Biology subjects

Yu, L.

Publications and source records attributed to Yu, L..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Co-Evolutionary Characterization of PBP2 as the Predominant Siderophore Recognizer in Diverse Gram-Positive Bacteria

Iron is a scarce yet essential nutrient for bacteria. Microbes often acquire iron by secreting siderophores, a diverse group of small molecules that form high-affinity complexes with iron for microbial uptake. Understanding microbial iron interaction networks requires detailed characterization of siderophore recognition specificity. In Gram-positive bacteria, substrate-binding proteins (SBPs) bind iron-siderophore complexes and deliver them to ABC transporters for import. However, the SBPs responsible for selective recognition remain poorly characterized, hindering large-scale data mining and network reconstruction. Here, we addressed this knowledge gap by systematically analyzing siderophore uptake systems, first in five representative genera and then across a comprehensive dataset of 16,232 Gram-positive genomes. Through a pipeline integrating genome mining, coevolutionary analysis, and structural modeling, we established PBP2 (Peripla_BP_2) subtype SBPs as the primary siderophore recognizer family. We revealed that, unlike the physically clustered systems in Gram-negative bacteria, synthetase and recognizer genes in Gram-positive bacteria are sometimes genomically decoupled yet display coordinated transcriptional regulation by iron-responsive transcription factors. Our findings underscore key differences between Gram-positive and Gram-negative iron acquisition systems, providing foundational knowledge for large-scale inference of siderophore-mediated microbial interactions. Impact StatementBacteria secrete siderophores to scavenge iron and import the siderophore-iron complex via specific receptors, a process that shapes microbial community dynamics. However, predicting these interactions has been challenging, because the specific siderophore receptors in Gram-positive bacteria remained largely uncharacterized. In this study, we opened this "black box" by analyzing a comprehensive dataset of 16,232 genomes spanning the majority of Gram-positive bacteria. Through coevolutionary analysis, we identified PBP2 proteins as the primary "locks" that recognize siderophore "keys." We further demonstrate that these receptors exhibit greater evolutionary flexibility than their Gram-negative counterparts, frequently decoupled genomically from siderophore biosynthesis genes yet linked by transcriptional regulation. This discovery fills a critical knowledge gap, providing the missing link needed to map the global landscape of siderophore uptake potential and enable "sequence-to-ecology" prediction of iron-interaction networks in Gram-positive bacteria.

microbiology↗

bioRxiv2025

Aspartate transaminases are required for blood development

Red blood cells (RBCs) have a limited lifespan of approximately 120 days. This necessitates continuous RBC production, resulting in [~]200 billion new RBCs made per day to maintain oxygen delivery. Despite this enormous biosynthetic demand, the metabolic pathways supporting erythropoiesis are poorly understood. We profiled metabolites across four independent models of elevated erythropoiesis and a consistent increase in aspartate levels emerged when compared to controls. This suggested a potential role for aspartate metabolism in RBC production. To test this, we deleted the aspartate aminotransferases Got1 or Got2 globally or in an erythroid-specific manner. Loss of either enzyme resulted in anemia, with Got2 deficiency producing a more severe phenotype. Individual loss of either Got or dual Got deletion led to an erythroid defect, where early progenitors accumulated. In human and mouse models of erythropoiesis, GOT1 and GOT2 loss had opposing impacts on aspartate despite exhibiting similar anemic phenotypes, suggesting an aspartate-independent function for these enzymes. GOT1 and GOT2 are also components of the malate-aspartate shuttle (MAS), which regulates NAD(H) homeostasis. However, conditional deletion of another MAS enzyme, Mdh1, did not cause anemia, and alleviating NADH reductive stress in GOT2-deficient cells with cytoplasmic bacterial NADH oxidase (LbNOX) failed to restore erythropoiesis. Instead, transcriptomic and epigenetic analyses revealed dysregulation of chromatin histone modifications in GOT-deficient erythroid cells, implicating epigenetic dysfunction as a driver of defective erythropoiesis. Collectively, these findings identify a previously unrecognized role for GOT1 and GOT2 as a central link between metabolism and epigenetic regulation during erythroid development. These insights may inform the development of new therapeutic strategies for anemia.

