Biology subjects

Lei, X.

Publications and source records attributed to Lei, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Modeling Post-Gastrula Development via Bidirectional Pluripotent Stem Cells

The absence of stem cells capable of efficiently generating both trophoblast and epiblast lineages has hindered precise recapitulation of embryonic development. Through high-content chemical screening, we established an AL medium to generate mouse and human bidirectional pluripotent stem cells (BPSCs) characterized by concurrent OCT4/CDX2 expression. Mouse BPSCs demonstrated high plastic differentiation into trophoblast, epiblast and primitive endoderm lineages in vitro within 48 hours without exogenous induction factors and efficiently contributed to the embryo and extraembryonic tissues in vivo. Mechanistically, hyperactivation of the Wnt signaling pathway breaks the early lineage differentiation barrier by initiating a Lef1-dependent bypass. Remarkably, BPSCs can efficiently generated E8.5 embryoids that completed gastrulation and displayed advanced features such as brain development, a closed neural tube, a beating heart, somite formation, and primordial germ cells. These findings highlight BPSCs as a powerful tool for investigating early lineage specification and post-gastrulation embryonic development, with potential applications across multiple species.

developmental biology↗

bioRxiv2025

Decoding ultrasensitive self-assembly of the calcium-regulated Tetrahymena cytoskeletal protein Tcb2 using optical actuation.

EF-hand calcium binding proteins are key macromolecular components of many unique filament systems and ultrafast contractile structures found in protists. However, our biochemical understanding of these cytoskeletal systems has been hindered by the need for assays that can controllably generate spatiotemporal calcium dynamics to probe their behavior. Here, we define the quantitative requirements for calcium-dependent self-assembly of the Tetrahymena cortical cytoskeletal protein Tcb2 using a microscopy-based spatiotemporally controlled optical calcium release assay. Light-driven uncaging of the photolabile calcium chelator DMNP-EDTA stimulates rapid localized self-assembly of Tcb2 into micron-scale protein networks. We quantify how the growth, size, and lifetime of Tcb2 networks is controlled by the duration and intensity of the applied light pulse. Incorporating the fluorescent calcium indicator Rhod-5N allows inference of the spatiotemporal distribution of calcium-bound Tcb2 monomers during the reaction and identifies a sharp, ultrasensitive transition to Tcb2 self-assembly. By applying this assay to mutants in Tcb2s four EF hand domains, we show that D184 is the key calcium binding site that licenses Tcb2 for self-assembly and define quantitative roles for other binding sites in tuning Tcb2s calcium-responsiveness. Our approach reveals a rich space of structures and regulation available to a single-protein system through coupling calcium-binding to ultrasensitive self-assembly, opening new paths forward to understanding other protist filament networks and contractile myonemes.

