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Lee, J.-H.

Publications and source records attributed to Lee, J.-H..

At least 37 records · Page 2Linked to original sources

Detection of astrocyte epigenetic memory in in vitro systems, experimental autoimmune encephalomyelitis and multiple sclerosis samples

We recently described astrocyte pro-inflammatory epigenetic memory based on multiple complementary in vivo and in vitro studies, and the analysis of multiple sclerosis samples. Based on bioinformatic analyses, ODea and Liddelow argued that the astrocyte epigenetic memory we described is the result of contamination with immune cells, particularly myeloid cells. We rebut ODea and Liddelow arguments as follows: (1) We show substantial purity of astrocytes analyzed in in vivo and in vitro systems; (2) We recapitulate astrocyte memory responses using five independent pure astrocyte in vitro systems, and show its dependency on the histone acetyl transferase p300; and (3) Using the Liddelow lab bioinformatic pipeline to implement purity and cell-quality criteria, we detect astrocyte epigenetic memory in five independent scRNA-seq experimental autoimmune encephalomyelitis (EAE) and multiple sclerosis (MS) astrocyte datasets. These additional analyses and studies provide further support for the existence of astrocyte pro-inflammatory epigenetic memory.

neuroscience↗

Prg4+ fibro-adipogenic progenitors in muscle are crucial for bone fracture repair

Clinically, compromised fracture healing often occurs at sites with less muscle coverage and muscle flaps can provide the necessary healing environment for appropriate healing in severe bone loss. However, the underlying mechanisms are largely unknown. Here, we established a mouse reporter model for studying muscle cell contribution to bone fracture repair. Analyzing skeletal muscle scRNA-seq datasets revealed that Prg4 marks a fibro-adipogenic progenitor (FAP) subpopulation. In mice, Prg4+ cells were specifically located in the skeletal muscle, but not at the periosteum or inside cortical bone. These cells expressed FAP markers, responded to muscle injury, and became periosteal cells under normal and muscle injury conditions. Fracture fragmented muscle fibers, rapidly expanded Prg4+ FAPs at the injury site and promoted their migration into the fracture site. Later, they gave rise to many chondrocytes, osteoblasts, and osteocytes in the outer periphery of callus next to muscle. In repaired bones, the descendants of Prg4+ FAPs were detected as mesenchymal progenitors in the periosteum and osteocytes at the prior fracture site. A second fracture activated those cells and stimulated them to become osteoblasts in the inner part of callus. Importantly, ablation of Prg4+ FAPs impaired fracture healing and functional repair. In an intramembranous bone injury model (drill-hole), Prg4+ FAPs became periosteal cells, but their contribution to bone defect repair was significantly less than in fractures. Taken together, we demonstrate the critical role of FAPs in endochondral bone repair and uncover a novel mechanism by which mesenchymal progenitors transform from muscle to cortical bone. Significance statementFracture healing is often impaired in areas with less muscle coverage, but the mechanisms behind this are poorly understood. In this work, we uncovered a critical role of specific muscle cells, known as Prg4+ fibro-adipogenic progenitors (FAPs), in bone regeneration. Using mouse models, we show that these muscle-resident mesenchymal progenitors expand after bone injury, migrate to the fracture site, transform into various bone cells in the fracture callus, and eventually become bone surface progenitors after the bone is healed. This finding highlights the importance of muscle cells in endochondral fracture repair and reveals a novel crosstalk mechanism between muscle and bone tissues. Future studies targeting these muscle progenitor cells could develop new treatments for delayed and nonunion fractures.

cell biology↗

H2O2-induced astrocytic collagen triggers neuronal death via fucosylation-dependent glial barrier formation upon ischemic stroke

The cascade of molecular and cellular events leading to neuronal death after a focal ischemic stroke remains enigmatic. Although astrocytes form glial barriers that may protect surrounding tissue, how barriers develop and contribute to neuronal death is unclear. Here, we show that H2O2 induces astrocytic type I collagen (COL1)-production via miR-29-mediated post-transcriptional and fucosylation-dependent post-translational regulations, leading to integrin activation and neuronal death. In photothrombosis (PT)-induced cortical stroke model, PT triggered H2O2-surge, astrogliosis, glial barrier formation, COL1 expression, fibrotic scarring, altered N-glycosylation, neuronal loss, and neurological deficits. Remarkably, these effects were reversed by astrocyte-specific COL1 or FUT8 gene-silencing or treatment with KDS12025, an H2O2-decomposing peroxidase enhancer. KDS12025s neuroprotective effects were also recapitulated in non-human primate stroke model. These findings delineate a previously unrecognized astrocyte-driven mechanism in which oxidative stress induces COL1 production, promoting neuronal death, and position H2O2 and astrocytic COL1 and FUT8 as promising therapeutic targets for ischemic stroke.

