yet unaltered speed. These results highlight the importance of cell-cell communication in microglia function (e.g., motility and A{beta} clearance) and the utility of the tri-culture model to further investigate microglia dysfunction in AD.

neuroscience↗

bioRxiv2024

CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.

cancer biology↗

bioRxiv2023

Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change

Oncogene amplification is a major driver of cancer pathogenesis. Breakage fusion bridge (BFB) cycles, like extrachromosomal DNA (ecDNA), can lead to high copy numbers of oncogenes, but their impact on intratumoral heterogeneity, treatment response, and patient survival are not well understood due to difficulty in detecting them by DNA sequencing. We describe a novel algorithm that detects and reconstructs BFB amplifications using optical genome maps (OGMs), called OM2BFB. OM2BFB showed high precision (>93%) and recall (92%) in detecting BFB amplifications in cancer cell lines, PDX models and primary tumors. OM-based comparisons demonstrated that short-read BFB detection using our AmpliconSuite (AS) toolkit also achieved high precision, albeit with reduced sensitivity. We detected 371 BFB events using whole genome sequences from 2,557 primary tumors and cancer lines. BFB amplifications were preferentially found in cervical, head and neck, lung, and esophageal cancers, but rarely in brain cancers. BFB amplified genes show lower variance of gene expression, with fewer options for regulatory rewiring relative to ecDNA amplified genes. BFB positive (BFB (+)) tumors showed reduced heterogeneity of amplicon structures, and delayed onset of resistance, relative to ecDNA(+) tumors. EcDNA and BFB amplifications represent contrasting mechanisms to increase the copy numbers of oncogene with markedly different characteristics that suggest different routes for intervention.

cancer biology↗

bioRxiv2023

Utility of T1 mapping and T2 mapping for non-invasive assessment of liver fibrosis: preclinical results

ObjectiveTo explore the potential of T1 and T2 mappings in assessing liver fibrosis (LF) and investigate the relationships between MRI and liver fibrogenesis markers. Materials and methods A total of 39 male C57BL/6 mice were divided into the control group (n = 9) and the model group (n = 10 per subgroup) with carbon tetrachloride (CCl4) administration for 2, 4, and 6 weeks. The METAVIR system (F0-4) was performed to stage fibrosis. MRI T1 and T2 mappings were performed and T1, and T2 values were calculated. One-way analysis of variance (ANOVA), Spearmans rank correlation analysis, and receiver operating characteristic (ROC) curves were performed. ResultsT1 and T2 values increased with progressing severity of fibrosis induction (P < 0.01). T1 and T2 were significantly correlated with LF stages ({rho} = 0.854, 0.697, P < 0.001). The area under the curves (AUCs) range of T1 and T2 for predicting [≥]F1, [≥]F2, [≥]F3, and F4 were 0.842-0.994 and 0.808-0.883, respectively. T1 and T2 showed moderate to strong correlations with collagen-associated protein and inflammatory factors. DiscussionT1 and T2 mappings can evaluate and differentiate LF stages in the CCl4-induced model. T1 is better correlated with collagen deposition and inflammation of LF than T2.

bioengineering↗

bioRxiv2023

Programmable delivery of fluoxetine via wearable bioelectronics for wound healing in vivo

The ability to deliver drugs with precise dosages at specific time points can significantly improve disease treatment while reducing side effects. Drug encapsulation for gradual delivery has opened up the doors for superior treatment regimen. To expand on this ability, programming bioelectronic devices to deliver small molecules enables ad-hoc personalized therapeutic profiles that are more complex than simple gradual release. Here, we introduce a wearable bioelectronic bandage with an integrated electrophoretic ion pump that affords on-demand drug delivery with precise dose control. Delivery of fluoxetine to wounds in mice resulted in a 27.2% decrease in the macrophage ratio (M1/M2) and a 39.9% increase in re-epithelialization, indicating a shorter inflammatory phase and faster overall healing. Programmable drug delivery using wearable bioelectronics in wounds introduces a broadly applicable strategy for the long-term delivery of a prescribed treatment regimen with minimal external intervention.

bioengineering↗

bioRxiv2023

Electrostatic modulation of signaling at cell membrane: Waveform- and time-dependent electric control of ERK dynamics

Different exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes with dielectric-coated microelectrodes, and show that the ERK signaling pathway of epithelial cells (MCF10A) can be both inhibited and activated by AC EF with different amplitude thresholds, peaking times and refractory periods. Interestingly, the ERK responses were sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.

biophysics↗

bioRxiv2023

CrWRKY42 positively regulates chlorophyll degradation and carotenoid biosynthesis in citrus