biophysics↗

bioRxiv2025

F-53B damages cell viability leading to impaired root development in Arabidopsis

The emerging contaminant chlorinated polyfluoroalkyl ether sulfonate (Cl-PFAES/F-53B) has been detected in many plant species, however, the impact of F-53B on the development in plants and the underpinning mechanisms remain largely unelucidated. In this study, we demonstrate by molecular biology, cytogenetics, and fluorescence microscopy mythologies that F-53B impairs cell viability leading to disrupted root development in Arabidopsis (Arabidopsis thaliana). We show that F-53B suppresses root length and the inhibitory effect is pronunanced at increasing concentrations. F-53B disrupts cell wall and microtubule-mediated cell plate formation and configuration in meristem cells, revealing its toxicity to cell division and cytoskeleton organization. F-53B induces cell death predominantly at the meristematic zone, however, gene exression and genetic studies indicate that F-53B does not trigger DNA double-strand breaks, implying a divergent effect on DNA stability across species. Moreover, we show that F-53B damages nuclei stability and viability, and induces Autophagy-Related 8 protein foci formation implying that it triggers autophagy-mediated cell responses. Taken together, this study provides cellular and molecular insights into the toxicity of F-53B to plant cells, which highlights its damage to agriculture and ecology security that deserve imperative environmental management actions. Environmental ImplicationF-53B has been detected in many plant species, which raises increasing concerns on its toxicity to plants and thus agriculture and ecology safety. However, the toxicity of F-53B to development in plants and the underpinning mechanisms remain largely unelucidated. Here, we demonstrate that F-53B damages nuclei stability and viability leading to cell death and impaired root development in the model plant species Arabidopsis thaliana. Our study provides cytogenetic and molecular insights into the F-53B toxicity to plant cells, which highlights imperative environmental management actions and can be referenced for developing F-53B control and management policies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/653422v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@159b211org.highwire.dtl.DTLVardef@1b99a95org.highwire.dtl.DTLVardef@53b964org.highwire.dtl.DTLVardef@b089be_HPS_FORMAT_FIGEXP M_FIG C_FIG One-sentence summaryF-53B triggers DNA double-strand break-free cell unviability leading to impaired meristematic cell division and root development in plants. HIGHLIGHTSO_LIF-53B impairs root development in Arabidopsis. C_LIO_LIF-53B prohibits mitotic cell division at root tips. C_LIO_LIF-53B damages cell viability predominantly at the meristematic zone in seedlings. C_LIO_LIF-53B does not induce DNA double-strand breaks in Arabidopsis seedlings. C_LIO_LIF-53B damages nuclei viability and stability in seedlings. C_LI

developmental biology↗

bioRxiv2025

A reference genome assembly of the alpine forage grass Elymus nutans

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans, representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred [~]3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies.

plant biology↗

bioRxiv2025

Light-induced reversible assembly and actuation in ultrafast Ca2+-driven chemomechanical protein networks

Programming rapid, repeatable motions in soft materials has remained a challenge in active matter and biomimetic design. Here, we present a light-controlled chemomechanical network based on Tetrahymena thermophila calcium-binding protein 2 (Tcb2), a Ca2+-sensitive contractile protein. These networks--driven by Ca2+-triggered structural rearrangements--exhibit dynamic selfassembly, spatiotemporal growth, and contraction rates comparable to actomyosin systems. By coupling light-sensitive chelators for optically triggered Ca2+ release, we achieve precise growth and repeatable mechanical contractility of Tcb2 networks, revealing emergent phenomena such as boundary-localized active regions and density gradient-driven reversals in motion. A coupled reaction-diffusion and elastic model explains these dynamics, highlighting the interplay between chemical network assembly and mechanical response. We further demonstrate active transport of particles via network-mediated forces in vitro and implement reinforcement learning to program seconds-scale spatiotemporal actuation in silico. These results establish a platform for designing responsive active materials with rapid chemomechanical dynamics and tunable optical control, with applications in synthetic cells, sub-cellular force generation, and programmable biomaterials.

bioengineering↗

bioRxiv2025

STAT3 Sustains Tumorigenicity Following Mutant KRAS Ablation

Oncogenic KRAS mutations underlie some of the deadliest human cancers. Genetic or pharmacological inactivation of mutant KRAS is not sufficient for long-term control of advanced tumors. Using a conceptual framework of pancreatic ductal adenocarcinoma, we find that CRISPR-mediated ablation of mutant KRAS can terminate tumor progression contingent on the concomitant inactivation of STAT3. STAT3 inactivation is needed to ensure that KRAS-ablated tumor cells lose their malignant identity. Mechanistically, the combined loss of mutant KRAS and STAT3 disrupts a core transcriptional program of cancer cells critical to oncogenic competence. This in turn impairs tumor growth in mice and enhances immune rejection, leading to tumor clearance. We propose that the STAT3 transcriptional program operating in cancer cells enforces their malignant identity, rather than providing classical features of transformation, and shapes cancer persistence following KRAS inactivation. Our findings establish STAT3 as a critical enforcer of oncogenic identity in KRAS-ablated tumors, revealing a key vulnerability that could be exploited for combination therapies. SignificanceThe limited clinical success of KRAS inhibitors points to the need to identify means by which tumor cells maintain stemness and immune evasion. We make an unprecedented finding that the STAT3 transcription factor can sustain tumorigenicity of pancreatic cancer cells following depletion of the KRAS oncogenic driver. The results have important implications for successful therapeutic intervention.

