Biology subjects

Song, K.

Publications and source records attributed to Song, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Coenzyme Q10 alleviates the mitochondrial damage by high-fat load in hepatocytes of spotted seabass (Lateolabrax maculatus) via promoting mitophagy

Coenzyme Q10, as a natural fat-soluble compound, can play a role in protecting mitochondria, but the mechanism is still unclear. Here, we explored the mechanism of coenzyme Q10 enhancing mitochondrial function using hepatocytes of spotted seabass. Three groups were set: normal medium as control group, fatty acid group containing 100 mol/L FA (FA group), and 100 mol/L FA and 5 mol/L coenzyme Q10 group (FA+COQ10). After the culture, the results showed that FA treatment significantly increased the triglyceride content in the cells. Bodipy staining showed that many lipid droplets appeared in the FA group, while coenzyme Q10 reduced triglycerides content and lipid droplets. Moreover, coenzyme Q10 significantly reduced the content of ROS in cells. After scavenging ROS, the liver cell damage caused by FA was alleviated, the mitochondrial membrane potential and its mitochondrial metabolic enzyme activity were restored, and the ATP content was increased. Further analysis showed that FA significantly down-regulated the expression of mitophagy key genes pink, parkin and lc3b, while up-regulated the expression of p62. Through mitochondrial fluorescence staining and mtDNA content detection, it was found that the number of mitochondria in FA-treated cells decreased significantly, while the number of mitochondria increased significantly after FA+COQ10 treatment. This indicates that coenzyme Q10 can significantly promote the mitophagy process. In order to further study whether the enhancement of mitochondrial function by coenzyme Q10 is related to the activation of autophagy, we set up FA group, FA+COQ10 group and FA+COQ10+Mdivi-1 group (pretreatment with mitophagy inhibitor Mdivi-1). After Mtphagy Dye staining, it was found that the number of autophagosomes in the FA+COQ10+Mdivi-1 group was lower than that in the FA+COQ10 group, indicating that the activation of mitophagy by coenzyme Q10 was inhibited. The results of this study indicate that coenzyme Q10 enhances mitochondrial function and alleviates excessive fat deposition dependent on PINK1-mediated mitophagy.

cell biology↗

bioRxiv2025

Integrative Multi-Scale Network Simulation forPrecision Drug Repurposing with PETS

Drug repurposing offers a promising strategy to accelerate therapeutic discovery for complex diseases; however, conventional approaches often overlook the multi-scale, dynamic nature of drug-induced perturbations. In this study, we introduce PETS (Pre-dictive Evaluation of Therapeutic Simulations), an innovative in silico framework that synergistically integrates curated pathway models with multi-layer network propagation, adaptive dampening, and memory mechanisms to simulate drug-gene interactions with high fidelity. By propagating perturbations through tissue- and cell-specific protein-protein interaction networks via iterative state updates, PETS robustly captures both proximal and distal regulatory feedback, enabling the identification and ranking of drug candidates capable of reversing disease-specific gene expression signatures. Validation against the SigCom L1000 dataset demonstrates that PETS achieves lower mean squared errors and higher predictive consistency compared to existing methods across models of Alzheimers disease, AD-expressing neuroblastoma, and glioblastoma multiforme. Moreover, PETS concurrently quantifies on-target therapeutic efficacy and potential off-target toxicity, providing mechanistic insights that are critical for candidate prioritization. Looking ahead, the integration of patient-specific multi-omics data and dynamic network topologies is expected to further enhance the translational impact of PETS. Our framework represents a significant advancement in the computational prediction of drug-gene perturbation effects, positioning it as a cornerstone tool for precision medicine and preclinical drug discovery.

bioinformatics↗

bioRxiv2025

Defined cellular reprogramming of androgen receptor-active prostate cancer to neuroendocrine prostate cancer

