Biology subjects

Yu, X.

Publications and source records attributed to Yu, X..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Structural basis of PPARγ-mediated transcriptional repression by the covalent inverse agonist FX-909

Hyperactivation of peroxisome proliferator-activated receptor gamma (PPAR{gamma})-mediated transcription promotes tumor growth in urothelial (bladder) cancer, which can be inhibited by pharmacological compounds that repress PPAR{gamma} activity. FX-909 is a covalent PPAR{gamma} inverse agonist currently in phase 1 clinical trials for advanced solid malignancies including muscle-invasive bladder cancer. Here, we compared the mechanism of action of FX-909 to other covalent inverse agonists including T0070907, originally reported more than 20 years ago and misclassified as an antagonist, and two recently reported improved covalent inverse agonist analogs, SR33068 and BAY-4931. Functional profiling and NMR studies reveal that FX-909 displays improved corepressor-selective inverse agonism and better stabilizes a transcriptionally repressive PPAR{gamma} LBD conformation compared to T0070907. The crystal structure of PPAR{gamma} LBD cobound to FX-909 and NCoR1 corepressor peptide reveals a repressive conformation shared by other covalent inverse agonists. These findings build on recent studies highlighting the pharmacological significance and clinical relevance of transcriptionally repressive PPAR{gamma} inverse agonists.

biophysics↗

bioRxiv2025

Non-visually-derived mental objects tax "visual" pointers

In daily life, we can construct mental objects from various modalities: we can create a cat in the mind from visual experience, or from what someone says or signs linguistically. Do mental objects derived from different input sources share the same set of "slots" (or pointers, indexicals)? Employing a novel imagine-one-then-more paradigm in a large EEG sample (N = 52) across two recording sites, we found that increasing the number of imagined objects derived from a non-visual source--auditory speech during eye closure--led to greater suppression of left posterior alpha power. This observation closely mirrors effects previously observed for visually-derived representations. Our results support the existence of a domain-general pointer system that functions as a modality-independent object register in moment-to-moment cognition.

neuroscience↗

bioRxiv2025

DICAR-JP Regulates Ribosome Migration, a New Theory of Mitochondrial Protein Production

BackgroundDICAR plays a cardioprotection of diabetic models. DICAR-JP, a short sequence of DICAR, may represent DICARs active functional domain. NAC is necessary for the heart tissue development. Addtionally, OGDHL is a metabolism regulator. In this study, we examine a new mechanism of DICAR via NAC/OGDHL on regulating cardiomyocyte metabolism in DCM. We also sought to elucidate the function of DICAR/DICAR-JP in modulating NAC-dependent production of OGDHL nascent peptides and their mitochondrial translocation, and we also aimed to optimize the DICAR-JP sequence to be better therapy on DCM. MethodsSPR was to investigate the binding interaction between DICAR-JP and NAC. The function of DICAR-JP and DICAR-JP45 on OGDHL nascent peptide transfection was detected by in vitro translation approach. Biotin-DICAR-JP was transfected to study the function of DICAR-JP, NAC and OGDHL. Untargeted metabolomics was utilized to characterize the metabolic reprogramming of cardiomyocytes. AAV9-DICAR-JP and DICAR-JP45 were constructed and administered to db/db mice for 1-2 months to assess their cardioprotective effects detected by Echocardiography confirmed mouse cardiac function. ResultsOur findings demonstrated that DICAR-JP be the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. Disruption of OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP facilitated the translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria, leading us to hypothesize that DICAR-JP plays a key role in regulating ribosomal migration from the endoplasmic reticulum to the mitochondria. We refer to this process as the Ribosome Migration. In our studies using AAV9-mediated DICAR-JP and DICAR-JP45 overexpression in heart tissue. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Empagliflozin. ConclusionsIn a conclusion, we propose a new endogenous nucleic acid candidate drug library, and a new molecular framework, the Ribosome Migration, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. This theory constructs a new mitochondrion protein from nuclear original protein. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSDICAR is a new protective circular noncoding RNA for diabetic cardiomyopathy. NAC is located in ribosome and regulates new peptide production, which is also a key factor in heart tissue development. OGDHL can regulate different energy metabolism in mitochondria. What New Information Does This Article Contribute?DICAR-JP is the functional domain that interacts with NAC to regulate OGDHL nascent peptide expression. There is an interaction between DICAR-JP and NAC. DICAR-JP sequence is protected by NAC and NAC function is mediated by DICAR-JP. We called this RNA functional domain. OGDHL expression reversed the metabolic reprogramming observed in diabetic cardiomyocytes, highlighting its crucial role in maintaining cardiac metabolic homeostasis. DICAR-JP takes part in tanscription and translocation of OGDHL nascent peptides from the cytoplasm to the mitochondria via plasma ribosome. We call this process the Ribosome Migration Theory. DICAR-JP and DICAR-JP45 both exhibited significant cardioprotective effects against diabetic cardiomyopathy (DCM), comparable to those observed with Dapagliflozin (DAPA). Our study revealed a novel molecular framework, the Ribosome Migration Theory, which implicates the DICAR-JP/NAC/OGDHL nascent peptide axis in metabolic reprogramming related to DCM. Moreover, DICAR-JP45 shows strong potential as a nucleic acid-based therapeutic candidate for treating DCM.