cancer biology↗

bioRxiv2025

Roles of Cro2 and CI2 binding to OR operators in controlling lysogeny stability during prophage induction

The lysogeny-lysis switch in bacteriophage lambda serves as a model for understanding cell fate decisions. The molecular network controlling this switch has been explored through extensive experimental and computational studies. Yet, the specific role of protein-DNA interactions, like the binding of CI2 and Cro2 proteins to operator sites, in regulating lysogeny stability during prophage induction remains less under-stood. This study employs a minimalistic model and the Accurate Chemical Master Equation (ACME) method to construct detailed probability landscapes of the networks behavior under varying conditions, such as different dissociation and CI2 degradation rates which simulate UV irradiation effects. Our findings indicate that Cro2 binding at OR3 and CI2 at OR1 significantly influence lysogeny stability, with the former destabilizing and the latter stabilizing it. Conversely, interactions at OR1 by Cro2 and OR3 by CI show minimal impact on this stability. Through the ACME approach, we could examine the networks global behavior under conditions unapproachable by conventional stochastic simulations. This study highlights the critical roles of specific protein-DNA interactions in maintaining lysogeny and provides insight into the broader dynamics of the lysogeny-lysis switch under various physiological stresses.

systems biology↗

bioRxiv2025

Pseudopaline-mediated zinc uptake by Pseudomonas aeruginosa determines specific clinically relevant phenotypes and infection outcome

AUTHOR SUMMARYThe host-pathogen interface is a biological niche in which two entities competes for essential resources. The hosts nutritional immunity restrict access to metals, while a successful pathogen overcomes these restrictions using dedicated uptake pathways. Pseudopaline is a high-affinity metallophore allowing Pseudomonas aeruginosa to acquire zinc in chelated environments. We demonstrate that this pathway is the last-resort solution to acquire zinc for this dreadful pathogen. The capacity to provide this metal to zinc-metalloproteins drives clinically relevant phenotypes, such as the capacity to form a mature and antibiotic-tolerant biofilm, or to affect the outcome of an infection. These results place pseudopaline as a potential drug target for blocking P. aeruginosa pathogenic capacity and resensitizing established biofilm to classic antibiotic treatment. ABSTRACTBiological metals are essential trace elements which are required by metalloproteins, involved in virtually every cellular, structural and catalytic function of the bacterial cell. Bacterial pathogenesis involves a tug-of-war between the host nutritional immunity, sequestering essential metals and the invading pathogens that deploy high-metal affinity uptake strategies in order to overcome these defence mechanisms. Metallophores are high-affinity, low-molecular mass metal chelators produced and secreted by bacteria to access chelated metals from the environment. Pseudopaline is a metallophore produced and secreted by Pseudomonas aeruginosa to acquire zinc when the bioavailability of this metal is severely restricted, as in the presence of a strong metal chelator such as EDTA, or during infections when the nutritional immunity of the host is active, in mammals through the production of the zing binding protein calprotectin. We show that under the conditions of metal deprivation, a pseudopaline-deficient P. aeruginosa strain exhibit a severe intracellular zinc deficiency, establishing that the pseudopaline pathway is the last-resort and unique pathway for the bacteria to acquire zinc under these restricted growth conditions. The present study explores the pleiotropic role of pseudopaline-mediated zinc acquisition on several clinically relevant phenotypes and its capacity to drive infection outcomes, placing this machinery as a promising therapeutic target for P. aeruginosas infection, acting synergistically as a pathogenicity determinant as well as an adaptative trait allowing the establishment of a mature and antibiotic resistance biofilm necessary for recalcitrant chronic infections.

