Biology subjects

Xie, M.

Publications and source records attributed to Xie, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Effects of different environments and microbial exposures on the adult immune system of the C57BL/6 laboratory mouse strain

The realization that the grossly underdeveloped immune system of laboratory mice may hinder their use as suitable models of human disease has led to the development of different strategies to "normalize" immune responses in these mice so that they more closely resemble those typical of the human population. In this study, we performed a comprehensive comparison of the adult immune systems and microbiomes of C57BL/6 laboratory mice exposed to different housing and microbial conditions. C57/BL6 mice housed in a facility of substandard health levels (herein termed "dirty") and C57BL/6 mice born after embryo transfer from females captured in the field ("wildings") were compared to C57BL/6 mice housed under standard SPF laboratory conditions. Microbiota and parasite burden varied widely between the three conditions, which also showed marked differences among populations of mature, antigen-experienced, memory, plasma, and germinal centre B cells. Interestingly, we observed discrepancies among T cell phenotypes, with antigen-experienced T cells present at higher frequencies in "dirty" mice. On the other hand, "wildlings" displayed significantly elevated frequencies of both naive and antigen-experienced spleen T cells. Interestingly, "dirty" and "wildlings" showed differences in the expansion of distinct myeloid cell types. Lastly, we observed that systemic immune traits reverted to a "cleaner" profile in the progenies (F2) of "wildlings" raised under laboratory conditions, indicating that such mice may not be suitable for human immune system modelling after prolonged housing in laboratory environments. Collectively, our results highlight the profound effects of varied microbial exposures and husbandry conditions on adult immunity of the common C57BL/6 laboratory mouse and suggest that complex microbial exposure in laboratory mice can provide a relevant tool for modelling immunological functions, thus enhancing their translational value.

immunology↗

bioRxiv2025

Neuroprotective function of astrocyte p75NTR in Alzheimer's Disease through regulation of cholesterol metabolism

Reactive astrogliosis in Alzheimers Disease (AD) involves profound changes in the morphology, metabolism and secretion profile of astrocytes, but whether astrogliosis is beneficial or harmful, and under which conditions, remain open questions. Here we report an unexpected neuroprotective function of death receptor p75NTR in astrocytes through its ability to regulate cholesterol metabolism. AD knock-in mice expressing signaling-deficient p75NTR variants in astrocytes showed enhanced A{beta} burden, brain histopathology and cognitive impairment, even when variants were introduced late in the disease process. Astrocytes expressing dysfunctional p75NTR variants showed impaired uptake of A{beta} oligomers, and their conditioned medium enhanced A{beta} production in AD neurons. p75NTR signaling negatively regulated astrocyte cholesterol biosynthesis and secretion, while cholesterol depletion restored A{beta} uptake in mutant astrocytes and reduced A{beta} production in AD neurons. In agreement with the role of astrocyte-derived cholesterol, statin treatment reverted the effects of astrocyte p75NTR mutants on AD neuropathology. Thus, although neuronal p75NTR has been widely recognized to amplify AD, astrocyte p75NTR plays a neuroprotective role.

neuroscience↗

bioRxiv2025

Amelioration of symptomatic Alzheimer's Disease after selective impairment of p75NTR function in adult forebrainexcitatory neurons

The p75 neurotrophin receptor (p75NTR) contributes to the development of Alzheimers Disease (AD) pathology by enhancing amyloid precursor protein (APP) cleavage and amyloid plaque formation. However, the cell type-specific and temporal roles of p75NTR in AD progression remain unclear. Here, we report that conditional knock-in of functionally impaired p75NTR variants lacking the death domain ({Delta}DD) or transmembrane Cys259 (C259A) specifically in forebrain excitatory neurons of 5xFAD mice significantly attenuated multiple AD-associated pathologies, including amyloid plaque accumulation, gliosis, neurite dystrophy, as well as learning and memory deficits. Hippocampal amyloid plaque burden was reduced to levels comparable to those found in whole-body knock-in mice. Strikingly, delaying introduction of p75NTR variants until advanced disease stages produced comparable beneficial effects, and rescued behavior performance in cognitively impaired animals. These findings suggest that blunting p75NTR function can have beneficial effects even during symptomatic stages of AD, offering a potential therapeutic approach complementary to passive vaccination.