neuroscience↗

Characterization of Human Anterior Neural Organoids as a Model for Investigating Cohen Syndrome

Neural organoids display three-dimensional (3D) structures that resemble in vivo neural architectures. Previously, we developed a novel two-dimensional (2D) neural induction-based protocol for culturing spinal cord organoids, enabling size control and recapitulating neural tube morphogenesis. In this study, we evaluated the application of this concept to induce the anterior regions of the brain and generate human anterior neural organoids (hANOs). By inducing neuroepithelial (NE) cells in 2D and re-aggregating them led to tube-forming morphogenesis similar to that posterior spinal cord induction. The transcriptome profiles of these hANOs resembled the frontal cortex of 20 weeks post-conception (PCW) human embryos. Using this hANOs protocol, we investigated microcephaly phenotypes associated with Cohen syndrome (CS), caused by biallelic loss-of-function variants in VPS13B gene. Deleting VPS13B in human pluripotent stem cells resulted in Golgi dispersion and growth retardation onset in mutant hANOs, akin to CS patients with postnatal microcephaly. This delay is partly linked to reduced neuronal growth. Additionally, mature CS organoids showed enhanced hyper-excitability associated with an excitatory/inhibitory imbalance. In conclusion, this protocol is suitable for studying microcephaly phenotypes from human genetic mutations due to its simplicity and scalability.

neuroscience↗

Cellular and Extracellular microRNA Dysregulation in LRRK2-Linked Parkinson's Disease

Background and objectiveThe discovery of cell-free micro-RNAs in body fluids has made them a promising biomarker target in the field of neurodegenerative diseases. Although they have been reported to be differentially expressed in biofluids and tissues from sporadic Parkinsons disease patients, it remains unclear whether similar observations can be made in patients with genetic forms of the disease and if miRNA profiles reflect mutation-specific pathogenic pathways. Since induced pluripotent stem cell-derived neurons represent a widely used research model for both sporadic and familial Parkinsons disease, we sought to assess the usability of this model for the identification of differentially expressed cell-free micro-RNAs in the context of the Parkinsons disease-related LRRK2 G2019S mutation in a proof-of-concept study. Materials and methodsWe isolated extracellular vesicles carrying cell-free RNA from patient-derived induced pluripotent stem cells carrying the LRRK2 G2019S mutation and their gene-corrected isogenic controls. After the generation of small-RNA libraries and differential expression analysis, we quantified expression levels of fourteen micro-RNAs in an independent batch of cell-free and cellular RNA via RT-qPCR. Finally, we quantified pRab10 levels as a proxy of LRRK2 activity and correlated observable changes to the miRNA expression levels. ResultsWe successfully isolated extracellular vesicles from induced pluripotent stem cell-derived human dopaminergic neurons. We detected over 2000 different micro-RNAs of which 56 were differentially expressed. Dysregulation of four micro-RNAs was confirmed in an independent batch of cell-free RNA. We discovered a high correlation between changes in the cell-free and cellular micro-RNAomes. Finally, we showed poor correlation between LRRK2 expression or activity and miRNA expression levels. ConclusionsOur results suggest that patients carrying the LRRK2 G2019S mutation display alterations in cellular and cell-free micro-RNA expression levels. Notably, the miRNA changes observed in this study did not follow a linear relationship with LRRK2 expression levels or kinase activity. Validation in larger cohorts will be necessary.

neuroscience↗

Processing reliant on granule cells is essential for motor learning but dispensable for many cerebellar-dependent behaviors

Cerebellar dysfunction leads to motor, learning, emotional, and social deficits. It is assumed that these deficits arise from impaired processing of mossy fiber inputs that activate granule cells (GCs) that in turn excite Purkinje cells (PCs). However, high-frequency spontaneous PC firing might also influence behaviors. To clarify how the cerebellum regulates behaviors, we compared the effects of disrupting either GC signaling, which selectively perturbs cerebellar processing, or PC signaling, which disrupts cerebellar processing and spontaneous PC firing. We find that both GC and PC signaling are required for eyeblink conditioning and vestibulo-ocular reflex (VOR) learning. However, disrupting PC signaling impairs baseline VOR, anxiety, and social behaviors, but abolishing GC signaling does not. This establishes that cerebellar processing is essential for motor learning, but is not required for many cerebellum-dependent behaviors. This suggests that such behaviors could be rescued by elevating firing in downstream targets, as shown previously for social deficits.