microbiology↗

bioRxiv2024

Dissociable neurofunctional and molecular characterizations of reward and punishment sensitivity

While the hyper-and hypo-reward or punishment sensitivities (RS, PS) have received considerable attention as prominent transdiagnostic features of psychopathology, the lack of an overarching neurobiological characterization currently limits their early identifications and neuromodulations. Here we combined microarray data from the Allen Human Brain Atlas with a multimodal fMRI approach to uncover the neurobiological signatures of RS and PS in a discovery-replication design (N=655 participants). Both RS and PS were mapped separately in the brain, with the intrinsic functional connectome in the fronto-striatal network encoding reward responsiveness, while the fronto-insular system was particularly engaged in punishment sensitivity. This dissociable functional connectome patterns related to RS and PS were also specific in differentiating decisions driven by social or monetary reward and punishment motivations. Further imaging transcriptomic analyses revealed that functional connectome variations for RS and PS were associated with topography of specific gene sets enriched in ontological pathways, including synaptic transmission, dopaminergic metabolism, immune response and stress adaptation. On the neurotransmitter level, the serotonin neuromodulator was identified as a pivotal hub regulating the intrinsic functional connectome patterns of RS and PS, with this process critically dependent on its interactions with dopaminergic, opioid and GABAergic systems. Overall, these findings indicate dissociable neural connectome mapping of RS and PS and highlight their linkage with transcriptomic profiles, which may offer valuable insights into the treatment evaluation for symptomatology relevant to reward/punishment processing deficits.

neuroscience↗

bioRxiv2024

Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing

Adenosine-to-Inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes. Despite its significance, the regulatory mechanisms controlling A-to-I editing remain largely unknown. In this study, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-based RNA EDITing regulator Screening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cell CRISPR-based RNA EDITing sequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations on dozens of selected genes. Through screening 1,350 RNA-binding proteins, we identified a series of known and novel A-to-I editing regulators. Detailed mechanistic investigation revealed DDX39B as a global repressor of A-to-I editing, which functions by preventing double-stranded RNA accumulation through its helicase and ATPase activities. We demonstrate that targeting DDX39B significantly enhances the efficiency of RNA editing-based tools like CellREADR and LEAPER, and represents a promising strategy for anti-HDV therapy by modulating viral genome editing. These technological advances not only expand our understanding of RNA editing regulation but also provide powerful tools for exploring tissue-specific and context-dependent RNA modification mechanisms, with broad implications for therapeutic development.

molecular biology↗

bioRxiv2024

ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types

Human endogenous retroviruses (HERVs) compose approximately 8% of the human genome, co-opted into the dynamic regulatory network of cellular potency in early embryonic development. In recent studies, resurgent HERVs transcriptional activity has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a web resource dedicated to querying the relationship between activation of HERVs and cancer development is lacking. Here, we have constructed a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently incorporates RNA sequencing (RNA-seq) data of 580 HERVs across 16246 samples, comprising 151 early embryonic data from the Gene Expression Omnibus (GEO) database, 8051 human adult tissues data from the Genotype-Tissue Expression (GTEx) project, 932 cancer cell lines data from the Cancer Cell Line Encyclopedia (CCLE) project, 6478 tumoral and 634 normal tissue samples data from The Cancer Genome Atlas (TCGA) project. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.

genomics↗

bioRxiv2024

Temporally resolved single-cell RNA sequencing reveals protective and pathological responses during herpes simplex virus 1 CNS infection