Neuroendocrine prostate cancer (NEPC) arises primarily through neuroendocrine transdifferentiation (NEtD) as an adaptive mechanism of therapeutic resistance. Models to define the functional effects of putative drivers of this process on androgen receptor (AR) signaling and NE cancer lineage programs are lacking. We adapted a genetically defined strategy from the field of cellular reprogramming to directly convert AR-active prostate cancer (ARPC) to AR-independent NEPC using candidate factors. We delineated critical roles of the pioneer factors ASCL1 and NeuroD1 in NEtD and uncovered their abilities to silence AR expression and signaling by remodeling chromatin at the somatically acquired AR enhancer and global AR binding sites with enhancer activity. We also elucidated the dynamic temporal changes in the transcriptomic and epigenomic landscapes of cells undergoing acute lineage conversion from ARPC to NEPC which should inform future therapeutic development. Further, we distinguished the activities of ASCL1 and NeuroD1 from the inactivation of RE-1 silencing transcription factor (REST), a master suppressor of a major neuronal gene program, in establishing a NEPC lineage state and in modulating the expression of genes associated with major histocompatibility complex class I (MHC I) antigen processing and presentation. These findings provide important, clinically relevant insights into the biological processes driving NEtD of prostate cancer.

cancer biology↗

bioRxiv2025

Transferring functional chromosomes between intergeneric yeast generates monochromosomal hybrids with improved phenotypes and transcriptional responses

Interspecific genetic exchanges caused by natural hybridization or horizontal gene transfer can lead to enhanced phenotypes, which are often of interest for industrial applications and evolutionary research. However, transferring genetic materials between distantly related species, such as intergeneric yeasts, presents technical challenges. In this study, we established a method to transfer individual chromosomes from Saccharomyces cerevisiae (Sc) into Kluyveromyces marxianus (Km), an emerging model for bioproduction. The Sc chromosome of interest was circularized, genetically modified to carry Km centromeres and replication origins, and transformed into Km via protoplast transformation. Using this method, we generated two synthetic strains, each containing a full set of Km chromosomes and either Sc chromosome I or III. The Sc chromosomes exhibited normal replication, segregation, and active transcription after the transfer. The synthetic strains displayed enhanced phenotypes in flocculation and salt tolerance, which were found to be caused by transgressive expression of FLO9 and SPS22 on the transferred Sc chromosomes, respectively. Transcriptomic analysis revealed that transgressive expression was prevalent among the transferred Sc genes, suggesting evolution of lineage-specific cis- and trans-regulatory interactions across a long evolutionary timescale. Our strategy has potential applications in optimizing cell factories, constructing synthetic genomes, and advancing evolutionary research.

synthetic biology↗

bioRxiv2025

Insights into the spool-like architecture and infectionstrategy of the archaeal virus SEV1

Archaeal viruses are well known for their diverse morphologies and extreme stability. In this study, we used cryo-electron tomography to analyze the structure of SEV1 and its infection strategies in its native state. The results show that SEV1 nucleocapsid adopts a coil-stacking architecture which displays a degree of flexibility. VP4, whose homologues are widespread in the thermo-acidic environment globally, is identified as the major capsid protein and binds genomic DNA forming a "beads-on-a-string" arrangement. Simulations in various extreme environments indicate that the envelope of SEV1 is crucial to the thermostability. SEV1 infects the host by membrane fusion revealed by the membrane fusion assay. The infected cell undergoes cytoplasm condensation to form a "viral factory", leading to the successive production of nascent virions. A series of assembly intermediates of SEV1 are identified revealing an integrated picture of the virus assembly process. The nascent virions are found to be released through virus-associated pyramids (VAPs), composed of unique proteins encoded by SEV1 distinct from other known VAP proteins. Our study provides novel insights to the survival strategies of SEV1, a flexible and enveloped archaeal virus, by using the unique "coil-stacking" architecture and the characteristic infection strategies.

microbiology↗

bioRxiv2024

Electron-density informed effective and reliable de novo molecular design and lead optimization with ED2Mol