biochemistry↗

bioRxiv2025

Convergent utilization of APN receptor by hedgehog merbecoviruses

Dipeptidyl peptidase-4 (DPP4) and angiotensin-converting enzyme 2 (ACE2) are well-established receptors for merbecoviruses, yet the receptor usage of merbecoviruses of European and Asian hedgehogs (EriCoVs) remains unknown. Here, by testing hedgehog orthologs of known coronavirus receptors, we identify hedgehog aminopeptidase N (APN) as a functional receptor for EriCoVs. Analysis of 94 APN orthologs indicates that EriCoVs have a limited host range, primarily utilizing hedgehog APN and, to a lesser extent, APN from certain felids, shaped by specific determinants at the virus-receptor interface. Cryo-EM reveals an APN-binding mode distinct from those used by alpha- and deltacoronaviruses. Functional assays indicate that hedgehog transmembrane serine protease 2 (TMPRSS2) enhances spike activation and promotes pseudovirus entry. Neutralizing antibodies targeting RBD and APN were developed and could effectively block EriCoV pseudovirus entry and propagation. These findings reveal an unexpected convergent evolution of APN utilization among merbecovirus, establishing a foundation for risk assessment and countermeasure development. Graphic abstractConvergent utilization of hedgehog APN by EriCoVs O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/676546v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1ea334aorg.highwire.dtl.DTLVardef@cd53bforg.highwire.dtl.DTLVardef@352102org.highwire.dtl.DTLVardef@a1eed_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Species-specific genetic routes to a shared phenotype: convergent adaptation of beans to European long days

The loss of photoperiod sensitivity was a key prerequisite for the adaptation of common bean (Phaseolus vulgaris) and scarlet runner bean (P. coccineus) to European environments. While the genetic architecture of this trait has been studied for decades, primarily through QTL mapping in RILs and NILs, its molecular basis remains incompletely resolved. Here, we combine whole-genome resequencing of over 200 P. vulgaris accessions spanning Mesoamerican, Andean, and European origins with 130 P. coccineus cultivars from Mesoamerica and Europe. Phenotyping under controlled long-day conditions revealed distinct distributions of photoperiod sensitivity across species and gene pools. Genome-wide association and haplotype analyses identified single nucleotide variants strongly linked to flowering under long days. Consistent with prior studies, signals of selection reflect independent domestication events in the Americas. Importantly, we detect species-specific selection on core photoperiod regulators, demonstrating that both species achieved similar adaptive outcomes via functionally convergent genetic routes. By explicitly accounting for major loci shaping growth habit in our analyses, we were able to unmask additional genomic regions contributing to flowering responses in European cultivars. Together, these results show that adaptation to long-day environments occurred through stepwise, species-specific genomic innovations, first during domestication in the Americas and later under European cultivation. Our findings highlight the role of pathway-level convergent evolution in shaping complex domestication traits and underscore the potential of parallel genomic strategies for crop adaptation.

plant biology↗

bioRxiv2025

A probabilistic functional atlas based on extraoperative electrocortical stimulation mapping

BackgroundDirect electrocortical stimulation (DES) is the clinical gold standard for identifying eloquent cortex and guiding neurosurgical intervention, yet prior intraoperative DES during awake craniotomies have been limited by intraoperative sampling constraints and density-based rather than probabilistic analyses. The probability of typical and atypical cortical organization has not been fully explored, especially in epilepsy populations. We sought to generate a probabilistic atlas of motor, sensory, and language functions using extraoperative DES in a large cohort of patients with epilepsy. MethodsWe retrospectively analyzed 2,124 extraoperative DES trials from 125 patients undergoing intracranial monitoring (2008-2023). Positive and negative trials were mapped to Montreal Neurological Institute space, parcellated with the Human Connectome Project atlas, and analyzed using probability mapping, bootstrapped region-of-interest hit probabilities, hierarchical clustering, and kernel density estimation. Mixed-effects models assessed clinical predictors of language disruption. ResultsProbabilistic maps revealed regions of increased likelihood for eliciting functional responses in expected sensorimotor and language territories, but also demonstrated marked variability and deviations from expected cortical locations. Language disruption occurred in 338 trials, motor in 520, and sensory in 370. Instead of observing high probabilities and low inter-patient variability isolated to classic perisylvian locations (e.g., Brocas and Wernickes areas), the likelihood of language disruption followed graded probabilistic gradients with high inter-patient variability. The middle frontal gyrus emerged as a consistent locus of naming and speech arrest. Motor phenomena extended into parietal association cortex. Higher-order experiences, including forced thoughts and feelings of presence, were reproducibly evoked from frontal and temporoparietal sites. Early seizure onset and temporal lobe lesions predicted lower naming disruption probabilities. ConclusionsThis extraoperative DES atlas, the largest to date, demonstrates that eloquent cortical functions are organized along probabilistic continua rather than fixed regions. Findings highlight the middle frontal gyrus as a critical language node, extend motor mapping into parietal cortex, and delineate reproducible experiential phenomena. Substantial inter-patient variability underscores the necessity of individualized mapping in surgical planning.