neuroscience↗

APOBEC3A, not APOBEC3B, drives deaminase mutagenesis in human gastric epithelium

Cancer genomes frequently carry APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like)-associated DNA mutations, suggesting APOBEC enzymes as innate mutagens during cancer initiation and evolution. However, the pure mutagenic impacts of the specific enzymes among this family that are responsible for APOBEC-associated mutagenesis remain unclear in human normal cell lineage, particularly the comparative mutagenic activities of APOBEC3A and APOBEC3B. Here, we investigated the mutagenic contributions of these enzymes through whole-genome sequencing of human normal gastric organoid lines carrying doxycycline-inducible APOBEC3A or APOBEC3B cassettes. Our findings demonstrated that transcriptional APOBEC3A upregulation led to the acquisition of a massive number of genomic mutations in a few cell cycles. By contrast, APOBEC3B upregulation did not generate a substantial number of mutations in gastric epithelium. APOBEC3B-associated mutagenesis remained insignificant even after a combined inactivation of TP53. Based on the spectrum of acquired mutations after APOBEC3A upregulation, we further analyzed APOBEC3A-associated mutational signatures, encompassing indels mainly composed of 1bp deletions, characteristics of clustered mutations, and selective pressures operative on cells carrying the mutations. Our observations provide a clear foundation for understanding the mutational impact of APOBEC enzymes in human cells.

genomics↗

Shift from visceral to subcutaneous fat in Cyp17a1 knockout rats prevent the progression of metabolic syndrome

In this study, we investigated the effects of Cyp17a1 gene knockout (KO) on obesity and metabolic syndrome. Cyp17a1 KO in rats using CRISPR-Cas9 resulted in sex dimorphism and obesity, and interestingly, idiopathic accumulation was found in subcutaneous adipose tissue. Surprisingly, an insulin tolerance test and oral glucose tolerance test did not show any issues with insulin sensitivity and secretion despite hyperglycemia. In addition, Cyp17a1 KO rats showed normal plasma insulin and free fatty acid levels compared to wild-type rats, and blood biochemistry analysis revealed normal triglyceride, total cholesterol, high-density lipoprotein, and low-density lipoprotein levels. Cyp17a1 KO adipose-tissue-derived stem cells from subcutaneous fat showed increased expression of KLF5, an early adipogenesis marker, which implies enhanced adipogenic potential in subcutaneous adipose tissue. When gene expression associated with lipid, glucose, and insulin metabolism as well as inflammation in adipose tissue was examined, a metabolic shift to subcutaneous adipose tissue was discovered in the Cyp17a1 KO group. In conclusion, in the Cyp17a1 KO rat models we generated for the first time, the phenotype promoted by obesity reflected health obesity hypothesis, but this did not result in metabolic syndrome due to enhanced metabolism in the subcutaneous fats.

physiology↗

IPMK Deficiency Reduces Skeletal Muscle Oxidative Metabolism and Exercise Capacity

Inositol phosphates are critical signaling messengers involved in a wide range of biological pathways in which inositol polyphosphate multikinase (IPMK) functions as a rate-limiting enzyme for inositol polyphosphate metabolism. IPMK has been implicated in cellular metabolism, but its function at the systemic level is still poorly understood. Since skeletal muscle is a major contributor to energy homeostasis, we have developed a mouse model in which skeletal muscle IPMK is specifically deleted and examined how a loss of IPMK affects whole-body metabolism. Here, we report that mice in which IPMK knockout is deleted, specifically in the skeletal muscle, displayed an increased body weight, disrupted glucose tolerance, and reduced exercise tolerance under the normal diet. Moreover, these changes were associated with an increased accumulation of triglyceride in skeletal muscle. Furthermore, we have confirmed that a loss of IPMK led to reduced beta-oxidation, increased triglyceride accumulation, and impaired insulin response in IPMK-deficient muscle cells. Thus, our results suggest that IPMK mediates the whole-body metabolism via regulating muscle metabolism and may be potentially targeted for the treatment of metabolic syndromes.