Herpes Simplex Virus 1 (HSV-1) is a common human neurotropic virus with the majority of adults harboring latent-recurrent infections. In rare cases, HSV-1 infection can access the central nervous system through the neuronal route and develop into life-threatening encephalitis. Here, we used a mouse model for HSV-1 infection to describe the transcriptomic profile of the infected brain stem at the single-cell level and with temporal resolution. Among resident brain cells, microglia increased in proportion during the course of infection, while astrocytes, pericytes, and endothelial cell levels decrease. At the levels of peripheral immune cells, we found notably monocytes to strongly influx the infected brain. Large dynamic changes were found in the abundance of subpopulations of the different cell types following virus infection. For instance, we identify one subpopulation of microglia exhibiting very high type I interferon and chemokine expression early during infection. This population was also enriched for viral transcripts, suggesting localization at foci of infection, and orchestrating recruitment of other immune cells. In contrast, for the infiltrating monocytes, we identified a larger panel of unique subpopulations with antiviral and inflammatory phenotypes, and found not all of these being highly positive for viral transcripts, thus indicating monocyte activities beyond the infected brain areas. Finally, investigation of endothelial cell cross-talk with other cell types revealed that cytokines derived from microglia and monocyte, but also T cells, contribute to disturbance of the blood brain barrier. Our work thus reveals for the first time the complex nature of the cellular response in the virus-infected brain, which seeks to eliminate infection but can also prime for pathological changes.

immunology↗

bioRxiv2024

Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer

Age is a major risk factor for liver cancer, as is the case for most adult human cancers. However, the underlying mechanisms are not well defined. A better understanding of the role of aging in liver and other cancers can facilitate approaches for risk assessment, early detection and prevention. We hypothesize that age-driven changes render aged liver more sensitive to oncogenic stress and hence tumorigenesis. To investigate how the liver changes with age, we documented the immune profile, transcriptome and epigenome of healthy livers from both young and aged mice, revealing pronounced alterations with aging. Notably, in aged hepatocytes, we identified heightened interferon (IFN) signaling, as well as simultaneous tumor suppressor and oncogene signaling at both bulk and single cell level, suggestive of an aged liver that is poised for neoplasia. To challenge this seemingly poised state, we employed adeno-associated virus (AAV)-mediated expression of a c-Myc oncogene in young and aged mouse liver hepatocytes in vivo. Analysis of aged hepatocytes expressing c-Myc revealed further elevated expression of IFN Stimulated Genes (ISGs). This ISG upregulation was evident in multiple models of oncogenic stress and transformation in older mice and also observed in aged humans with Metabolic dysfunction-Associated Steatohepatitis (MASH). We determined that Stat1 is both necessary and sufficient for the age specific elevated ISG expression in old wild type mice. Remarkably, inhibiting Jak/Stat signaling alongside ectopic c-Myc expression led to high-grade hepatocyte dysplasia and tumor formation, selectively in aged mice. Together, these results suggest that an aged liver is in a state of "precarious balance", due to concurrent activation of oncogenic and tumor suppressor pathways, but protected against neoplastic progression by IFN-signaling. Age-dependent activation of IFN signaling has been observed in many tissues and recent studies have demonstrated its detrimental consequences on aging, raising the question as to why IFN-signaling is activated during aging. We propose that aged tissues are intrinsically at higher risk of cancer and age-dependent activation of IFN-signaling is an adaptive process to protect from tumorigenesis, but one that also has maladaptive consequences.

cancer biology↗

bioRxiv2024

Genetic variation in the species Arabidopsis thaliana reveals the existence of natural heat resilience factors for meiosis