Generative drug design opens new avenues for discovering novel compounds within the vast chemical space rather than conventional screening against limited compound libraries. However, the practical utility of the generated molecules is frequently constrained, as many designs prioritize a narrow range of pharmacological properties while neglecting physical reliability, which hinders the success rate of subsequent wet-lab evaluations. To address this, we propose ED2Mol, a deep learning-based approach that leverages fundamental electron density information to improve de novo molecular generation and lead optimization. The extensive evaluations across multiple benchmarks demonstrate that ED2Mol surpasses existing methods in terms of generation success rate and >97% physical reliability. It also facilitates automated lead optimization that is not fully implemented by other methods using fragment-based strategies. Furthermore, ED2Mol exhibits generalizability to more challenging, unseen allosteric pocket benchmarks, attaining consistent performance in both de novo molecule generation and lead optimization. More importantly, ED2Mol has been applied to various real-world essential targets, successfully identifying wet-lab validated bioactive compounds, ranging from FGFR3 orthosteric inhibitors to CDC42 allosteric inhibitors and GCK allosteric activators. The directly generated binding modes of these compounds with target proteins are close to predictions through molecular docking and further validated via the X-ray co-crystal structure. All these results highlight ED2Mols potential as a useful tool in realistic drug design with enhanced effectiveness, physical reliability, and practical applicability.

bioinformatics↗

bioRxiv2024

Structural and antigenic characterization of novel and diverse Henipavirus glycoproteins

Henipaviruses, a genus within the Paramyxoviridae family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease. Recent discoveries of several new Paramyxoviridae species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and studied their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain appended to the conserved 6-bladed, {beta}-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.

biochemistry↗

bioRxiv2024

Effect of the daily exposure of 1.7 GHz LTE electromagnetic field in early fetal brain development using a human brain organoid model of the cerebral cortex

Wireless communication technologys ubiquity means constant exposure to radiofrequency electromagnetic fields (RF-EMF). While concerns exist about RF-EMFs effects on fetal brain development, studying this in pregnant women poses ethical and safety challenges. Our study examined 1.7 GHz LTE RF-EMFs impact on early human fetal brain development using brain organoids derived from human induced pluripotent stem cells (hiPSCs). Previous research showed that 100-day-old human cerebral cortical brain organoids correspond to 19-24 weeks post-conception of fetal brain development. We exposed organoids to 1.7 GHz LTE RF-EMF at 8 W/kg specific absorption rate (SAR) for 5 hours daily up to 100 days. We monitored size, developmental morphology, and developmental stage markers using immunofluorescence microscopy and qPCR analysis. Comparing RF-EMF-exposed organoids with controls showed no significant differences in size, development, or expression of key markers: SOX2 and PAX6 (pluripotent cell markers), NEUN (mature neuronal marker), MAP2 (dendrite marker), and SYN1 (synapse marker). Results suggest that daily exposure to 1.7 GHz LTE RF-EMF at 8 W/kg SAR may not significantly affect early human fetal brain development.

developmental biology↗

bioRxiv2024

Citalopram exhibits immune-dependent anti-tumor effects by modulating C5aR1+ TAMs and CD8+ T cells

Administration of selective serotonin reuptake inhibitors (SSRIs) is associated with a reduced cancer risk and shows significant anti-tumor effects across multiple tumor types, suggesting the potential for repurposing SSRIs in cancer therapy. Nonetheless, the specific molecular target and mechanism of action of SSRIs remain to be fully elucidated. Here, we reveal that citalopram exerts an immune-dependent anti-tumor effects in hepatocellular carcinoma (HCC). Interestingly, the anti-HCC effects of citalopram are not reliant on its conventional target, the serotonin transporter. Through various drug repurposing approaches, including global reverse gene expression profiling, drug affinity responsive target stability assay, and molecular docking, the complement component 5a receptor 1 (C5aR1) is identified as a new target of citalopram. C5aR1 is predominantly expressed by tumor-associated macrophages (TAMs), and citalopram treatment enhances local macrophage phagocytosis and elicits CD8+ T anti-tumor immunity. C5aR1 deficiency or depletion of CD8+ T cells hinders the anti-HCC effects of citalopram. Collectively, our study reveals the immunomodulatory roles of citalopram in inducing anti-tumor immunity, and provides a basis for considering the repurposing of SSRIs as promising anticancer agents for HCC treatment.