neuroscience↗

bioRxiv2025

Loss of tight junction protein claudin 18 uncovers alveolar epithelial stem cell plasticity and emergence of non-fibrogenic transitional progenitors

Persistence of senescent alveolar transitional progenitors following lung injury is implicated in the pathogenesis of fibrosis. We identified transitional cells in uninjured Cldn18 knockout (KO) mouse lungs distinct from previously reported damage-associated transitional progenitors (DATPs) with a less fibrogenic transcriptomic profile. Cldn18 KO mice are protected from bleomycin-induced fibrosis, with early restoration of cellular homeostasis. Lineage tracing implicates accelerated differentiation as a mechanism for protection from fibrosis, leading us to name these cells regeneration-associated transitional progenitors (RATPs). Multiome confirms that RATPs and DATPs are epigenetically distinct, with RATPs comprised of RATP2s and RATP1s based on epigenomic proximity to AT2s and AT1s, respectively, and suggests dynamic regulatory remodeling during AT2-to-AT1 differentiation, with NKX2.1 and AP-1 active in early transitions and TEAD factors in later stages. These results reveal an unexpected role for Cldn18 in regulation of AEC plasticity, while identification of RATPs challenges the notion that persistence of transitional alveolar cells is invariably pathologic.

cell biology↗

bioRxiv2025

Beckwith-Wiedemann syndrome multiomic analysis of hepatoblastoma uncovers unique tumor heterogeneity and cellular landscapes, including transition cells leading to tumor formation

BackgroundBeckwith-Wiedemann syndrome (BWS) is an overgrowth and cancer predisposition syndrome caused by epigenetic alterations on chromosome 11p15 that predisposes children to multiple cancer types, including hepatoblastoma. Hepatoblastoma is heterogenous in nature, and the 11p15 changes that cause BWS can also be found as a somatic alteration in nonBWS hepatoblastomas, further adding complexity to this disease. MethodsTo understand the impact of the predisposition molecular cues in BWS hepatoblastoma, we interrogated BWS and nonBWS hepatoblastomas, as well as adjacent normal liver, using a multiomic approach [single nuclei RNA-sequencing (snRNA-seq) + single nuclei assay for transposable-accessible chromatin sequencing (snATAC-seq)]. ResultsOur approach identified an enrichment of the WNT signaling pathway in BWS hepatoblastoma. Despite similar histology, we found greater tumor heterogeneity and embryonic transcriptional signatures in BWS hepatoblastoma. Furthermore, using pseudotime analysis, we identified a population of transition cells in BWS, with unique molecular profiles, which likely promote the precancer to cancer neoplastic transition in BWS. ConclusionsThis study highlights key signaling pathways, particularly WNT, and identifies a unique population of transition cells that may drive neoplastic transformation in BWS hepatoblastoma. These findings provide new insights into the molecular events leading to cancer in BWS and suggest potential targets for early intervention and prevention strategies.

cancer biology↗

bioRxiv2025

Fluorescent protein-based ticker tapes for multiplexed recordings of transcriptional histories in single cells in culture and in vivo