pharmacology and toxicology↗

bioRxiv2025

Distinct yet Overlapping Functions of VMP1 and TMEM41B in Modulating Hepatic Lipoprotein Secretion and Autophagy in MASH

BackgroundTransmembrane protein 41B (TMEM41B) and vacuolar membrane protein 1 (VMP1) are endoplasmic reticulum (ER) scramblases that shuttle phospholipids between the inner and outer leaflets of the ER membrane. Both TMEM41B and VMP1 also play critical roles in regulating hepatic lipoprotein secretion and autophagy. Despite these similarities, whether TMEM41B and VMP1 exhibit different roles in very low-density lipoprotein (VLDL) secretion and autophagy in the pathogenesis of metabolic-associated steatotic liver disease (MASLD) remains unclear. MethodsWe created liver- and hepatocyte-specific single knockout (KO) and double knockout (DKO) mice for Tmem41b and Vmp1, as well as overexpression knock-in (KI) mice with hepatic overexpression of TMEM41B, Tmem41b KO/Vmp1 KI, and Vmp1 KO/Tmem41b KI. We conducted lipidomic, metabolomic, biochemical, and functional studies in these mice, fed either a chow diet or a MASLD diet. ResultsTMEM41B protein levels were decreased in the livers of human subjects with MASLD. The loss of hepatic Tmem41b impaired VLDL secretion, resulting in steatosis, inflammation, and fibrosis. Vmp1 KO mice exhibited similar phenotypes to DKO mice, displaying a more severe defect in VLDL secretion and greater liver injury than Tmem41b KO mice. Lipidomic analysis revealed decreased levels of phosphatidylcholine and phosphatidylethanolamine, along with increased neutral lipids in both Tmem41b KO and Vmp1 KO mice; however, these changes were generally more pronounced in Vmp1 KO mice. VMP1 and TMEM41B localized at the mitochondrial-associated membrane (MAM), and a reduction in mitochondria-ER contact was observed in hepatocytes deficient in either VMP1 or TMEM41B. Ultrastructural electron microscopy analysis showed increased accumulation of "lipid droplet" in the ER membrane bilayer and ER lumen in both Vmp1 KO and Tmem41b KO hepatocytes, with greater ER luminal "lipid droplet" accumulation in Tmem41b KO hepatocytes. The loss of hepatic Vmp1 or Tmem41b led to elevated levels of LC3-II and p62, with significantly higher levels of both markers in Vmp1 KO and DKO mouse livers compared to Tmem41b KO mouse livers. Restoring Vmp1 in Tmem41b KO mice partially improved defective VLDL secretion; however, high expression levels of VMP1 did not correct the hepatic autophagy defect. In contrast, restoring Tmem41b in Vmp1 KO mice dose-dependently enhanced both defective VLDL secretion and autophagy. Importantly, overexpression of hepatic TMEM41B mitigated diet-induced MASLD in mice. ConclusionThe loss of hepatic Vmp1 or Tmem41b decreases hepatic MAM and phospholipid content, leading to decreased VLDL secretion and promoting MASLD. While VMP1 and TMEM41B have overlapping functions, VMP1 appears to play a more critical role in regulating VLDL secretion and autophagy in mouse livers than TMEM41B.