neuroscience↗

bioRxiv2025

Toward Precision Detection of Pyrazinamide Resistance: Critical Concentration Assessment and Rapid Molecular Method Validation

This study aimed to evaluate the diagnostic performance of broth microdilution (BMD) and fluorescence PCR melting curve analysis (MeltPro MTB/PZA assay) for detecting pyrazinamide (PZA) resistance in rifampicin-resistant tuberculosis (RR-TB).RR-TB strains isolated from patients in TB prevention and control in stitutions and designated hospitals in Beijing from January to December 2009 were analyzed. PZA susceptibility was assessed using BMD, MeltPro MTB/PZ A assay (targeting pncA mutations), and whole-genome sequencing (WGS). The sensitivity, specificity, agreement rate, and Kappa value of BMD (at critical c oncentrations (CCs) of 100 g/mL and 200 g/mL)and MeltPro MTB/PZA assa y were evaluated using WGS as the reference standard. At CCs of 100 g/mL and 200 g/mL, BMD showed resistance rates of 63.6% (70/110) and 45.5% (50/110), respectively. Compared to WGS, BMD demonstrated sensitivities of 96 .1% and 92.2%, specificities of 64.4% and 94.9%, with {kappa} values of 0.590 and 0.872, respectively. The MeltPro assay detected resistance in 44.5% (53/119) of strains, with 89.7% sensitivity, 98.4% specificity, and {kappa} value of 0.882. The MeltPro MTB/PZA assay demonstrates high diagnostic accuracy for PZA resista nce screening in RR-TB patients, supporting its utility as a frontline detection t ool. BMD at 200 g/mL showed better concordance with WGS. Additionally, f ive novel pncA mutations (Ile5Thr, Leu27Gln, Ser67stop, Pro69Arg, Trp119Ser) identified in this study expand the catalog of known resistance-associated vari ants and offer new targets for mechanistic investigations. IMPORTANCEThis study evaluates the diagnostic performance of broth micr odilution and a rapid molecular assay in detecting pyrazinamide resistance in R R-TB, providing insight into reliable testing approaches and resistance profiles.

microbiology↗

bioRxiv2025

Zolpidem restores sleep and slows Alzheimer's progression in a mouse model

STRUCTURED ABSTRACTO_ST_ABSINTRODUCTIONC_ST_ABSDeficits in Non-Rapid Eye Movement (NREM) sleep facilitate Alzheimers disease (AD) progression. Enhancing GABAergic signaling can restore sleep. Unbiased computational analysis identified zolpidem as high-affinity GABA receptor modulator facilitating chloride transport that could slow AD. METHODSZolpidems effects on sleep and Alzheimers progression were evaluated in young APP/PS1 mice. Sleep was monitored with EEG/EMG telemetry. Widefield imaging with voltage-sensitive dyes was used to track sleep-dependent brain rhythms. Multiphoton microscopy allowed assessments of amyloid plaque load and basal neuronal calcium levels. Behavioral assays were used to measure memory and cognitive function. RESULTSZolpidem restored NREM sleep and rescued sleep-dependent brain rhythm, slow oscillation. Zolpidem administration reduced cortical amyloid plaque burden, mitigated neuronal calcium overload, and enhanced sleep-dependent memory consolidation without adverse effects on locomotion. DISCUSSIONZolpidem effectively slowed Alzheimers progression in young APP/PS1 mice. This supports zolpidems therapeutic promise as an intervention strategy at early stages of AD.