cancer biology↗

bioRxiv2024

Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography

Influenza viruses are enveloped, negative sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80-90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of receptor-free and receptor-bound HA in vitro, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryo-electron tomography (cryoET) to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even inter-glycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8-10 [A] reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present new structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.

biophysics↗

bioRxiv2024

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples

Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions, while more modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab(R) test. Remnant clinician-collected NuSwab(R) vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab(R) test. Community State Types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab(R) panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). Sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab(R) assay microbe quantification was strongly concordant with quantification by sequencing (p << 0.01). Samples in CST-I (18 of 18, 100%), CST-II (3 of 3, 100%), CST-III (15 of 17, 88%), and CST-V (1 of 1, 100%) were largely categorized as BV-negative via the NuSwab(R) panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings show that 16S V3-V4 rRNA gene sequencing robustly reproduces PCR-based BV diagnostic testing results, accurately discriminates vaginal microbiome CSTs dominated by distinct Lactobacilli, and further elucidates BV-associated bacterial and metabolic signatures. ImportanceBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either physical and microscopic evaluations by technicians or panels of select microbes. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab(R) test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can reproduce targeted panel diagnostic results, while also broadly characterizing healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.

microbiology↗

bioRxiv2024

Serum Amyloid P Secreted by Bone Marrow Adipocytes Drives Skeletal Amyloidosis

The accumulation of amyloid fibrils has been identified in tissues outside the brain, yet little is understood about the formation of extracerebral amyloidosis and its impact on the aging process of these organs. Here, we demonstrate that both transgenic mice modeling Alzheimers disease (AD) and naturally aging mice exhibit accumulated senescent bone marrow adipocytes (BMAds), accompanied by amyloid deposits surrounding the BMAds. Senescent BMAds acquire a secretory phenotype, resulting in a marked increase in the secretion of serum amyloid P component (SAP), also known as pentraxin 2 (PTX2). SAP/PTX2 colocalizes with amyloid deposits around senescent BMAds in vivo and is sufficient to promote the formation of insoluble amyloid deposits from soluble A{beta} peptides in in vitro and ex vivo 3D BMAd-based culture experiments. Additionally, Combined treatment with SAP/PTX2 and A{beta} peptides promotes osteoclastogenesis but inhibits osteoblastogenesis of the precursor cells. Transplantation of senescent BMAds into the bone marrow cavity of healthy young mice is sufficient to induce bone loss. Finally, pharmacological depletion of SAP/PTX2 from aged mice abolishes bone marrow amyloid deposition and effectively rescues the low bone mass phenotype. Thus, senescent BMAds, through the secretion of SAP/PTX2, contribute to the age-associated development of skeletal amyloidosis and resultant bone deficits.

cell biology↗

bioRxiv2024

SSRI antidepressant citalopram reverses the Warburg effect to inhibit hepatocellular carcinoma by directly targeting GLUT1