Recording and imaging of promoter activities in real time is critical for deciphering cellular states and dynamic signaling crosstalk, but technologies capable of simultaneously capturing multiple transient events in living cells are lacking. Here, we custom-design fluorescent protein-based ticker tapes (FPTT) for multiplexed and longitudinal recording of physiological activities in single cells. FPTT integrates multi-spectral monomeric fluorescent proteins with self-assembling protein fibers, enabling massively parallel analysis of signaling dynamics under varying cellular conditions. Using FPTT, we were able to log dose-dependent and reversible transcriptional histories of endogenous cFos signaling in primary hippocampus neurons at a 3-hour temporal resolution via biological timestamps and an extended recording time of over 8 days. Furthermore, we expanded the imaging toolset by engineering genetically encoded FPTT variants for human NF{kappa}B, JAK/STAT3, mTOR, NFAT and cAMP signaling, allowing for the quantification of potential crosstalk between cFos and NF{kappa}B pathways in neurons, multiplexed recording of STAT3- and cAMP-specific promoters during drug-induced liver injury in mice, as well as simultaneous analysis of up to four major signaling pathways involved in experimental T-cell activation. This platform advances single-cell analysis by providing a versatile tool to investigate transcriptional histories and signaling interplay across diverse biological contexts, with broad applications in developmental biology and disease modeling.

synthetic biology↗

bioRxiv2025

Interstitial macrophages prevent tuberculosis relapse by restricting Mycobacterium tuberculosis immune evasion

Alveolar macrophages (AMs) are the first immune cells to encounter Mycobacterium tuberculosis (Mtb) in the lungs, but they frequently fail to eliminate this causative agent of tuberculosis (TB), allowing Mtb to persist or replicate. Interstitial macrophages (IMs) are recruited to restrict Mtb growth and limit immune evasion. While IMs have been implicated in the control of acute Mtb infection, their role during latent tuberculosis infection (LTBI) has not yet been explored. We hypothesized that IMs contribute to maintaining latency and that their depletion during LTBI would promote Mtb reactivation, leading to TB relapse and disease. To test this, we utilized our previously established mouse model of paucibacillary Mtb infection that mimics aspects of LTBI in humans to selectively deplete IMs during the latent phase. IM depletion led to TB relapse in 26% of mice compared to 2% in control mice. The transitory depletion of this macrophage subset transiently affected both pulmonary macrophage and neutrophil populations. Mice that relapsed exhibited an increased proportion of pro-inflammatory IMs and elevated concentrations of G-CSF, GM-CSF, IL3, IL-12, IL-13, IL-17A and KC in the lung. These findings indicate that IMs play a critical role in controlling latent Mtb and preventing TB relapse.

immunology↗

bioRxiv2025

Hypobaric hypoxia drives citrate cycle reprogramming to suppress tumor progression

High altitude residents present lower tumor incidence and mortality than plain residents, suggesting that hypobaric hypoxia displays protective effect against tumor development. The results of our studies showed that hypobaric hypoxia exposure significantly suppressed tumor progression in subcutaneous bearing and lung metastasis tumor models. With single-cell transcriptome analysis, we identified HIF-1 pathway was significantly downregulated in tumor tissues with high altitude hypoxia, leading to decreased glycolysis and angiogenesis and improved antitumor immune response. Mechanistically, systemic hypoxia rewired citric acid cycle, with enhanced CS and IDH2 expression and reduced OGDH and SUCLG2 expression, to induce -ketoglutarate accumulation and succinate decline in tumor microenvironment, further mediating HIF-1 pathway inhibition. Moreover, hypobaric hypoxia treatment significantly improved the antitumor effects of adjuvant therapies (including chemotherapy, anti-angiogenic therapy and immunotherapy). Our findings reveal the role and mechanism of hypobaric hypoxia for tumor regression and yield new insights into tumor therapy.

cancer biology↗

bioRxiv2025

GIN-CRC-Pareto: A graph-based Pareto-optimal multi-task learning framework to identify miRNA-target interactions in colorectal cancer