Chlorophyll degradation and carotenoid biosynthesis, which occur almost simultaneously during fruit ripening, are essential for coloration and nutritional value of fruits. However, the synergistic regulation of these two processes at transcriptional level remains largely unknown. Here, we identified a novel WRKY transcription factor CrWRKY42 from the transcriptome data of the yellowish bud mutant Jinlegan tangor (MT) and its wild type Shiranuhi tangor (WT), which was involved in the transcriptional regulation of both chlorophyll degradation and carotenoid biosynthesis pathways. CrWRKY42 activated the expression of {beta}-carotene hydroxylase 1 (CrBCH1) by directly binding to its promoter. Overexpression and interference of CrWRKY42 in citrus calli demonstrated that CrWRKY42 promoted carotenoid accumulation by inducing the expression of multiple carotenoid biosynthetic genes. Further assays confirmed that CrWRKY42 also directly bound to and activated the promoters of the genes involved in the carotenoid biosynthesis, including phytoene desaturase (CrPDS) and lycopene {beta}-cyclase 2 (CrLCYB2). In addition, CrWRKY42 could also bind to the promoter of STAY-GREEN (CrSGR) and activated its expression, thus promoting chlorophyll degradation. Overexpression and silencing of CrWRKY42 in citrus fruits indicated that CrWRKY42 positively regulated chlorophyll degradation and carotenoid biosynthesis by synergistically activating the expressions of genes involved in both pathways. In conclusion, our data revealed that CrWRKY42 acted as a positive regulator of chlorophyll degradation and carotenoid biosynthesis to alter the conversion of citrus fruit color. Our findings provide insight into the complex transcriptional regulation of chlorophyll and carotenoid metabolism during fruit ripening. One Sentence SummaryThe CrWRKY42 transcription factor coordinates chlorophyll degradation and carotenoid biosynthesis by directly regulating genes involved in these pathways to alter the conversion of citrus fruit color.

molecular biology↗

bioRxiv2023

PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities

PARP14 is a mono-ADP-ribosyl transferase involved in the control of immunity, transcription and DNA replication stress management. However, little is known about the ADP-ribosylation activity of PARP14, including its substrate specificity or how PARP14-dependent ADP-ribosylation is reversed. Here we show that PARP14 is dual function enzyme with both ADP-ribosyl transferase and hydrolase activity acting on both protein and nucleic acid substrates. In particular, we show that the PARP14 macrodomain 1 is an active ADP-ribosyl hydrolase. We also demonstrate hydrolytic activity for the first macrodomain of PARP9. We reveal that expression of a PARP14 mutant with the inactivated macrodomain 1 results in a dramatic increase in mono(ADP-ribosyl)ation of proteins in human cells, including PARP14 itself and antiviral PARP13. Moreover, we demonstrate that the closely related hydrolytically active macrodomain of SARS2 Nsp3, Mac1, efficiently reverses PARP14 ADP-ribosylation in vitro and in cells, supporting the evolution of viral macrodomains to counteract PARP14-mediated antiviral response. TeaserPARP14 is an antiviral PARP that combines ADP-ribosylation writer, reader and eraser functions in one polypeptide.

cell biology↗

bioRxiv2023

TREM2 promotes glioma progression and angiogenesis mediated by microglia/brain macrophages

TREM2, a myeloid cell-specific signaling molecule, controls essential functions of microglia and impacts on the pathogenesis of Alzheimers disease and other neurodegenerative disorders. TREM2 is also highly expressed in tumor-associated macrophages and plays detrimental roles in an experimental mouse sarcoma model. Here we studied whether TREM2 influences glioma progression. We found a sex- dependent effect of TREM2: the glioma volume is significantly attenuated in TREM2- deficient male but not female mice injected with GL261-EGFP glioma cells. The accumulation of glioma-associated microglia/macrophages (GAMs) and vascularization is reduced in male TREM2-deficient mice. A transcriptomic analysis of glioma tissue revealed that TREM2 deficiency suppresses angiogenic genes and MHC clusters. In an organotypic slice model devoid of functional vascularization, the tumor size was not affected by TREM2-deficiency. In human resection samples from glioblastoma, TREM2 is upregulated in GAMs. Based on the TCGA and CGGA databases, the TREM2 expression levels are negatively correlated with survival. Thus, the TREM2-dependent crosstalk between GAMs and the vasculature formation promotes glioma growth. Graphic abstractTREM2-dependent crosstalk between glioma-associated microglia/macrophages and the vasculature formation promotes glioma growth in male glioma mouse model. Created with BioRender.com O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/540621v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@65bec7org.highwire.dtl.DTLVardef@1d00961org.highwire.dtl.DTLVardef@117ee5eorg.highwire.dtl.DTLVardef@227994_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

Disrupting microglial TGF-β signaling triggers region-specific pathology in the spinal cord