Although there is growing appreciation for effective repurposing of selective serotonin reuptake inhibitors (SSRIs) for cancer therapy, particularly hepatocellular carcinoma (HCC), efforts are hampered by limited knowledge of their molecular targets and mechanism of action. Global inverse gene-expression profiling method, drug affinity responsive target stability assay, and in silico molecular docking analysis was performed to identify the targets of SSRIs. Murine subcutaneous, orthotopic models, and patient-derived xenograft were employed to explore the therapeutic effects and underlying mechanisms of SSRIs in HCC. The clinical relevance of SSRI use was verified with real world data. SSRIs exhibit significant anti-HCC effects independent of their known target serotonin reuptake transporter. The glucose transporter 1 (GLUT1) is identified as a new target of SSRIs. Citalopram binds to and antagonizes GLUT1, resulting in reduced glycolytic flux and ATP generation. Mutant GLUT1 in the binding site E380 of citalopram compromises the inhibitory effects of citalopram on the Warburg effect and tumor growth. In preclinical models, citalopram dampens the growth kinetics of GLUT1high liver tumors and displays a synergistic effect with anti-PD-1 therapy. Retrospective analysis of health records found that SSRIs use is associated with a lower risk of metastasis among HCC patients. Our study reveals an unprecedented role of SSRIs in cancer metabolism, and establishes a rationale for repurposing SSRIs as potential anticancer drugs for HCC.

cancer biology↗

bioRxiv2024

Continuous exposure to 60 Hz extremely low frequency electromagnetic field at 10 to 16 mT promotes various human cell proliferation by activating extracellular-signal-regulated kinase

We previously showed that continuous exposure to 60 Hz extremely low-frequency electromagnetic fields (ELF-EMF) at 6 mT promotes cell proliferation. Here, we investigated the cellular effect of 60 Hz ELF-EMF at over 10 mT. We revised the ELF-EMF-generating device to increase the magnetic flux density of the ELF-EMF stably without thermal effect. We investigated the cellular effect of 10-16 mT ELF-EMF on various mammalian cells including human cervical carcinoma HeLa, rat neuroblastoma B103, liver cancer stem cells Huh7 and Hep3B, immortalized normal hepatic cell MIHA, and normal fibroblast IMR-90. Cell proliferation was promoted around 20% or more in all cells through continuous ELF-EMF exposure at 10 and 14 mT for 72 h, compared with the sham exposure group. In the cells whose proliferation was activated by 14 mT ELF-EMF, the MEK-ERK pathway and NF-{kappa}B were activated but not Akt. These cells showed a slight increase in the S phase population in BrdU incorporation and Ki-67 expression. In these cells, intracellular and mitochondrial ROS levels were not changed, and the proliferation-activating cellular effects of ELF-EMF were maintained even when oxidative phosphorylation was interrupted by CCCP. Additionally, no changes in intracellular calcium levels were observed in ELF-EMF-exposed cells and the proliferation-activating cellular effects of ELF-EMF were maintained in the presence of a calcium chelator, BAPTA-AM. These observations suggested that ROS and intracellular calcium do not mediate ELF-EMFs proliferation-activating physiological effect. Altogether, we demonstrated that 60 Hz ELF-EMF at 10 to 14 mT promotes cell proliferation by activating ERK1/2 and does not affect intracellular ROS and calcium levels.

cell biology↗

bioRxiv2024

TRPV4-Expressing Tissue-Resident Macrophages Regulate the Function of Collecting Lymphatic Vessels via Thromboxane A2 Receptors in Lymphatic Muscle Cells

