Sci Adv. 2025 Jan 3;11(1):eado9970. doi: 10.1126/sciadv.ado9970. Epub 2025 Jan 3.

ABSTRACT

Fluid shear stress (FSS) from blood flow sensed by vascular endothelial cells (ECs) determines vessel behavior, but regulatory mechanisms are only partially understood. We used cell state transition assessment and regulation (cSTAR), a powerful computational method, to elucidate EC transcriptomic states under low shear stress (LSS), physiological shear stress (PSS), high shear stress (HSS), and oscillatory shear stress (OSS) that induce vessel inward remodeling, stabilization, outward remodeling, or disease susceptibility, respectively. Combined with a publicly available database on EC transcriptomic responses to drug treatments, this approach inferred a regulatory network controlling EC states and made several notable predictions. Particularly, inhibiting cell cycle-dependent kinase (CDK) 2 was predicted to initiate inward remodeling and promote atherogenesis. In vitro, PSS activated CDK2 and induced late G1 cell cycle arrest. In mice, EC deletion of CDK2 triggered inward artery remodeling, pulmonary and systemic hypertension, and accelerated atherosclerosis. These results validate use of cSTAR and identify key determinants of normal and pathological artery remodeling.

PMID:39752487 | DOI:10.1126/sciadv.ado9970

Geroscience. 2025 Jan 3. doi: 10.1007/s11357-024-01478-5. Online ahead of print.

ABSTRACT

Using whole-genome sequencing (WGS) might offer insights into rare genetic variants associated with healthy aging and extreme longevity (EL), potentially pointing to useful therapeutic targets. In this study, we conducted a genome-wide association study using WGS data from the Long Life Family Study and identified a novel longevity-associated variant rs6543176 in the SLC9A2 gene. This SNP also showed a significant association with reduced hypertension risk and an increased, though not statistically significant, cancer risk. The association with cancer risk was replicated in the UK Biobank and FinnGen. Metabolomic analyses linked the rs6543176 longevity allele to higher serine levels, potentially associated with delayed mortality. Our findings warrant further investigation of SLC9A2's role in both longevity and cancer susceptibility, and they highlight the need for careful evaluation in developing anti-aging therapies based on EL-associated alleles.

PMID:39751714 | DOI:10.1007/s11357-024-01478-5

Alzheimers Dement. 2024 Dec;20 Suppl 1:e090392. doi: 10.1002/alz.090392.

ABSTRACT

BACKGROUND: Progressive supranuclear palsy (PSP) is a devastating primary tauopathy with rapid progression to death. Although several therapies currently in the development pipeline show promising safety profiles and robust target engagement, few demonstrated significant efficacy in patients, underscoring the need to interrogate additional targets with novel therapeutic modalities to expand the potential therapeutic arsenal. To diversify the therapeutic avenues for PSP and related tauopathies (e.g. Alzheimer's disease), we systematically integrated multi-omics data from human brains of PSP and control donors with cross-species validation to nominate high-confidence therapeutic targets. We plan to translate our findings into safe and effective treatments for PSP using antisense oligonucleotides (ASO).

METHOD: We analyzed brain gene expression profiles in PSP and control individuals at bulk tissue (N = 408) and single-cell levels (snRNAseq, N = 36). Cell-type-specific expression perturbations were systematically prioritized using a cross-species validation paradigm, including rTG4510 tau mice and tau-overexpressing Drosophila models. We conducted in vitro screening of ASO candidates against our prioritized target genes. ASO efficacy and toxicity were measured. RNAseq experiments will be performed to interrogate off-target effects. The safety and efficacy of the lead ASOs will be assessed in PSP-patient-derived iPSC models.

RESULT: We previously reported discovery of novel genes with significant differential expression in PSP brains, characterized their brain cell-specificity and validated them using snRNAseq data. We prioritized 21 genes using gene expression data from a mouse tauopathy model. Validation of these 21 high-priority genes using a Drosophila tau model nominated astrocytic STOM, KANK2, and DDR2 as potential therapeutic targets for PSP. Knocking down their expression in Drosophila significantly rescues tau-mediated neurodegenerative pathology. In vitro screening identified ASO leads that reduced the target expressions at mRNA and protein levels with low cellular toxicity.

CONCLUSION: We developed a systems biology pipeline and nominated STOM, KANK2, and DDR2 as candidate gene targets for PSP. We identified ASOs that modulate these targets' expression without cellular toxicity, suggesting they may be suitable as potential therapeutic candidates. Importantly, the shared pathophysiology and molecular aberrations between PSP and other tauopathies, such as Alzheimer's disease, suggests that such therapeutic candidates may be repurposed for multiple neurodegenerative diseases, further accelerating, and streamlining the therapeutic pipeline.