molecular biology↗

Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis

Aging is associated with a decline in the number and fitness of adult stem cells1-4. Aging-associated loss of stemness is posited to suppress tumorigenesis5,6, but this hypothesis has not been tested in vivo. Here, using physiologically aged autochthonous genetically engineered mouse models and primary cells7,8, we demonstrate aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. This phenotype is underpinned by aging-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, leading to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1--lipocalin-2 axis or iron supplementation rescue stemness and promote tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1-- lipocalin-2 axis is detrimental to young alveolar cells via induction of ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites associates with elevated NUPR1 expression, which is recapitulated in young alveolar cells by inhibition of DNA methylation. We uncover that aging drives a functional iron insufficiency, which leads to loss of stemness and tumorigenesis, but promotes resistance to ferroptosis. These findings have significant implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate in young individuals, revealing a critical window for such cancer prevention efforts.

cancer biology↗

Mechanism of nucleus-chloroplast communication by alternative promoter usage and stromules to establish photomorphogenesis in Arabidopsis

Interorganellar communication is essential for maintaining cellular and organellar functions and adapting to dynamic environmental changes in eukaryotic cells. In plants, light triggers photomorphogenic development, including chloroplast biogenesis and the inhibition of hypocotyl elongation, through photoreceptors such as the red/far-red-sensing phytochromes and their downstream signaling pathways. However, the mechanism of interorganellar crosstalk underlying photomorphogenesis remains elusive. Here, we investigate the role of light-regulated alternative promoter usage in NUCLEAR CONTROL OF PEP ACTIVITY (NCP), a gene encoding a phytochrome signaling component that is dual-localized to the nucleus and chloroplasts. The long transcript variant (NCP-L) is upregulated under high red light, while the short variant (NCP-S) predominates in dark or low red light conditions. This light-regulated alternative transcription initiation of NCP is dependent on PHYTOCHROME-INTERACTING FACTORS (PIFs). The NCP-L isoform primarily localizes to chloroplasts, whereas the NCP-S isoform is found in the cytoplasm and nucleus. Notably, chloroplast-localized NCP-L translocates to the nucleus via stromules. Consequently, NCP-L, present in both chloroplasts and the nucleus, initiates chloroplast biogenesis and inhibits hypocotyl growth during photomorphogenesis, whereas NCP-S is nonfunctional and degraded by the 26S proteasome. Taken together, our findings elucidate the mechanisms by which light-regulated NCP alternative promoter usage and NCP retrotranslocation via stromules control photomorphogenesis in Arabidopsis. These mechanisms provide insights into interorganellar communication, orchestrating organ-specific developmental processes in response to fluctuating light environments.

plant biology↗

Intestinal epigenomic alterations are associated with a dysregulated nutrient absorption phenotype in obesity

Obesity is an epidemic with myriad health effects, but little is understood regarding individual obese phenotypes and how they may respond to therapy. Epigenetic changes associated with obesity have been detected in blood, liver, pancreas, and adipose tissues. Previous work using human organoids found that dietary glucose hyperabsorption is a steadfast trait in cultures derived from some obese subjects, but detailed transcriptional or epigenomic features of the intestinal epithelia associated with this persistent phenotype are unknown. This study evaluated differentially expressed genes and relative chromatin accessibility in intestinal organoids established from donors classified as non-obese, obese, or obese hyperabsorptive by body mass index and glucose transport assays. Transcriptomic analysis indicated that obese hyperabsorptive subject organoids have significantly upregulated dietary nutrient absorption transcripts and downregulated type I interferon targets. Chromatin accessibility and transcription factor footprinting predicted that enhanced HNF4G binding may promote the obese hyperabsorption phenotype. Quantitative RT-PCR assessment in organoids representing a larger subject cohort suggested that intestinal epithelial expression of CUBN, GIP, SLC5A11, and SLC2A5 were highly correlated with hyperabsorption. Thus, the obese hyperabsorption phenotype was characterized by transcriptional changes that support increased nutrient uptake by intestinal epithelia, potentially driven by differentially accessible chromatin. Recognizing unique intestinal phenotypes in obesity provides a new perspective in considering therapeutic targets and options to manage the disease.

genomics↗

Acoustic target strengths and swimbladder morphology of Chub mackerel Scomber japonicus in the Northwest Pacific Ocean