RationaleTRPV4 channels are critical regulators of blood vascular function and have been shown to be dysregulated in many disease conditions in association with inflammation and tissue fibrosis. These are key features in the pathophysiology of lymphatic system diseases, including lymphedema and lipedema; however, the role of TRPV4 channels in the lymphatic system remains largely unexplored. TRPV4 channels are calcium permeable, non-selective cation channels that are activated by diverse stimuli, including shear stress, stretch, temperature, and cell metabolites, which may regulate lymphatic contractile function. ObjectiveTo characterize the expression of TRPV4 channels in collecting lymphatic vessels and to determine the extent to which these channels regulate the contractile function of lymphatics. Methods and ResultsPressure myography on intact, isolated, and cannulated lymphatic vessels showed that pharmacological activation of TRPV4 channels with GSK1016790A (GSK101) led to contractile dysregulation. The response to GSK101 was multiphasic and included, 1) initial robust constriction that was sustained for [≥]1 minute and in some instances remained for [≥]4 minutes; and 2) subsequent vasodilation and partial or complete inhibition of lymphatic contractions associated with release of nitric oxide. The functional response to activation of TRPV4 channels displayed differences across lymphatics from four anatomical regions, but these differences were consistent across different species (mouse, rat, and non-human primate). Importantly, similar responses were observed following activation of TRPV4 channels in arterioles. The initial and sustained constriction was prevented with the COX inhibitor, indomethacin. We generated a controlled and spatially defined single-cell RNA sequencing (scRNAseq) dataset from intact and microdissected collecting lymphatic vessels. Our data uncovered a subset of macrophages displaying the highest expression of Trpv4 compared to other cell types within and surrounding the lymphatic vessel wall. These macrophages displayed a transcriptomic profile consistent with that of tissue-resident macrophages (TRMs), including differential expression of Lyve1, Cd163, Folr2, Mrc1, Ccl8, Apoe, Cd209f, Cd209d, and Cd209g; and at least half of these macrophages also expressed Timd4. This subset of macrophages also highly expressed Txa2s, which encodes the thromboxane A2 (TXA2) synthase. Inhibition of TXA2 receptors (TXA2Rs) prevented TRPV4-mediated contractile dysregulation. TXA2R activation on LMCs caused an increase in mobilization of calcium from intracellular stores through Ip3 receptors which promoted store operated calcium entry and vasoconstriction. ConclusionsClinical studies have linked cancer-related lymphedema with an increased infiltration of macrophages. While these macrophages have known anti-inflammatory and pro-lymphangiogenic roles, as well as promote tissue repair, our results point to detrimental effects to the pumping capacity of collecting lymphatic vessels mediated by activation of TRPV4 channels in macrophages. Pharmacological targeting of TRPV4 channels in LYVE1-expressing macrophages or pharmacological targeting of TXA2Rs may offer novel therapeutic strategies to improve lymphatic pumping function and lymph transport in lymphedema. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/595189v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1ce67fforg.highwire.dtl.DTLVardef@dd1beorg.highwire.dtl.DTLVardef@1454c78org.highwire.dtl.DTLVardef@9f76a1_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2024

Roles and mechanisms of leptomeningeal collaterals in human distal MCA territory ischemia

BackgroundLeptomeningeal collaterals (LMCs) provided hemodynamic support and reperfusion during acute ischemic stroke (AIS). Although regulation details have been deeply acquired from animal models, human cortex may share limited hemodynamic patterns due to larger physical scale that needs further investigation. MethodsWe performed sequential hierarchical blocking during awake craniotomy on fourteen human subjects to mimic AIS in middle cerebral artery (MCA) M4 segment territory. Widefield microscope was applied to reveal microcirculation of LMCs. Relative flow rate (RFR) was measured to evaluate the impact of LMCs hierarchy on microcirculation maintenance. Single-cell sequencing and spatial transcriptomics were further performed to analyze the mechanism of different LMCs recruitment abilities. ResultsLMCs RFR decreased to 30.75% immediately (95% CI, 6.64 - 54.86%, P < 0.001), and about 80.25% RFR was finally recovered within 5 minutes (95% CI, 55.2 - 105.3%, P = 0.0034) during M4 occlusion. For M5 and pial branches occlusion, RFR decreased to 55.78% with no further recovery (95% CI, 22.50-89.05%, P = 0.014), and 4 in 11 subjects had no valid microcirculation. For subjects with better recruitment ability, the proportion of arteriole is much higher in leptomeninx (76 - 79% vs. 36 - 56%). There were more significant interaction pairs associated with key signaling pathways between arteriole and neuron/astrocyte (TGF-beta signaling pathway, ECM-receptor interaction) ConclusionsAbundant LMCs supported hemodynamic stability during AIS in human subjects. The proportion of arteriole is much higher in leptomeninx for subjects with better recruitment ability. The Active neuron/astrocyte - arteriole interaction may improve LMCs recruitment. GRAPH ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/594043v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@eb7fb8org.highwire.dtl.DTLVardef@10e10aforg.highwire.dtl.DTLVardef@6954c7org.highwire.dtl.DTLVardef@13ceb98_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Single cell regulatory architecture of human pancreatic islets suggests sex differences in β cell function and the pathogenesis of type 2 diabetes.