Colorectal cancer (CRC) ranks as the third highest incidence among malignancies in humans and the second most common cause of cancer-related mortality in the United States. Accumulating evidence has established microRNAs (miRNAs) as critical regulators of cancer development and therapeutic response. Understanding miRNA-mRNA interactions is critical for elucidating the molecular mechanisms driving CRC and other malignancies. In this study, we proposed GIN-CRC-Pareto, a graph-based, Pareto-optimal multi-task learning framework that simultaneously predicts miRNA-mRNA binding pairs, identifies seed match pairings, and classifies seed match subtypes. By leveraging the power of graph neural networks and Pareto-optimal gradient balancing strategy, GIN-CRC-Pareto dynamically adjusted the task weights during training to optimize each task without compromising the others. Experimental results demonstrated that our framework consistently outperforms traditional deep learning models and existing state-of-the-art tools across multiple evaluation metrics, with 0.909 in accuracy, 0.909 in precision and 0.968 in AUC in the miRNA-mRNA binding pairs prediction task. Additionally, we further validated the generalizability of the framework in combination with transfer learning techniques to identify miRNA-target interactions across other cancers. These findings highlight the effectiveness of the proposed framework to comprehensively identify the miRNA-target interactions in CRC, with the potential to serve as a scalable and generalizable tool across diverse cancer types, ultimately facilitating the development of miRNA-based therapeutics for cancer treatment.

bioinformatics↗

bioRxiv2025

CLASHub: an integrated database and analytical platform for microRNA-target interactions

MicroRNAs (miRNAs) are [~]22-nucleotide RNAs that regulate gene expression, critical for development and disease. Residing in Argonaute (AGO) proteins, miRNAs target messenger RNAs via complementary base-pairing. Current miRNA-target databases rely on indirect data from AGO crosslinking immunoprecipitation (AGO-CLIP). In contrast, CLASH (Crosslinking, Ligation, and Sequencing of Hybrids) employs proximity ligation within AGO complexes, providing direct miRNA-target interaction evidence. Existing CLASH datasets remain limited to few human and mouse samples. CLASHub integrates CLASH-defined interactions with gene and miRNA expression data from human, mouse, Drosophila, and C. elegans, covering over 20 cell types and tissues. The datasets also include samples with ZSWIM8-knockout, an essential component in target RNA-directed miRNA degradation (TDMD)--a specialized mechanism for miRNA turnover triggered by basepairing with specific target RNA--thereby providing unique insights into miRNA turnover mechanisms. CLASHub also features a user-friendly Analyzer interface for CLASH, RNA-seq, miRNA-seq, and cumulative fraction curve analysis. Leveraging these tools, we uncovered a novel TDMD "trigger" for miR-335-3p degradation in ATP6V1G1s 3' UTR. Thus, CLASHub offers an online platform for miRNA research, enabling discovery of novel miRNA targets and triggers across diverse contexts. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/668543v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@6766e4org.highwire.dtl.DTLVardef@940f40org.highwire.dtl.DTLVardef@75499dorg.highwire.dtl.DTLVardef@33f938_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

A lncRNA drives developmentally-timed decay of all members of an essential microRNA family

The spatiotemporal expression patterns of microRNAs (miRNAs) are crucial to their function. Target-directed miRNA degradation (TDMD) is an emerging regulatory module that contributes to these expression patterns wherein a specialized RNA (TDMD trigger) drives miRNA decay through base pairing and resulting recruitment of E3 ubiquitin ligase ZSWIM8/EBAX-1. Extensive base pairing to the miRNA seed region and 3 end has been proposed as a key feature that distinguishes TDMD triggers from conventional mRNA targets of miRNAs, which primarily pair with the seed. Here we identify the long noncoding RNA, tts-2, as a TDMD trigger for mir-35-42, the most abundant miRNA family in C. elegans early embryos. We demonstrate that a single site in tts-2 drives decay through base pairing with the seed sequence shared by all eight family members. A second site in tts-2 supports decay of mir-38 with incomplete seed complementarity. Our findings demonstrate that extended base pairing is not a universal requirement for TDMD, and that TDMD drives developmentally-timed clearance of abundant miRNAs at the exit of C. elegans embryogenesis.