neuroscience↗

bioRxiv2025

A Multi-Disciplinary Framework for Decoding S1PR1-Selective Agonism

Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphingosine-1-phosphate receptors (S1PRs), which include five subtypes (S1PR1-5), thereby activating these receptors and their downstream signaling pathways. Understanding the molecular determinants that govern agonist selectivity among different S1PR subtypes is vital for the rational and precise development of targeted therapeutic agents. Here, four cryo-electron microscopy structures of agonist-bound S1PR1-Gi complexes are reported. Through an integrated approach combining structural analysis, molecular dynamics simulations, and pharmacological assays, the molecular basis for the selectivity of CYM5442, HY-X-1011, Ponesimod, and SAR247799 toward S1PR1 over S1PR3 and S1PR5 is uncovered. Specifically, the selectivity arises from a combination of non-conserved residues within the ligand-binding pocket and at the Gi-protein interface, distinct curved agonist-binding modes oriented toward transmembrane helices 5-7 that cause steric clashes with S1PR3, and the presence of branched moieties at the lower part of three agonists. These features collectively enhance agonist potency and efficacy for S1PR1 while reducing activity at S1PR3 and S1PR5. These findings establish a structural framework for the rational design of next-generation S1PR1 highly selective agonists with improved therapeutic potential.

biochemistry↗

bioRxiv2025

Characterizing Post-Mortem Brain Molecular Taxonomy of Cognitive Resilience and Translating it to Living Humans

Here, we define cognitive resilience as slower or faster cognitive decline after we regress out the effects of common brain neuropathologies. Its understanding could provide important insights into the biology underlying cognitive health, enabling the development of more effective strategies to prevent cognitive decline and dementia. However, this requires the development of a practical method to quantify resilience and measure it in living individuals, as well as identifying heterogenous pathways associated with resilience in different individuals. Here, we approach this problem by using a data-driven framework to quantify and characterize molecular signatures underlying cognitive resilience. Using multimodal contrastive trajectory inference (mcTI) on bulk RNA sequencing and tandem mass tag (TMT) proteomic data from 898 post- mortem brain samples from the Religious Orders Study and the Rush Memory and Aging Project (ROSMAP), we derived individual-level molecular pseudotime values reflecting the molecular path from high to low resilience across individuals. Additionally, we identified two distinct molecular subtypes of resilience, each characterized by unique transcriptomic and proteomic signatures, and differing associations with several phenotypes. To translate our brain-derived pseudotime and subtypes to living individuals, we developed prediction models with paired genetics, ante-mortem blood omics, clinical, psychosocial, imaging and device data from the same individuals, demonstrating the potential to predict brain molecular resilience profiles in living persons. Our findings establish a framework for quantifying resilience based on multi- level molecular signatures, identify molecularly distinct resilience subtypes, and demonstrate the feasibility of translating brain-derived molecular profiles to living individuals--laying the groundwork for the development of targeted resilience-promoting interventions in cognitive aging.

neuroscience↗

bioRxiv2025

GT61 β-1,2-xylosyltransferases define a conserved xylan modification in gymnosperm and Arabidopsis primary cell walls

Plant primary and secondary cell walls differ in molecular composition, structure, and mechanical properties. While secondary wall xylan has been extensively characterised, the structure of xylan in primary walls remains less well understood, particularly in gymnosperms. Here, we identify a previously uncharacterised {beta}-1,2-linked xylosyl side chain in conifer and Arabidopsis thaliana xylan. Using enzymatic fingerprinting, NMR, and mass spectrometry, we show that this structure is positioned two xylose residues away from glucuronic acid substitutions, forming an evenly patterned substituted xylan. This spacing pattern is consistent with xylan-cellulose interaction, suggesting a structural role in primary wall architecture. This modification, found in primary wall-rich tissues of diverse conifer species, including needles and pro-embryogenic mass (PEM), is also present in Arabidopsis callus. We demonstrate that conifer Group III GT61 glycosyltransferases introduce this modification with consistent positional specificity. In Arabidopsis, three closely related GT61 enzymes act redundantly to generate the same structure, and their combined loss results in its complete absence. These findings uncover a conserved primary wall xylan modification in seed plants and define the GT61 enzymes responsible for its biosynthesis, opening new avenues to explore how xylan structure contributes to primary wall function. Significance StatementXylan structure is well characterised in secondary walls, but its primary wall counterpart remains poorly understood. We identified a conserved {beta}-1,2-xylosyl modification on xylan in the primary walls of conifers and Arabidopsis. This side chain is positioned at a defined position from a glucuronic acid substitution and is introduced by GT61 glycosyltransferases that cluster in one phylogenetic subclade. Our findings revealed a previously unrecognised xylan structural pattern and the biosynthetic enzymes responsible for its addition. This work expands the current understanding of primary wall architecture across seed plants.