The Northwest Pacific chub mackerel (Scomber japonicus) is one of the most productive, economically important fishery resources worldwide. Due to fluctuations in their abundance and distribution, there is a pressing need to accurately assess this species and to ensure total allowable catch limits are followed. Acoustic target strength (TS; dB) measurements of Scomber japonicus were conducted at 38, 70, and 120 kHz using a split-beam echosounder of individuals from nine size groups (mean fork length, 10.8[~]28.3 cm) swimming freely in a net cage within a seawater tank. An underwater camera was utilized to simultaneously measure the swimming angle. A least-squares regression analysis revealed that when the slope was constrained to 20, as per the generally applicable morphometric equation, the resulting values for the constant term (b20) were -67.7, -66.6, and - 67.3 dB at 38, 70, and 120 kHz, respectively. The mean swimming angle of S. japonicus across the groups was -10.5[~]9.6{degrees} (standard deviation (SD), 16.3[~]33.3{degrees}). In addition, the ratio of swimbladder height to swimbladder length, swimbladder length to fork length, and tilt angle of the swimbladder (mean {+/-} SD) were 0.191 {+/-} 0.060, 0.245 {+/-} 0.055, and 9.6 {+/-} 3.0{degrees}, respectively. These results can be used for the acoustic stock assessment of S. japonicus in the Northwest Pacific Ocean.

animal behavior and cognition↗

Self-Assembled Origami Neural Probes for Scalable, Multifunctional, Three-Dimensional Neural Interface

Flexible intracortical neural probes have drawn attention for their enhanced longevity in high-resolution neural recordings due to reduced tissue reaction. However, the conventional monolithic fabrication approach has met significant challenges in: (i) scaling the number of recording sites for electrophysiology; (ii) integrating of other physiological sensing and modulation; and (iii) configuring into three-dimensional (3D) shapes for multi-sided electrode arrays. We report an innovative self-assembly technology that allows for implementing flexible origami neural probes as an effective alternative to overcome these challenges. By using magnetic-field-assisted hybrid self-assembly, multiple probes with various modalities can be stacked on top of each other with precise alignment. Using this approach, we demonstrated a multifunctional device with scalable high-density recording sites, dopamine sensors and a temperature sensor integrated on a single flexible probe. Simultaneous large-scale, high-spatial-resolution electrophysiology was demonstrated along with local temperature sensing and dopamine concentration monitoring. A high-density 3D origami probe was assembled by wrapping planar probes around a thin fiber in a diameter of 80[~]105 m using optimal foldable design and capillary force. Directional optogenetic modulation could be achieved with illumination from the neuron-sized micro-LEDs (LEDs) integrated on the surface of 3D origami probes. We could identify angular heterogeneous single-unit signals and neural connectivity 360{degrees} surrounding the probe. The probe longevity was validated by chronic recordings of 64-channel stacked probes in behaving mice for up to 140 days. With the modular, customizable assembly technologies presented, we demonstrated a novel and highly flexible solution to accommodate multifunctional integration, channel scaling, and 3D array configuration.

neuroscience↗

Mosaic display of stable hemagglutinin monomers induces broad immune responses

The nature of the interplay between immunity and viral variation is infinitely adaptive. Infection frequently induces immune responses against variation-prone epitopes, rather than against spatially hidden conserved epitopes. It thus remains a substantial challenge to elicit the immune responses to the conserved epitopes providing broad-spectrum immunity. We developed an approach of scaffold-mediated mosaic display to present monomeric influenza virus hemagglutinins (HAs), which exposes highly conserved stem and interface epitopes. Stable monomers were rationally engineered from H1 and H3 subtypes and B type HA trimers, with amino acid mutations at the monomer-monomer interface and for disulfide bond formation, and fused to a self-assembling scaffold, to generate a mosaic HA monomer-displaying nanoparticle, 3HA-np. Immunization with 3HA-np induced broadly neutralizing antibodies (bnAbs) in mice and ferrets and protected against challenges with H1N1 and H3N2 viruses. Competitive immunoassays revealed that 3HA-np induced high interface- and stem-binding Ab titers as compared to head Ab titers, indicating that the monomeric and mosaic nature of 3HA-np elicit cross-reactive Abs. Our results suggest that exposure of the hidden conserved epitope by monomer-displaying nanoparticles is a promising approach to generate a universal influenza vaccine.

bioengineering↗

Matrix-rigidity cooperates with biochemical cues in M2 macrophage activation through increased nuclear deformation and chromatin accessibility