cell biology↗

bioRxiv2025

MKFGO: Integrating Multi-Source Knowledge Fusion with Pre-Trained Language Model for High-Accuracy Protein Function Prediction

Accurately identifying protein functions is essential to understand life mechanisms and thus advance drug discovery. Although biochemical experiments are the gold standard for determining protein functions, they are often time-consuming and labor-intensive. Here, we proposed a novel composite deep-learning method, MKFGO, to infer Gene Ontology (GO) attributes through integrating five complementary pipelines built on multi-source biological data. MKFGO was rigorously benchmarked on 1522 non-redundant proteins, demonstrating superior performance over 11 state-of-the-art function prediction methods. Comprehensive data analyses revealed that the major advantage of MKFGO lies in its two deep-learning components, HFRGO and PLMGO, which derive handcraft features and protein large language model (PLM)-based features, respectively, from protein sequences in different biological views, with effective knowledge fusion at the decision-level. HFRGO leverages an LSTM-attention network embedded with handcraft features, in which the triplet loss-based guilt-by-association strategy is designed to enhance the correlation between feature similarity and function similarity. PLMGO employs the PLM to capture feature embeddings with discriminative functional patterns from sequences. Meanwhile, another three components provide complementary insights for further improving prediction accuracy, driven by protein-protein interaction, GO term probability, and protein-coding gene sequence, respectively. The source codes and models of MKFGO are freely available at https://github.com/yiheng-zhu/MKFGO.

bioinformatics↗

bioRxiv2025

A Single-Cell Atlas of RNA Alternative Splicing in the Glioma-Immune Ecosystem

Single-cell analysis has refined our understanding of cellular heterogeneity in glioma, yet RNA alternative splicing (AS)--a critical layer of transcriptome regulation--remains underexplored at single-cell resolution. Here, we present a pan-glioma single-cell AS analysis in both tumor and immune cells through integrating seven SMART-seq2 datasets of human gliomas. Our analysis reveals lineage-specific AS across glioma cellular states, with the most divergent AS landscapes between mesenchymal- and neuronal-like glioma cells, exemplified by AS in TCF12 and PTBP2. Comparison between core and peripheral glioma cells highlights AS-redox co-regulation of cytoskeleton organization. Further analysis of glioma-infiltrating immune cells reveals potential isoform-level regulation of protein glycosylation in regulatory T cells and a link between MS4A7 AS in macrophages and clinical response to anti-PD-1 therapy. This study emphasizes the role of AS in glioma cellular heterogeneity, highlighting the importance of an isoform-centric approach to better understand the complex biological processes driving tumorigenesis.

genomics↗

bioRxiv2025

Wnt/Beta-Catenin Signaling Is Active in Neuroendocrine Prostate Cancer

Wnt/beta-Catenin signaling plays a critical role in prostate cancer (PCa) progression, yet its precise contributions in neuroendocrine prostate cancer (NEPCa) remain incompletely understood. In this study, we utilized TRAMP/Wnt-reporter mice to monitor Wnt/beta-Catenin activity and investigated transcriptional alterations associated with NEPCa development. RNA sequencing and pathway enrichment analyses identified neuroactive ligand-receptor interaction, MAPK, calcium, and cAMP signaling as key pathways enriched in NEPCa. Although Wnt signaling was not among the top-enriched pathways, elevated Axin2 expression and increased Wnt-reporter activity suggest its involvement in NEPCa progression. We observed upregulated expression of Wnt3, Wnt6, Dvl2, Dvl3, and Lef1 in NEPCa, coupled with reduced expression of Yap1 and Frat1, which are involved in beta-Catenin degradation. Pharmacological inhibition of Wnt/beta-Catenin signaling using FC101 significantly suppressed PCa growth, underscoring its potential as a therapeutic target. These findings reveal that Wnt/beta-Catenin signaling is active in NEPCa through multiple mechanisms and highlight the need for further investigation into the regulatory interplay between Wnt and YAP1 in prostate cancer.