plant biology↗

bioRxiv2025

Functional screening of TCR-like antibodies for targeted cancer immunotherapy

Although hybridomas and display technologies have long been used in antibody discovery, identifying TCR-like antibodies that recognize major histocompatibility (MHC)-presented neoantigens remains an inefficient process. Here, we present a functional screening approach for antibody discovery based on T cell-specific functionality. By constructing Synthetic T cell receptor and Antigen Receptor (STAR)-T cells expressing antibody libraries and co-culturing them with target cells, we observed distinct antigen-specific STAR endocytosis and T cell activation. These two indicators are combined into an E-A functional index, which we demonstrate as an effective screening strategy for identifying antibodies with strict antigen sensitivity and specificity. Using this E-A functional screening method, we successfully discovered antibodies or nanobodies targeting cell-surface tumor antigens and neoantigens presented by human leukocyte antigen (HLA). These antibodies exhibited potent anti-tumor efficacy both in vitro and in vivo. Moreover, converting these antibodies into chimeric antigen receptors (CARs) and bispecific antibodies also induced T cell activation and tumor killing. In summary, our study establishes a robust functional screening strategy for identifying antibodies or TCR-like nanobodies targeting tumor-specific neoantigens, offering significant potential for advancing targeted cancer therapies.

immunology↗

bioRxiv2025

Development of Anti-Inflammatory Extracellular Vesicles by Surface Expression of Syndecan-4

The biological functions of extracellular vesicles (EVs) depend on their cellular source. Further, different subpopulations of EVs from the same cells carry different cargo, but differences in their biological functions are less understood. We here identify a very small EV subpopulation released by HEK293F cells (miniEVs). These EVs, in contrast to the larger EVs, were found to have anti-inflammatory properties. Quantitative proteomics identified a potential anti-inflammatory molecule, Syndecan-4 (SDC4), on the surface of the miniEVs, but not larger EVs. We engineered HEK293F cells to overexpress SDC4, which results in the molecule being highly expressed in all EV subpopulations. Expression of SDC4, a proteoglycan, also increased the presence of heparan sulfate on the EV surface. Furthermore, these EVs were found to have potent anti-inflammatory effects in vitro, which heparinase treatment could slightly reduce. Furthermore, the SDC4 EVs showed anti-inflammatory effects in vivo in a model of peritonitis. We conclude that HEK293F EVs can be engineered to become anti-inflammatory, and that SDC4-expressing HEK293F-EV potentially could become an anti-inflammatory therapeutic.

cell biology↗

bioRxiv2025

PromptBio: A Multi-Agent AI Platform for Bioinformatics Data Analysis

PromptBio is a modular AI platform for scalable, reproducible, and user-adaptable bioinformatics analysis, powered by generative AI and natural language interaction. It supports three complementary modes of analysis designed to meet diverse research needs. PromptGenie is a multi-agent system that enables stepwise, human-in-the-loop workflows using prevalidated domain-standard tools. Within PromptGenie, specialized agents--including DataAgent, OmicsAgent, AnalysisAgent, and QAgent--collaborate to manage tasks such as data ingestion, pipeline execution, statistical analysis, and interactive summarization. DiscoverFlow provides integrated, automated workflows for large-scale multi-omics analysis, offering end-to-end execution and streamlined orchestration. ToolsGenie complements these modes by dynamically generating executable bioinformatics code for custom, user-defined analyses, enabling flexibility beyond standardized workflows. PromptGenie and DiscoverFlow leverage a suite of domain-specific tools, including Omics Tools for standardized omics pipelines, Analysis Tools for downstream statistical interpretation, and MLGenie for machine learning and multi-omics modeling. We present the design, capabilities, and validation of these components, highlight their integration into automated and customizable workflows, and discuss extensibility, monitoring, and compliance. PromptBio aims to democratize high-throughput bioinformatics through a large language model-powered, natural language understanding, workflow generation and agent orchestration.

bioinformatics↗

bioRxiv2025

Epigenetic Programming of Estrogen Receptor in Adipose Tissue by High Fat Diet Regulates Obesity-Induced Inflammation