Heat interferes with multiple meiotic processes leading to genome instability and sterility in flowering plants, including many crops. Despite its importance for food security, the mechanisms underlying heat tolerance of meiosis are poorly understood. In this study, we analyzed different meiotic processes in the Arabidopsis (Arabidopsis thaliana) accessions Columbia (Col) and Landsberg erecta (Ler), their F1 hybrids and F2 offspring under heat stress (37{degrees}C). At 37{degrees}C, Col exhibits significantly reduced formation of double-stand breaks (DSBs) and completely abolished homolog pairing, synapsis and crossover (CO) formation. Strikingly, Ler and Ler/Col hybrids are much less affected than Col. Interestingly, only 10% [~] 20% of F2 offspring exhibit the same heat tolerance of meiotic recombination as parents, indicating that heat resilience in Ler is controlled by the interplay of several loci. Moreover, F2 offspring show defective chromosome condensation in interkinesis, and untimely sister-chromatid segregation and/or chromosome fragmentation, the levels of which exceed those in either inbreds and/or hybrids thus implying a transgressive effect on heat tolerance of meiosis. Furthermore, correlation and cytogenetic analysis suggest that homolog pairing and/or synapsis have an impact on heat tolerance of chromosome morphology and stability during post-recombination stages under heat stress. Taken together, this study reveals the existence of natural heat resilience factors for meiosis in Arabidopsis, which have the great potential to be exploited in breeding programs. Author summaryEnvironmental temperature alterations affect meiotic recombination and/or chromosome segregation thus perturbing genetic makeup and genome stability in plants. We have previously reported that CO formation is fully abolished in Arabidopsis thaliana accession Col under heat stress (36{degrees}C-38{degrees}C) due to reduced DSB formation and impaired homolog pairing. Here, we show that in Arabidopsis thaliana accession Ler under the same high temperature conditions, both DSB and CO formation occur normally, and homolog pairing is mildly impacted, which indicate a striking difference in heat tolerance of meiotic recombination from Col. Remarkably, Col/Ler hybrids display the same heat tolerance as Ler, however, only 10% [~] 20% of F2 offspring behave the same as parents. Moreover, we found higher levels of defects in chromosome morphology and integrity, and sister-chromatid segregation in F2 population than those in both inbreds and hybrids, which suggest a transgressive effect influencing heat tolerance of meiosis. Our findings reveal that heat resilience in Arabidopsis is controlled by the interplay of multiple genomic loci, holding a great potential to be exploited in crop breeding.

plant biology↗

bioRxiv2024

A high-continuity and annotated reference genome of allotetraploid Siberian wildrye (Elymus sibiricus L., Poaceae: Triticeae)

Elymus sibiricus L. (Siberian wildrye, Es), a species belonging to the wheat tribe, is extensively employed as forage and for the reclamation of degraded grasslands within the Qinghai-Tibet Plateau (QTP). This study provides a high-quality reference genome assembly for the allotetraploid Es, which is composed of 14 pseudomolecules with the total genome size of 6.57 Gb. Our finding suggest that large-scale bursts of retrotransposons are critical for the genome expansion of Es. We discovered a translocation event between the Es4H and Es6H chromosomes with a low frequency of combination. Phylogenetic analyses of 90 Es accessions and 25 diploid accessions representing proposed ancestors from various habitats revealed the existence of four distinct populations. We further provided support for the hypothesis that the QTP is the center of origin and genetic diversity for Es. Collectively, our study offers valuable insights into the evolution of Es, as well as providing genomic resources for genetic enhancement in the Elymus genus and wheat tribe.

genomics↗

bioRxiv2024

ACSS2 upregulation enhances neuronal resilience to aging and tau-associated neurodegeneration

Epigenetic mechanisms, including histone acetylation, are pivotal for learning and memory, with a role in neuronal function in Alzheimers disease and Related Dementia (ADRD). Acetyl-CoA synthetase 2 (ACSS2), an enzyme that generates acetyl-CoA, is central to histone acetylation and gene regulation, particularly in neurons, due to their unique metabolic demands and postmitotic state. ACSS2 can be recruited to the nucleus and chromatin, locally supplying acetyl-CoA to directly fuel histone acetyltransferase enzymes and key neuronal gene expression. This regulatory mechanism may be a promising target for therapeutic intervention in neurodegenerative diseases. Previously we showed that systemic ACSS2 deletion in mice, although largely normal in physiology, is greatly impaired in memory. Here we investigated whether increasing ACSS2 levels could protect neurons against disease and age-associated cognitive decline. Given the role of tau in ADRD, we used primary hippocampal neurons that mimic the sporadic development of tau pathology and the P301S transgenic mouse model for tau-induced memory decline. Our results show that ACSS2 upregulation mitigates tau-induced transcriptional alterations, enhances neuronal resilience against tau pathology, improves long-term potentiation, and ameliorates memory deficits. Expanding upon these findings, we reveal that increasing histone acetylation through ACSS2 upregulation improves age-associated memory decline. These findings indicate that increasing ACSS2 is highly effective in countering age- and tau-induced transcriptome changes, preserving elevated levels of synaptic genes, and safeguarding synaptic integrity. We thus highlight ACSS2 as a key player in the epigenetic regulation of cognitive aging and ADRD, providing a foundation for targeted therapeutics to enhance brain resilience and function. SummaryACSS2 upregulation protects neurons from disease and age-related decline by enhancing synaptic and longevity gene expression.