cancer biology↗

bioRxiv2025

Androgen Deprivation-Induced TET2 Activation Fuels Prostate Cancer Progression via Epigenetic Priming and Slow-Cycling Cancer Cells

Advanced prostate cancer (PCa) frequently develops resistance to androgen deprivation therapy through various mechanisms including lineage plasticity. Slow-cycling cells (SCCs) have emerged as key players in adaptive responses to therapy, yet their role in PCa remains unclear. Through in silico analysis of single-cell RNA sequencing (scRNA-seq) data, we discovered that SCCs are enriched during pivotal stages of PCa progression, including the transition from androgen-dependent to castration-resistant states and the emergence of neuroendocrine PCa (NEPC). Using a tetracycline-inducible H2BeGFP reporter system, we confirmed SCC enrichment following androgen deprivation in both in vitro and in vivo models. Furthermore, we identified TET2 as a key regulator of SCCs, with its expression upregulated by androgen deprivation and positively correlated with SCC signature scores in PCa. Genome-wide 5-hydroxymethylcytosine (5hmC) profiling revealed increased hydroxymethylation after androgen deprivation, while TET2 knockdown reduced 5hmC levels at specific loci. Functional studies demonstrated that TET2 governs SCC maintenance, cell cycle progression, and DNA damage repair. Targeting TET2, either alone or in combination with an ATM inhibitor, significantly suppressed tumor growth, highlighting TET2 as a promising therapeutic target. Our study provides the first single-nucleotide resolution map of 5hmC dynamics in PCa, identifies a cell state driving epigenetic rewiring, and underscores the transformative potential of novel therapeutic strategies for advanced PCa.

cancer biology↗

bioRxiv2025

One Tracer, Dual Platforms: Unlocking Versatility of Fluorescent Probes in TR-FRET and NanoBRET Target Engagement Assays

Target engagement assays are essential for drug discovery, utilizing Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) and Nano Bioluminescence Resonance Energy Transfer (NanoBRET) as complementary methods for biochemical and cellular evaluation. Traditional platforms require distinct fluorescent tracers, increasing costs and complexity. This study systematically evaluates the cross-platform performance of T2-BODIPY-FL and T2-BODIPY-589, tracers developed for receptor-interacting protein kinase 1 (RIPK1) target engagement in TR-FRET and NanoBRET applications, respectively. Our results demonstrate both tracers effectively bridge biochemical and cellular assays, providing reliable measurements. T2-BODIPY-589 demonstrates superior performance in NanoBRET (Z up to 0.80) and acceptable functionality in TR-FRET (Z=0.53). Conversely, T2-BODIPY-FL performs optimally in TR-FRET (Z=0.57) and exhibits NanoBRET potential (Z up to 0.72). Competition assays with an unlabeled inhibitor yielded consistent binding constants across all combinations. These findings suggest a single tracer can integrate diverse assay platforms, enhancing consistency and comparability in drug discovery. Table of Content Graphic O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/645143v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1cad1eforg.highwire.dtl.DTLVardef@9ccef0org.highwire.dtl.DTLVardef@d611c1org.highwire.dtl.DTLVardef@279f90_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Towards a unified molecular mechanism for ligand-dependent activation of NR4A-RXR heterodimers