Adipose inflammation plays a key role in obesity-induced metabolic abnormalities. Epigenetic regulation, including DNA methylation, is a molecular link between environmental factors and complex diseases. Here we found that high fat diet (HFD) feeding induced a dynamic change of DNA methylome in mouse white adipose tissue (WAT) analyzed by reduced representative bisulfite sequencing. Interestingly, DNA methylation at the promoter of estrogen receptor (Esr1) was significantly increased by HFD, concomitant with a down-regulation of Esr1 expression. HFD feeding in mice increased the expression of DNA methyltransferase 1 (Dnmt1) and Dnmt3a, and binding of DNMT1 and DNMT3a to Esr1 promoter in WAT. Mice with adipocyte-specific Dnmt1 deficiency displayed increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity upon HFD challenge; while mice with adipocyte-specific Dnmt3a deficiency showed a mild metabolic phenotype. Using a modified CRISPR/RNA-guided system to specifically target DNA methylation at the Esr1 promoter in WAT, we found that reducing DNA methylation at Esr1 promoter increased Esr1 expression, decreased adipose inflammation and improved insulin sensitivity in HFD-challenged mice. Our study demonstrates that DNA methylation at Esr1 promoter plays an important role in regulating adipose inflammation, which may contribute to obesity-induced insulin resistance.

physiology↗

bioRxiv2025

Multi-Omics Analysis of Heat Stress-Induced Memory in Arabidopsis

In their natural environment, plants experience temperature fluctuations, including intensified heat waves driven by climate change, which pose significant threats to their productivity. To adapt, plants have evolved diverse mechanisms to withstand heat stress (HS), minimizing potential damage and ensuring survival. One such adaptation is acquired thermotolerance (AT), where prior exposure to HS primes plants to withstand subsequent severe HS. AT can persist for several days and involves a recovery period during which plants establish heat stress memory (HSM), reorganize cellular processes, and strengthen stress resilience. The molecular mechanisms underlying HSM remain the subject of active investigation. In this study, we employ a high-throughput comparative multi-omics approach to unravel the transcriptome, metabolome, and proteome of Arabidopsis thaliana seedlings during distinct intervals of the HSM phase. Our findings provide insights into the intricacies of HS recovery and the memory process. Notably, distinct temporal responses emerge at both the transcriptional and protein levels during the early and late recovery phases. Transcripts associated with HSM are upregulated during the early HS recovery phase, indicating a rapid response crucial for initial memory formation, while corresponding protein levels remain elevated throughout the recovery period, supporting memory consolidation. Additionally, metabolite profiles reveal distinctive patterns across the HS memory phase. This marks the first detailed multi-omic analysis of the HSM phase in Arabidopsis seedlings, providing insights into the multifaceted nature of this complex process. These comprehensive datasets hold promise in elucidating regulators of HS resilience, thereby enhancing efforts in breeding HS-tolerant crops

plant biology↗

bioRxiv2025

Deconvolution of multiplexed peptidoform mass spectra enables high-resolution profiling of complex protein modification patterns

Combinatorial patterns of post-translational modifications (PTMs), like the histone code, play critical roles in regulating protein functionality. However, in bottom-up proteomics, isobaric modification peptidoforms (IMPs) frequently co-elute and co-fragment during liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), resulting in multiplexed mass spectra that cannot be properly analyzed by conventional protein identification and quantification methods. Existing solutions are either limited to highly narrow scenarios or unavailable for public use. Here, we introduce PTMdecoder, a robust and versatile software tool for discriminating and quantifying IMPs by deconvoluting their multiplexed MS/MS spectra and ion chromatograms without requiring a spectral library of individual peptidoforms. Tested on 34 samples of synthesized IMPs, PTMdecoder achieved an overall sensitivity of 95.7% for IMP identification and root mean square errors mostly <0.05 for quantification. In human histone samples, it detected and quantified 36.7-44.8% more IMPs than conventional methods, providing a higher-resolution view of histone modification patterns.

bioinformatics↗

bioRxiv2025

A lipid metabolism defect is an underlying contributor to Diamond Blackfan anemia syndrome