Biological sex affects the pathogenesis of type 2 and type 1 diabetes (T2D, T1D) including the development of {beta} cell failure observed more often in males. The mechanisms that drive sex differences in {beta} cell failure is unknown. Studying sex differences in islet regulation and function represent a unique avenue to understand the sex-specific heterogeneity in {beta} cell failure in diabetes. Here, we examined sex and race differences in human pancreatic islets from up to 52 donors with and without T2D (including 37 donors from the Human Pancreas Analysis Program [HPAP] dataset) using an orthogonal series of experiments including single cell RNA-seq (scRNA-seq), single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq), dynamic hormone secretion, and bioenergetics. In cultured islets from nondiabetic (ND) donors, in the absence of the in vivo hormonal environment, sex differences in islet cell type gene accessibility and expression predominantly involved sex chromosomes. Of particular interest were sex differences in the X-linked KDM6A and Y-linked KDM5D chromatin remodelers in female and male islet cells respectively. Islets from T2D donors exhibited similar sex differences in differentially expressed genes (DEGs) from sex chromosomes. However, in contrast to islets from ND donors, islets from T2D donors exhibited major sex differences in DEGs from autosomes. Comparing {beta} cells from T2D and ND donors revealed that females had more DEGs from autosomes compared to male {beta} cells. Gene set enrichment analysis of female {beta} cell DEGs showed a suppression of oxidative phosphorylation and electron transport chain pathways, while male {beta} cell had suppressed insulin secretion pathways. Thus, although sex-specific differences in gene accessibility and expression of cultured ND human islets predominantly affect sex chromosome genes, major differences in autosomal gene expression between sexes appear during the transition to T2D and which highlight mitochondrial failure in female {beta} cells.

genomics↗

bioRxiv2024

PGC-1α drives small cell neuroendocrine cancer progression towards an ASCL1-expressing subtype with increased mitochondrial capacity

Adenocarcinomas from multiple tissues can evolve into lethal, treatment-resistant small cell neuroendocrine (SCN) cancers comprising multiple subtypes with poorly defined metabolic characteristics. The role of metabolism in directly driving subtype determination remains unclear. Through bioinformatics analyses of thousands of patient tumors, we identified enhanced PGC-1--a potent regulator of oxidative phosphorylation (OXPHOS)--in various SCN cancers (SCNCs), closely linked with neuroendocrine differentiation. In a patient-derived prostate tissue SCNC transformation system, the ASCL1-expressing neuroendocrine subtype showed elevated PGC-1 expression and increased OXPHOS activity. Inhibition of PGC-1 and OXPHOS reduced the proliferation of SCN lung and prostate cancer cell lines and blocked SCN prostate tumor formation. Conversely, enhancing PGC- 1 and OXPHOS, validated by small-animal Positron Emission Tomography mitochondrial imaging, tripled the SCN prostate tumor formation rate and promoted commitment to the ASCL1 lineage. These results establish PGC-1 as a driver of SCNC progression and subtype determination, highlighting novel metabolic vulnerabilities in SCNCs across different tissues. STATEMENT OF SIGNIFICANCEOur study provides functional evidence that metabolic reprogramming can directly impact cancer phenotypes and establishes PGC-1-induced mitochondrial metabolism as a driver of SCNC progression and lineage determination. These mechanistic insights reveal common metabolic vulnerabilities across SCNCs originating from multiple tissues, opening new avenues for pan-SCN cancer therapeutic strategies.

cancer biology↗