Transforming growth factor-{beta} (TGF-{beta}) signaling is critical for microglial maturation during development and the maintenance of microglial homeostasis in adulthood. It remains unclear whether regional susceptibilities to the loss of TGF-{beta} signaling in microglia also exist, and the contributing factors have yet to be identified. We find that deletion of Tgfbr2 on microglia leads to microglial activation and demyelination in mouse spinal cords, primarily in the dorsal column (DC). Tgfbr2-deficient microglia exhibit distinct transcriptomic changes, and those sorted from the DC display a more proinflammatory profile compared to those from the ventral column (VC) and grey matter (GM). Single nucleus RNA sequencing (snRNA-seq) of the spinal cord uncovers a microglial subtype that emerges exclusively following Tgfbr2 deletion (termed TGF{beta} signaling-suppressed microglia, TSM), exhibiting high expression of Mmp12, Gpnmb, Lgals3, Mgll, and Alcam, predominantly located in the DC. Phenotypically, disruption of microglial TGF-{beta} signaling results in behavioral deficits that are more severe in female and older mice, whereas young male mice are less affected. Mechanistically, we reveal a significantly higher level of TGF-{beta}1/TGFBR2 in the spinal cords of normal older mice compared to the young mice, with the DC region richer in genes of the TGF-{beta} signaling pathway than the VC and GM regions. This indicates that older mice and the DC region require more TGF{beta}1 to maintain tissue homeostasis and, reciprocally, are more responsive and sensitive to the disruption of TGF-{beta} signaling in microglia. Herein, we report a demyelinating disease with region-specificity and its susceptibility to the loss of microglial TGF-{beta} signaling with gender and age differences. Our findings contribute valuable information to our understanding of the importance of microglia in regulating myelin health, especially during the aging process.

neuroscience↗

bioRxiv2023

A network of CD163+ macrophages monitors enhanced permeability at the blood-dorsal root ganglion barrier

In dorsal root ganglia (DRG), macrophages reside in close proximity to sensory neurons, and their functions have largely been explored in the context of pain, nerve injury and repair. In this study, however, we discovered that the majority of macrophages in DRGs are in direct contact with the vasculature where they constantly monitor the circulation, efficiently phagocytosing proteins and macromolecules from the blood. Characterization of the DRG endothelium revealed a specialized vascular network spanning the arteriovenous axis, which gradually transformed from a barrier type endothelium in arteries to a highly permeable endothelium in veins. Macrophage phagocytosis spatially aligned with peak endothelial permeability and we identified caveolar transcytosis as a mechanism regulating endothelial permeability. Profiling of the DRG immune landscape revealed two subsets of perivascular macrophages with distinct transcriptome, turnover and function. CD163 expressing macrophages self-maintained locally, specifically participated in vasculature monitoring, displayed distinct responses during peripheral inflammation and were conserved in mouse and Man. Our work provides a molecular explanation for the permeability of the blood-DRG barrier and identifies an unappreciated role of macrophages as integral components of the DRG-neurovascular unit.

immunology↗

bioRxiv2023

Simulating Rumen Conditions using an Anaerobic Dynamic Membrane Bioreactor to Enhance Hydrolysis of Lignocellulosic Biomass

An anaerobic dynamic membrane bioreactor (AnDMBR) was used to mimic rumen conditions to enhance the hydrolysis of lignocellulosic materials and the production of volatile fatty acids (VFA) when treating food waste. The AnDMBR was inoculated with cow rumen content and operated at a 0.5-day hydraulic retention time, 2 to 4-day solids retention time, a temperature of 39 {degrees}C, and a pH of 6.3, characteristics similar to those of a rumen. An operational strategy of repeating settle-permeate-mix cycles was utilized to simulate the regurgitation of ruminant animals. Removal rates of neutral detergent fiber (NDF) and acid detergent fiber (ADF) of 58.9 {+/-} 8.4 % and 69.0 {+/-} 8.6 %, respectively, and a VFA yield of 0.55 {+/-} 0.12 g VFA/g CODfed were observed when operating at an organic loading rate of 18 {+/-} 2 kg VS/m3/day. Sequencing results of both 16S rRNA gene and 16S rRNA revealed that a microbial community resistant to both disruption and reinoculation developed six weeks after inoculation. Up to 66.7 {+/-} 5.7 % of the active microbial populations (based on 16S rRNA sequence data) and 51.0 {+/-} 7.0 % of the total microbial populations (based on 16S rRNA gene sequence data) present in the rumen-mimicking AnDMBR originated from the rumen inoculum. This study offers a reliable strategy to leverage the unique features of a rumen; the rumen-mimicking AnDMBR achieved high hydrolysis and acidogenesis rates even when treating substrates drastically different from those fed to ruminants.