molecular biology↗

bioRxiv2025

Evolutionary Genomics Guides Scalable Coral Probiotics for Climate Resilience

A universal bottleneck limiting probiotic efficacy in medicine, aquaculture, agriculture, and wildlife conservation is uncertain long-term colonization, necessitating repeated administration. We present an evolution-guided framework for probiotic identification based on genomic hallmarks of emerging host dependency, including widespread pseudogenization and insertion sequence proliferation driving genomic restructuring. Applied to coral reefs, we screened over 1,200 coral-associated bacterial isolates and identified Ruegeria MC10 as exhibiting these signatures. Its presence was associated with increased thermal tolerance of a model cnidarian. Following nursery application, MC10 persisted in reef corals for an 8-month monitoring period through a natural bleaching event, improving color retention and retaining algal photosynthesis performance. This work establishes a predictive, scalable pipeline for selecting persistent probiotics, directly addressing a central constraint on microbiome-based interventions across host systems.

microbiology↗

bioRxiv2025

Simulating Iron Deficiency in Plant Plastids With a Flexible Physics-Informed Neural Network Approach

Flux balance analysis has proven to be a successful approach in metabolic engineering and systems biology to predict intracellular fluxes of large genome-scale networks and the essentiality of genes encoding enzymes and regulatory factors. Flux balance analysis (FBA) relies on a key assumption of a metabolic state being persistent ("steady") over a given time frame. This assumption works well for microbial growth because of the ease with which microbial media can be fixed, biomass can be decomposed, and growth rates can be measured. However, the assumption is far less tenable for the cells and tissues of complex multicellular organisms, particularly if any integrated data is sampled from a heterogeneous collection of developing cells continually interacting between and across tissues. These will likely exhibit transient metabolic states equilibrating over varying timescales, and many FBA studies in complex organisms typically either ignore time as a parameter, or integrate data taken over long timescales (days/weeks). In this work, we adopt and modify a previously published machine learning approach originally developed to hybridize several aspects of a constraint-based approach with machine-learning in order to predict growth. This approach accommodates transient state dynamics, at the cost of tolerating a controlled amount of slack in the steady-state assumption, in order to enable transcript-constrained flux estimation in plant tissues without optimizing a growth objective. For our case study, we reconstruct the metabolism of the plastid of Poplar and Sorghum, integrating data sampled from leaf tissue under varying levels of iron bioavailability. The two species diverge sharply: Sorghum suppresses its photosynthetic electron transport and Calvin cycle abruptly at day 7 and its carbon delivery to biomass collapses to a third of control by day 21, whereas Poplar declines gradually and retains roughly 70%. Normalizing each reaction score to the plastid proteome pool makes the two species comparable and exposes reallocation as the pool contracts, including a split within Sorghums sulfate assimilation that tracks which enzymes carry iron cofactors.

bioinformatics↗

bioRxiv2025

Nephron segmentation and patterning in kidney organoids can be modulated by distinct FGF subfamily members

Human pluripotent stem cell-derived kidney organoids replicate embryonic nephrogenesis in a 3D-culture system. Recent advances suggest that refining the culture environment to replicate spatiotemporal cues present during embryonic organogenesis improves patterning. Here, this paradigm was applied to FGF signalling, a key regulator of embryonic nephron progenitor maintenance, nephrogenesis and ureteric branching. Both FGF8b and FGF10 signalling is sufficient to support nephrogenesis, with each having distinct effects on nephron patterning. FGF10 enhanced the initial WT1+ mesenchymal population, leading to proximally biased nephrons, while FGF8b biased toward early distal patterning, leading to the formation of cells with connecting segment identity. The addition of both FGF8b and FGF10 together had an additive effect, leading to a balance of proximal and distal patterning. This differential patterning was retained in tissue transplanted under the murine renal capsule, with FGF8b-treated organoids displaying increased distal/connecting segments. These findings highlight plasticity during organoid nephrogenesis that can be modulated by FGF signalling and identify an approach to refine nephrogenesis toward key cell types.

developmental biology↗

bioRxiv2025

Breaking the Link: Neural Dissociation of Attention and Working Memory through Inhibitory Control