A subset of nuclear receptors (NRs) function as permissive heterodimers with retinoid X receptor (RXR), defined by transcriptional activation in response to RXR agonist ligands. Permissive NR-RXR activation is generally understood to operate through a classical pharmacological mechanism in which RXR agonist binding enhances coactivator recruitment to the heterodimer. However, we previously demonstrated that transcriptional activation of permissive Nurr1-RXR (NR4A2-NR2B1) heterodimers by an RXR ligand set, which included pharmacological RXR agonists and selective Nurr1-RXR agonists that function as antagonists of RXR homodimers, is explained by a non-classical activation mechanism involving ligand-binding domain (LBD) heterodimer dissociation (Yu et al., 2023). Here, we extend mechanistic ligand profiling of the same RXR ligand set to the evolutionarily related Nur77-RXR{gamma} (NR4A1-NR2B3) heterodimer. Biochemical and NMR protein-protein interaction profiling, together with cellular transcription studies, indicate that activation of Nur77-RXR{gamma} transcription by the RXR ligand set, which lacks selective Nur77-RXR{gamma} agonists, is consistent with contributions from both classical pharmacological activation and LBD heterodimer dissociation. However, reanalysis of our previously published data for Nurr1-RXR revealed that inclusion of selective Nurr1-RXR agonists was essential for elucidating the LBD heterodimer dissociation mechanism. Together, our findings highlight the importance of using a more functionally diverse RXR ligand set to define the mechanism of Nur77-RXR{gamma} activation and to further evaluate whether LBD heterodimer dissociation represents a shared activation mechanism among NR4A-RXR heterodimers relevant to neurodegenerative and inflammatory diseases.

biochemistry↗

bioRxiv2025

Unleashing the potential of OPM-MEG to study event-related fields against low-frequency artifacts: the case of sentence processing

OPM-MEG (optically pumped magnetometers-magnetoencephalography) offers unprecedented opportunity in its proximity to the brain and in mobility, outperforming other human MEG systems. However, movements induce low-frequency artifacts (up to [~] 3 Hz) in this system, calling for pipelines that could efficiently reduce these low-frequency noises. Although a high-pass filter of e.g., 4 Hz may minimize these artifacts, it may also eliminate many event-related field (ERF) components, such as the N400 response in sentence processing studies. Moreover, as an emerging technology with expensive sensors, many labs are starting with an experimental setup with fewer sensors (e.g., [~] 10), making it challenging to reject principal components based on visually inspecting the topographic field maps. In the current paper, we show that a combination of moderate high-pass filtering (1 Hz) and evoked-biased denoising source separation (evoked-biased DSS) can effectively reveal typical N400 deflections and effects (between nouns and verbs), with a nine-sensor OPM-MEG setup. Our current pipeline paves the way to studying ERFs with OPM-MEG in more budget-friendly setups with a small number of sensors.

neuroscience↗

bioRxiv2025

ClairS-TO: A deep-learning method for long-read tumor-only somatic small variant calling

Accurate identification of somatic variants in tumor is crucial but challenging, and typically requires a matched normal sample for reliable detection, which is often unavailable in real-world research and clinical scenarios, necessitating proficient algorithms to tell real somatic variants from germline variants and background noises. However, existing tumor-only somatic variant callers that were designed for short-read data dont work well with long-read. To fill the gap, we present ClairS-TO, a deep-learning-based method for long-read tumor-only somatic variant calling. ClairS-TO uses an ensemble of two disparate neural networks that were trained from the same samples but for opposite tasks - how likely/not likely a candidate is a somatic variant. ClairS-TO also applies multiple post-calling filters, including 1) nine hard-filters, 2) four public plus any number of user-supplied PoNs, and 3) a module that statistically separates somatic and germline variants using tumor purity and copy number profile. Benchmarks using COLO829 and HCC1395 show that ClairS-TO outperforms DeepSomatic in long-read. ClairS-TO is also applicable to short-read and outperforms Mutect2, Octopus, Pisces, and DeepSomatic. Extensive experiments across various sequencing coverages, VAF ranges, and tumor purities support that ClairS-TO has a broad coverage of usage scenarios. ClairS-TO is open-source, available at https://github.com/HKU-BAL/ClairS-TO.

bioinformatics↗

bioRxiv2025

Comparative Transcriptomic Analysis of Embryonic Stem Cells (ESCs) across Mammalian Species