Analysis of neither Diamond Blackfan anemia syndrome (DBAS) cohorts nor animal models has revealed a potential mechanism for the variable anemia phenotype, a key feature of this disease. Here, we utilized an established Rpl5Skax23-Jus/+ murine DBAS model in order to study this dynamic erythropoiesis deficiency. These haploinsufficient mice exhibit variably penetrant craniofacial and cardiac defects mimicking the phenotypes of DBAS patients bearing RPL5 mutations. We additionally discovered that this specific heterozygous splicing mutation is pathogenic and leads to partial intron retention. By examining the transcriptome of fetal liver erythroid progenitors at E12.5, we demonstrate that the downregulation of erythroid differentiation pathways is consistent with the DBAS phenotype. We also identified dysregulated transcription of lipid metabolism genes with significant reduction in the abundance of Scd1 in a subset of E12.5 mutant embryos at risk for erythroid failure. SCD1, a key enzyme that converts saturated to monounsaturated fatty acids, has not been previously linked to erythropoiesis or DBAS. When anemia was induced in adult mice, pretreatment with an SCD1 inhibitor resulted in improved erythropoiesis. This analysis suggests a key role of lipid metabolism in the variable anemia penetrance in DBAS and highlights a previously unappreciated pathway that may serve as a potential target for drug development. Key PointsO_LIThe variable anemia in Rpl5Skax23-Jus/+mice is triggered by intrinsic/extrinsic stress C_LIO_LIRpl5 haploinsufficient murine and human erythroid progenitors exhibit a lipid metabolism signature with downregulation of Scd1/SCD. C_LI

developmental biology↗

bioRxiv2025

Brain Multi-Omic Subtypes of Neuroticism Reveal Molecular Signatures linked to Alzheimer's Disease

ImportanceMolecular mechanisms linking neuroticism with Alzheimers disease traits are unknown. ObjectiveTo identify molecular subtypes of neuroticism and examine their association with ADRD traits. DesignThree ongoing cohort studies were used; Religious Orders Study (ROS), Rush Memory and Aging Project (MAP) and Minority Aging Research Study (MARS), that began enrollment in 1994, 1997, and 2004, respectively. SettingOlder priests, nuns, and brothers from across the U.S. (ROS), older adults (MAP) and older African-American adults (MARS) from across the greater Chicago metropolitan area. Participants1,028 decedents with multi-omic data from the dorsolateral prefrontal cortex (DLPFC), the anterior cingulate cortex (AC), and the posterior cingulate gyrus (PCG). Exposure(s)Eight layers of omics (DNA methylation and histone acetylation from DLPFC; RNA seq from AC, DLPFC, and PCG, single-nucleus RNA, TMT proteomics and metabolomics from DLPFC) and Neuroticism using the 12-item version from the NEO Five-Factor Inventory. Main outcome(s) and measure(s)Person-specific multi-omic molecular pseudotime representing molecular progression from low to high phenotypic expression of neuroticism, and three multi-omic brain molecular subtypes of neuroticism which represent distinct omic pathways from no/low neuroticism to high neuroticism that differ by their omic constituents. Participants are exclusively assigned to the subtype which aligns mostly with their multi-omic profile. ResultsThe top drivers of subtype differentiation were transcriptomic alterations across three brain regions (DLPFC, AC, PCG) which extensively and differentially characterized the subtypes. The subtypes were also differentially associated with AD pathology, temporal lobe atrophy, and AD dementia, with subtype N1 showing the strongest associations. Conclusions and RelevanceNeuroticism may be driven by three distinct molecular subtypes, with subtype N1 driving ADRD-related associations, N2 showing some ADRD associations, and N3 being completely independent of these outcomes. Our data provide novel insights into the biology of individual differences in predispositions of neuroticism and its associations with ADRD traits. Key pointsO_ST_ABSQuestionC_ST_ABSWhat are the brain multi-omics molecular signatures linking neuroticism with Alzheimers diseases and related dementias (AD/ADRDs)? FindingsWe identified three distinct brain multi-omic molecular subtypes reflecting different molecular pathways underlying neuroticism. Top omic features of the subtypes were extensively and differentially characterized by transcriptomic alterations across three brain regions - dorsolateral prefrontal cortex, anterior cingulate cortex, and posterior cingulate gyrus. Subtype N1 was strongly associated with AD pathology, AD dementia, and temporal lobe atrophy. MeaningThe association we typically observe between phenotypic neuroticism and ADRD clinical traits might be largely driven by a molecular pathway underlying this trait.

neuroscience↗