Macrophages encounter a myriad of biochemical and mechanical stimuli across various tissues and pathological contexts. Notably, matrix rigidity has emerged as a pivotal regulator of macrophage activation through mechanotransduction. However, the precise mechanisms underlying the interplay between mechanical and biochemical cues within the nuclear milieu remain elusive. Here we elucidate how the increased matrix rigidity drives macrophages to amplify alternatively-activated (M2 phenotype) signalings cooperatively with biochemical cues (e.g., IL4/13) through altered nuclear mechanics. Notably, we found that reconstructed podosome-like F-actins and contractility induced nucleus deformation, opening nuclear pores, which facilitates nuclear translocation of the key transcription factor STAT6. Furthermore, the altered nuclear mechanics increased chromatin accessibility induced by H3K9 methylation, particularly of M2-associated gene promoters. These cooperative events of the mechano-chemical signaling at the cytoskeletal-to-nuclear domains facilitated M2 transcriptional activation and cellular functions. We further evidenced the rigidity-primed M2 macrophages were immunosuppressive and accumulated in stiffened tumor tissues. This study proposes a mechanism by which matrix mechanics crosstalks with biochemical signals to potentiate macrophage activation through nuclear mechanosensing and chromatin modifications, offering insights into macrophage mechanobiology and its therapeutic modulations.

bioengineering↗

Circadian regulation of endoplasmic reticulum calcium response in mouse cultured astrocytes

The circadian clock, an internal time-keeping system orchestrates 24-hour rhythms in physiology and behavior by regulating rhythmic transcription in cells. Astrocytes, the most abundant glial cells, play crucial roles in central nervous system (CNS) functions, but the impact of the circadian clock on astrocyte functions remains largely unexplored. In this study, we identified 412 circadian rhythmic transcripts in cultured mouse cortical astrocytes through RNA sequencing. Gene Ontology analysis indicated that genes involved in Ca2+ homeostasis are under circadian control. Notably, Herpud1 (Herp) exhibited robust circadian rhythmicity at both mRNA and protein levels, a rhythm disrupted in astrocytes lacking the circadian transcription factor, BMAL1. HERP regulated endoplasmic reticulum (ER) Ca2+ release by modulating the degradation of inositol 1,4,5-trisphosphate receptors (ITPRs). ATP-stimulated ER Ca2+ release varied with the circadian phase, being more pronounced at subjective night phase, likely due to the rhythmic expression of ITPR2. Correspondingly, ATP-stimulated cytosolic Ca2+ increases were heightened at the subjective night phase. This rhythmic ER Ca2+ response led to circadian phase-dependent variations in the phosphorylation of Connexin 43 (Ser368) and gap junctional communication. Given the role of gap junction channel (GJC) in propagating Ca2+ signals, we suggest that this circadian regulation of ER Ca2+ responses could affect astrocytic modulation of synaptic activity according to the time of day. Overall, our study enhances the understanding of how the circadian clock influences astrocyte function in the CNS, shedding light on their potential role in daily variations of brain activity and health.

neuroscience↗

scGND: Graph neural diffusion model enhances single-cell RNA-seq analysis

Single-cell sequencing technologies have played a pivotal role in advancing biomedical research over the last decade. With the evolution of deep learning, a variety of models based on deep neural networks have been developed to improve the precision of single-cell RNA sequencing (scRNA-seq) analysis from multiple angles. However, deep learning models currently used in scRNA-seq analysis frequently suffer from a lack of interpretability. In this study, we present a novel physics-informed graph generative model, termed Single Cell Graph Neural Diffusion (scGND). This model is founded on solid mathematical concepts and provides enhanced interpretability. Unlike methods that focus solely on gene expression in individual cells, scGND concentrates on the cell-cell interaction graph, incorporating two key physical concepts: local and global equilibrium. We show that achieving a balance between local and global equilibrium significantly improves the geometric properties of the graph, aiding in the extraction of inherent biological insights from the cell-cell interaction graph at multiple scales. The effectiveness of scGND has been proven through benchmark tests involving five independent scRNA-seq datasets from various tissues and species. scGND consistently achieves better or comparable results comparing with several established competitors in both clustering and trajectory analysis. scGND represents a comprehensive generative model based on cell graph diffusion, demonstrating considerable promise for both theoretical and practical applications in scRNA-seq data analysis.

bioinformatics↗