Pluripotency, the ability of cells to self-renew and differentiate into all the cell types in an animals body, is vital for mammalian early development. This study presented a comprehensive comparative transcriptomic analysis of embryonic stem cells across multiple mammalian species, defining their progression through expanded/extended, naive, formative, and primed pluripotency states. Our findings revealed both conserved and species-specific mechanisms underlying pluripotency regulation. We also emphasized the limitations of existing state-specific markers and their limited cross-species applicability, while identifying de novo pluripotency markers that can inform future research. Despite variability in gene expression dynamics, gene co-expression networks showed remarkable conservation across species. Among pluripotency states, the primed state demonstrated the highest conservation, evidenced by shared markers, preserved gene networks, and stronger selective pressures acting on its genes. These findings provide critical insights into the evolution and regulation of pluripotency, laying a foundation for refining stem cell models to enhance their translational potential in regenerative medicine, agriculture, and conservation biology.

genomics↗

bioRxiv2025

Shifting the PPARγ conformational ensemble towards a transcriptionally repressive state improves covalent inhibitor efficacy

The nuclear receptor peroxisome proliferator-activated receptor gamma (PPAR{gamma}) regulates transcription in response to ligand binding at an orthosteric pocket within the ligand-binding domain (LBD). We previously showed that two covalent ligands, T0070907 and GW9662--extensively used as PPAR{gamma} inhibitors to assess off-target activity--weaken but do not completely block ligand binding via an allosteric mechanism associated with pharmacological inverse agonism (Shang et al., 2024). These covalent inhibitors shift the LBD towards a repressive conformation, where the activation function-2 (AF-2) helix 12 occupies the orthosteric pocket, competing with orthosteric ligand binding. Here, we provide additional support for this allosteric mechanism using two covalent inverse agonists, SR33065 and SR36708, which better stabilize the repressive LBD conformation and are more effective inhibitors of--but also do not completely inhibit--ligand cobinding. Furthermore, we show that ligand cobinding can occur with a previously reported PPAR{gamma} dual-site covalent inhibitor, SR16832, which appears to weaken ligand binding through a direct mechanism independent of the allosteric mechanism. These findings underscore the complex nature of the PPAR{gamma} LBD conformational ensemble and highlight the need to develop alternative methods for designing more effective covalent inhibitors.

biochemistry↗

bioRxiv2025

Ultradeep N-glycoproteome Atlas of Mouse Reveals Spatiotemporal Signatures of Brain Aging and Neurodegenerative Diseases

The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieved an ultradeep and precision analysis of the N-glycoproteome of mouse tissues by integrating multiple workflows. The largest N-glycoproteomic dataset to date was established on mice, which contained 91,972 precursor glycopeptides, 62,216 glycoforms, 8,939 glycosites and 4,563 glycoproteins. The database consisted of 6.8 million glyco-spectra (containing oxonium ions), among which 160,928 were high-quality spectra with confident N-glycopeptide identifications. The large-scale and high-quality dataset enhanced the performance of current artificial intelligence models for glycopeptide tandem spectrum prediction. Using this ultradeep dataset, we observed tissue specific microheterogeneity and functional implications of protein glycosylation in mice. Furthermore, the region-resolved brain N-glycoproteomes for Alzheimers Diseases, Parkinson Disease and aging mice revealed the spatiotemporal signatures and distinct pathological functions of the N-glycoproteins. A comprehensive database resource of experimental N-glycoproteomic data from this study and previous literatures were further established. This N-glycoproteome atlas serves as a promising tool for revealing the role of protein glycosylation in biological systems.