Attention and working memory (WM) encoding have traditionally been considered inseparable processes with shared neural mechanisms. Here, using an innovative experimental design and a multimodal approach, we provide the first direct neural evidence that attention and WM encoding are dissociable. Functional MRI identifies the supramarginal gyrus (SMG) as the key region enabling this dissociation, while dynamic causal modeling reveals the neural circuitry through which the SMG exerts inhibitory control over attentional representations, regulating their integration into WM. Furthermore, neuromodulation via transcranial direct current stimulation (tDCS) demonstrates that enhancing SMG activity strengthens this inhibitory control, providing causal evidence for the dissociation mechanism. A second tDCS experiment with varied stimuli confirms the generalizability of this mechanism and reinforces the robustness of our results. These findings challenge the long-standing view that attention and WM encoding form a continuous process, demonstrating instead that they constitute two dissociable neural processes of information selection.

neuroscience↗

bioRxiv2025

Treatment of human oocytes with extracellular vesicles from follicular fluid during rescue in vitro maturation enhances maturation rates and modulates oocyte proteome and ultrastructure

Study questionCould follicular fluid-derived extracellular vesicles (ffEVs) benefit human oocyte rescue in vitro maturation (rIVM)? Summary answerSupplementation of rIVM culture with ffEVs isolated from mature follicles enhanced oocyte maturation rates by >20%, inducing changes in oocyte protein profile and organelle distribution. What is already knownIVM involves the culture of immature germinal vesicle (GV) oocytes under set laboratory conditions to allow for their transition to mature metaphase II (MII) stage, which is confirmed by the extrusion of the first polar body. Efficient IVM could circumvent aggressive controlled ovarian stimulation (COS), reduce the cost and broaden the repertoire of infertility treatments. Animal studies suggest that extracellular vesicles (EVs), membranous nanosized vesicles containing different molecular content (e.g. nucleic acids, proteins) and present in the ovarian follicular fluid could enhance oocyte maturation. The uptake of ffEVs by bovine, equine and feline oocytes, but not human, has been demonstrated. Study design, size, durationWomen undergoing transvaginal oocyte retrieval after COS (n=83) were recruited to donate follicular fluid (n=54 single follicles) and/or immature GV oocytes (n=95). We aimed to: a) define differences in the protein cargo of ffEVs derived from human follicles containing mature (MII-ffEVs, n=10) versus immature (GV-ffEVs, n=5; metaphase I MI-ffEVs, n=5) oocytes, b) demonstrate the capacity of human GV oocytes to uptake MII-ffEVs and c) determine the effect of MII-ffEVs supplementation on oocyte maturation. Participants/materials, setting, methodsffEVs were isolated by ultracentrifugation. The protein content of ffEVs was analysed by mass spectrometry. The uptake of fluorescently-labelled MII-ffEVs by GV oocytes (n=15) was assessed by confocal microscopy. GVs were cultured for rIVM in a timelapse incubator with MII-ffEVs (n=45 GVs) or without (n=40 GVs) and extrusion of polar body denoted maturation. The impact of MII-ffEVs supplementation on IVM-matured oocytes was assessed through single-cell proteomics and intracellular organelles appearance on transmission electron microscopy (TEM). Main results and the role of chanceWe identified 1340 proteins in ffEVs, with proteins such as F12, IGKV1-39, FREM2, and C1QC being significantly enriched in MII-ffEVs. GV oocytes internalised MII-ffEVs, and their supplementation for 48 hours increased the oocyte maturation rate compared to control by 22.8{+/-}9.4% (77.8% vs 55% maturation rate respectively; p-value=0.0372). Proteomic analysis of ffEV-supplemented mature oocytes (n=6) revealed 56 differentially abundant proteins (DAPs) compared to not supplemented mature oocytes (n=5). Among them, 37 DAPs were in higher abundance in ffEVs- supplemented mature oocytes including Hyaluronan Synthase 1 (HAS1) that is associated with oocyte maturation (6.55 fold increase). Electron microscopy showed differences in oocyte organelle distribution and appearance, particularly that of endoplasmic reticulum (RE) and RE-mitochondria complexes. Functional enrichment analysis of differentially abundant proteins during ffEV-oocyte interaction revealed regulation of endoplasmic reticulum, steroid biosynthesis, and keratin organisation pathways. Large scale dataN/A Limitations, reasons for cautionThis study utilised immature oocytes from COS cycles, therefore the results should be interpreted within the context of rIVM potential. Winder implications of the findingsThese results provide new insights into the role of ffEVs in enhancing oocyte maturation, offering potential improvements for clinical rIVM protocols and inspire the development of global IVM supplements based on ffEVs or associated specific cargo. Study funding/competing interest(s)This work was funded by an EMDO research fellowship and a FAN research grant (Fonds zur Forderung des akademischen Nachwuchses) from the University of Zurich. What does it mean for the patientsInfertility rates are rising, with 17% of couples worldwide needing help to get pregnant, often through treatments like in vitro fertilisation (IVF). IVF usually involves using hormones to stimulate the ovaries to produce multiple eggs, which can be tough on a womans health, both physically and emotionally, and can be very expensive. In vitro oocyte maturation (IVM) is a gentler alternative, where eggs are matured outside the body, reducing risks and costs. However, IVM isnt as effective as IVF yet, mainly because the current methods are not perfect. Our research is exploring a new approach to improve IVM by adding extracellular vesicles from follicular fluid to the egg culture. This could help the eggs mature better, leading to higher success rates and giving more options to couples struggling with infertility.