neuroscience↗

bioRxiv2024

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

RNA binding proteins (RBPs) containing intrinsically disordered regions (IDRs) are present in diverse molecular complexes where they function as dynamic regulators. Their characteristics promote liquid-liquid phase separation (LLPS) and the formation of membraneless organelles such as stress granules and nucleoli. IDR-RBPs are particularly relevant in the nervous system and their dysfunction is associated with neurodegenerative diseases and brain tumor development. Serpine1 mRNA-binding protein 1 (SERBP1) is a unique member of this group, being mostly disordered and lacking canonical RNA-binding domains. We defined SERBP1s interactome, uncovered novel roles in splicing, cell division and ribosomal biogenesis, and showed its participation in pathological stress granules and Tau aggregates in Alzheimers brains. SERBP1 preferentially interacts with other G-quadruplex (G4) binders, implicated in different stages of gene expression, suggesting that G4 binding is a critical component of SERBP1 function in different settings. Similarly, we identified important associations between SERBP1 and PARP1/polyADP-ribosylation (PARylation). SERBP1 interacts with PARP1 and its associated factors and influences PARylation. Moreover, protein complexes in which SERBP1 participates contain mostly PARylated proteins and PAR binders. Based on these results, we propose a feedback regulatory model in which SERBP1 influences PARP1 function and PARylation, while PARylation modulates SERBP1 functions and participation in regulatory complexes.

genomics↗

bioRxiv2024

Immunomagneto-activated hepatocyte-specific tissue vesicle profiling reveals message diversification from regenerating liver

Background & AimsThe liver possesses a remarkable regenerative capacity involving intricate intercellular communication, the mechanisms of which remain poorly understood. Extracellular vesicles (EVs) emerge as important messengers in diverse pathophysiological conditions. However, tissue-derived, cell-specific functional EV populations in regeneration have not been robustly investigated. MethodsBulk and single-cell RNA sequencing analyses of the regenerating liver after partial hepatectomy (PHx), ultrastructural examinations of in situ liver tissue EVs (LT-EVs), and nanoscale and proteomic profiling of hepatocyte-derived tissue EVs (Hep-EVs) were integrated. Targeted inhibition of Hep-EV release in vivo was performed via AAV-mediated shRNA knockdown of Rab27a, and Hep-EVs were intravenously infused for therapeutically use. Gross, histological, and immunofluorescent examinations of livers with evaluating in vivo and ex vivo hepatocyte proliferation were conducted. ResultsLT-EVs contribute to the liver regenerative process after PHx, and hepatocytes serve as the major origin of tissue EVs in the regenerating liver. Moreover, Hep-EVs play an indispensable role to orchestrate liver regeneration, which is strengthened to release with proliferative messages identified after PHx. Mechanistically, Hep-EVs from the regenerating liver reciprocally promote hepatocyte proliferation, which are hallmarked by and function based on the Cyclin dependent kinase 1 (Cdk1) activity. Importantly, replenishment of Hep-EVs from the regenerating liver holds translational promise and rescues insufficient liver regeneration. ConclusionsOur study establishes a functional and mechanistic framework that release of regenerative Hep-EVs govern rapid hepatocyte proliferation through cell cycle control, shedding light on investigation of physiological and endogenous tissue EV populations in organ regeneration and therapy.

cell biology↗