neuroscience↗

bioRxiv2025

Structure-based analysis unveils co-origin of LPOR and nitrogenase-like proteins

Structures of nitrogenases, dark-operative protochlorophyllide oxidoreductases, and light-dependent protochlorophyllide oxidoreductases (LPOR) have been resolved. However, their evolutionary relatedness remains elusive. Here, we show, through structural alignment, that all subunits of nitrogenase-like proteins originated from a co-ancestral archaic one-subdomain precursor. LPOR evolved from the BchX/BchY subunits of nitrogenase-like chlorophyllide a oxidoreductase (COR), and the intermediary retinol dehydrogenase through possible genetic recombination. We thus establish previously unknown structural links among key enzymes involved in biological nitrogen-fixation (BNF) and photosynthesis, unraveling structure-guided functional evolution from a single-subunit iron protein to multi-subunit nitrogenase-like COR, and to the single-subunit LPOR for phototrophic metabolism via bacteriochlorophyll, retinal, and chlorophyll. This work also demonstrates structural similarities are imperative for inferring distant origins of functionally divergent proteins, particularly those lacking primary amino-acid sequence identity. Moreover, our findings coupled with AI may be exploited to design innovative light-driven CORs and/or light-utilizing nitrogenases with enhanced efficacy of photosynthesis and BNF. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/634645v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@9f9a2aorg.highwire.dtl.DTLVardef@4243ecorg.highwire.dtl.DTLVardef@796b4corg.highwire.dtl.DTLVardef@17373da_HPS_FORMAT_FIGEXP M_FIG C_FIG Video abstracthttps://www.youtube.com/watch?v=b0qBE1JMaH0 HighlightsO_LILPOR evolves from BchX and BchY subunits of the nitrogenase-like protein (NGLP) COR C_LIO_LIAll subunits of NGLPs can be traced back to the ancestral one-subdomain precursor C_LIO_LIRetinol dehydrogenase acts as a crucial intermediate in the COR to LPOR evolution C_LIO_LIStructure-based design of LUN is showcased to revolutionize protein engineering C_LI

evolutionary biology↗

bioRxiv2025

Aging directs the differential evolution of KRAS-driven lung adenocarcinoma

Lung adenocarcinoma (LUAD), the most common histological subtype of lung cancer(1, 2), is a disease of the elderly, with an average age of diagnosis of about 70 years of age(3). Older age is associated with an increased incidence of KRAS-driven LUAD(4), a particularly deadly type of LUAD characterized by treatment resistance and relapse. Despite this, our understanding of how old age shapes KRAS-driven LUAD evolution remains incomplete. While the age-related increase in cancer risk was previously ascribed to the accumulation of mutations over time, we are now beginning to consider the role of host biology as an independent factor influencing cancer. Here, we use single-cell RNA-Sequencing of KP (KrasG12D/+; Trp53flox/flox) LUAD transplanted into young and old mice to define how old age affects LUAD evolution and map the changes that old age imposes onto LUADs microenvironment. Our data demonstrates that the aged lung environment steers LUAD evolution towards a primitive stem-like state that is associated with poor prognosis. We ascribe this differential evolution, at least in part, to a population of rare and highly secretory damage-associated alveolar differentiation intermediate (ADI) cells that accumulate in the aged tumor microenvironment (TME) and that dominate the niche signaling received by LUAD cells. Overall, our data puts aging center stage in coordinating LUAD evolution, highlighting the need to model LUAD in its most common context and creating a framework to tailor future cancer therapeutic strategies to the age of the patient to improve outcomes in the largest and most vulnerable LUAD patient population, the elderly.

cancer biology↗

bioRxiv2025

Impact of infusion conditions and anesthesia on CSF tracer dynamics in mouse brain

Tracer imaging has been instrumental in mapping the brains solute transport pathways facilitated by cerebrospinal fluid (CSF) flow. However, the impact of tracer infusion parameters on CSF flow remains incompletely understood. This study evaluated the influence of infusion location, rate, and anesthetic regimens on tracer transport using dynamic contrast-enhanced MRI with Gd-DTPA as a CSF tracer. Infusion rate effects were assessed by administering Gd-DTPA into the cisterna magna (ICM) at two rates under isoflurane anesthesia. Anesthetic effects were evaluated by comparing transport patterns between isoflurane and ketamine/xylazine (K/X) anesthesia at the slower rate. Gd-DTPA transport was also examined after lateral ventricle (ICV) infusion, the primary site of CSF production. The results demonstrate that, besides anesthesia, both the location and rate of infusion substantially affected solute transport within the brain. ICV infusion led to rapid, extensive transport into deep brain regions, while slower ICM infusion resulted in more pronounced transport to dorsal brain regions. Cross-correlation and hierarchical clustering analyses of region-specific Gd-DTPA signal time courses revealed that ICM infusion facilitated transport along periarterial spaces, while ICV infusion favored transport across the ventricular-parenchymal interface. These findings underscore the importance of experimental conditions in influencing tracer kinetics and spatial distribution in the brain.

physiology↗