cell biology↗

bioRxiv2024

Data-driven discovery of cell-type-directed network-correcting combination therapy for Alzheimer's disease

Alzheimers disease (AD) is a multifactorial neurodegenerative disorder characterized by heterogeneous molecular changes across diverse cell types, posing significant challenges for treatment development. To address this, we introduced a cell-type-specific, multi-target drug discovery strategy grounded in human data and real-world evidence. This approach integrates single-cell transcriptomics, drug perturbation databases, and clinical records. Using this framework, letrozole and irinotecan were identified as a potential combination therapy, each targeting AD-related gene expression changes in neurons and glial cells, respectively. In an AD mouse model, this combination therapy significantly improved memory function and reduced AD-related pathologies compared to vehicle and single-drug treatments. Single-nuclei transcriptomic analysis confirmed that the therapy reversed disease-associated gene networks in a cell-type-specific manner. These results highlight the promise of cell-type-directed combination therapies in addressing multifactorial diseases like AD and lay the groundwork for precision medicine tailored to patient-specific transcriptomic and clinical profiles. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/627436v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1e67fd5org.highwire.dtl.DTLVardef@1d2b779org.highwire.dtl.DTLVardef@10b6efforg.highwire.dtl.DTLVardef@1a44394_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families

While much is known about miRNA biogenesis and canonical miRNA targeting, relatively less is understood about miRNA decay. The major miRNA decay pathway in metazoans is mediated through target-directed miRNA degradation (TDMD), in which certain RNAs can "trigger" miRNA decay. All known triggers for TDMD base pair with the miRNA seed, and extensively base pair on the miRNA 3' end, a pattern that supposedly induces a TDMD-competent conformational change of Argonaute (Ago), allowing for miRNA turnover. Here, we utilized Ago1-CLASH to find that the Drosophila transcript Kah contains at least two triggers, a "trigger cluster", against miR-9b and the miR-279 family. One of these triggers contains minimal/non-canonical 3' end base pairing but is still sufficient to induce TDMD of the entire miR-279 family. We found that these clustered triggers likely lack cooperativity, the minimal 3' pairing is required for miR-279 family turnover, and probed the in-cell RNA structure of the Kah trigger cluster. Overall, this study expands the list of endogenous triggers and the unexpectedly complex regulatory network governing miRNA degradation.

molecular biology↗