bioengineering↗

bioRxiv2022

Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma

Early-stage lung adenocarcinoma is typically treated by surgical resection of the tumor. While in the majority of cases surgery can lead to cure, approximately 30% of patients progress. Despite intense efforts to map the genetic landscape of early-stage lung tumors, there has been limited success in discovering accurate biomarkers that can predict clinical outcomes. Meanwhile, the role of the tumor-adjacent tissue in cancer progression has been largely ignored. To test whether tumor-adjacent tissue can be informative of progression-free survival and to probe the underlying molecular pathways involved, we designed a multi-omic study in both tumor and matched tumor-adjacent histologically normal lung tissue from the same patient. Our study includes 143 treatment naive stage I cases with long-term patient follow-up and is, to our knowledge, the largest such study with the longest follow-up. We performed a comprehensive histologic characterization of all tumors, mapped the mutational landscape and probed the transcriptome of both tumor and adjacent normal tissue. We evaluated the predictive power of each data modality and showed that the transcriptome of tumor-adjacent histologically normal lung tissue is the only reliable predictor of clinical outcome. Unbiased discovery of co-expressed gene modules revealed that inflammatory pathways are upregulated in the tumor-adjacent tissue of patients at high risk for disease progression. Furthermore, single-cell transcriptome analysis in the tumor-adjacent lung demonstrated that progression-associated inflammatory signatures were broadly expressed by both immune and non-immune cells including mesothelial cells, alveolar type 2 cells and fibroblasts, CD1 dendritic cells and MAST cells. Collectively, our studies suggest that molecular profiling of tumor-adjacent tissue can identify patients that are at high risk for disease progression.

bioinformatics↗

bioRxiv2022

Predictive Network Analysis Identifies JMJD6 and Other Novel Key Drivers in Alzheimer Disease

Despite decades of genetic studies on late onset Alzheimers disease (LOAD), the molecular mechanisms of Alzheimers disease (AD) remain unclear. Furthermore, different cell types in the central nervous system (CNS) play distinct roles in the onset and progression of AD pathology. To better comprehend the complex etiology of AD, we used an integrative approach to build robust predictive (causal) network models which were cross-validated over multiple large human multi-omics datasets in AD. We employed a published method to delineate bulk-tissue gene expression into single cell-type gene expression and integrated clinical and pathologic traits of AD, single nucleotide variation, and deconvoluted gene expression for the construction of predictive network models for each cell type in AD. With these predictive causal models, we are able to identify and prioritize robust key drivers of the AD-associated network state. In this study, we focused on neuron-specific network models and prioritized 19 predicted key drivers modulating AD pathology. These targets were validated via shRNA knockdown in human induced pluripotent stem cell (iPSC) derived neurons (iNs), in which 10 out of the 19 neuron-related targets (JMJD6, NSF, NUDT2, YWHAZ, RBM4, DCAF12, NDRG4, STXBP1, ATP1B1, and FIBP) significantly modulated levels of amyloid-beta and/or phosphorylated tau peptides in the postmitotic iNs. Most notably, knockdown of JMJD6 significantly altered the neurotoxic ratios of A{beta}42 to 40 and p231-tau to total tau, indicating its potential therapeutic relevance to both amyloid and tau pathology in AD. Molecular validation by RNA sequencing (RNAseq) in iNs further confirmed the network structure, showing significant enrichment in differentially expressed genes after knockdown of the validated targets. Interestingly, our network model predicts that these 10 key drivers are upstream regulators of REST and VGF, two recently identified key regulators of AD pathogenesis.

neuroscience↗

bioRxiv2022

Novel Master Regulators of Microglial Phagocytosis and Repurposed FDA-approved Drug for Treatment of Alzheimer Disease

Microglia, the innate immune cells of the brain, are essential determinants of late-onset Alzheimers Disease (LOAD) neuropathology. Here, we developed an integrative computational systems biology approach to construct causal network models of genetic regulatory programs for microglia in Alzheimers Disease (AD). This model enabled us to identify novel key driver (KDs) genes for microglial functions that can be targeted for AD pharmacotherapy. We prioritized FCER1G, HCK, LAPTM5, ITGB2, SLC1A2, PAPLN, GSAP, NTRK2, and CIRBP as KDs of microglial phagocytosis promoting neuroprotection and/or neural repair. In vitro, shRNA knockdown of each KD significantly reduced microglial phagocytosis. We repurposed riluzole, an FDA-approved ALS drug that upregulates SLC1A2 activity, and discovered that it stimulated phagocytosis of A{beta}1-42 in human primary microglia and decreased hippocampal amyloid plaque burden/phosphorylated tau levels in the brain of aged 3xTg-AD mice. Taken together, these data emphasize the utlility of our integrative approach for repurposing drugs for AD therapy.

neuroscience↗