PMID:39751534 | DOI:10.1002/alz.090392

Alzheimers Dement. 2024 Dec;20 Suppl 1:e085676. doi: 10.1002/alz.085676.

ABSTRACT

BACKGROUND: Alzheimer's disease (AD), characterized by tau lesions and amyloid plaques, has traditionally been investigated within the cortical domain. Recent neuroimaging studies have implicated micro- and macrostructural abnormalities in cortical layers during the progression of AD. While examinations from diverse brain regions have contributed to comprehending the regional severity, these approaches have constrained the ability to delineate cortical alterations in AD. Our study employed a single-cell resolution approach to characterize transcriptomic and epigenomic alternations in the human brain affected by the disease.

METHOD: We conducted a comprehensive analysis utilizing snRNA-Seq and single-nucleus epigenomic profiling on samples obtained from more than 2 million cells over 100 individuals with early and late-stage AD cases, along with controls. Four samples were procured from each participant, derived from the human pre-frontal cortex (PFC) and temporal cortex (TCX). Our analysis utilized multi-ome profiling, which simultaneously profiles gene expression and epigenomic changes. Data processing utilized Scanpy and Signac for gene expression and histone processing. Cicero identified cis-regulatory elements (cCREs), overlaid with GWAS variants, creating a genome-wide map. Transcription factor (TF) footprinting was done for cell types and disease-associated subclusters.

RESULT: UMAP and Leiden clustering on batch-corrected data identified discrete cell-type clusters from snRNA-Seq and additional multi-ome profiling. Enhancer-promoter links were identified, constructing disease-enriched, region-specific, and shared TF regulatory networks in AD. Pseudotime trajectory analysis revealed changes from early to late-stage AD.

CONCLUSION: The single nucleus multi-ome data produced in this study represents a valuable asset for the AD research community. Compared to bulk ATAC-seq, our single-nucleus epigenomic data provides precise insights into active and repressive activities. The study illuminates crucial TFs and their roles in AD, offering insights into cell-specific and region-specific mechanisms in AD pathology. Experimental validation underscores the functional relevance of the targeted TF in AD, highlighting its potential medical significance.

PMID:39751410 | DOI:10.1002/alz.085676

Elife. 2025 Jan 3;12:RP91422. doi: 10.7554/eLife.91422.

ABSTRACT

The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in Chinese hamster and mouse cell lines. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors, although Jag1-Notch1 signaling was substantially weaker than other ligand-receptor combinations. Cis-interactions were predominantly inhibitory, with the exception of the Dll1- and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.

PMID:39751380 | DOI:10.7554/eLife.91422

Alzheimers Dement. 2024 Dec;20 Suppl 1:e093497. doi: 10.1002/alz.093497.

ABSTRACT

BACKGROUND: The immerging role of CD8+T cells, interferon and the adaptive immune response in AD is consistent with previous observations of the putative role of neurotrophic herpesvirus family infections contributing to Alzheimer's Disease pathophysiology. An outstanding question is how chronic viral infections over decades may contribute to AD pathogenesis. Our HSV-1 reactivation model aims to provide insights to this question.

METHOD: We infected 2 month old C57B6/J mice containing humanized APP and APOE4 with 106 PFU HSV-1 strain 17 via corneal scarification. We reactivated the virus with the bromo-domain compound JQ1 at 4, 7 and 10 months, with 1x, 3x and 6x reactivations respectively and harvested the brainstem, hippocampus, entorhinal cortex and dural sinuses, for RNAseq. To identify common changes in gene expression between our HSV-1 reactivation model and AD, we compared the gene expression profiles of our mice to both human and mouse model gene profiles using 19 AD-specific categories (BioDomains).

RESULT: We found reactivation by JQ1 resulted in increased HSV-1 detection by qPCR in a progressive manner, emanating outward from the trigeminal ganglion, towards more distal brain regions. We observed changes in RNAseq expression profiles in a time-dependent manner, with the greatest number of differentially expressed genes at 7 months. We observed changes in synaptic and immune genes in both the entorhinal cortex and hippocampus. We also saw decreases in gene expression in lipid metabolism, myelination, and the endolysosomal pathways.

CONCLUSION: Our HSV-1 reactivation mouse model identifies changes in gene expression that are similar to those observed in humans and mouse AD models, with observed, distinct changes in synaptic- and immune-associated genes in multiple brain regions. Activation of immune genes was highest in the brain stem, where detection of HSV-1 was highest. The greatest changes in gene expression occurred at 7 months, with fewer changes following at 10 months. These changes are most similar to changes in early disease and support the role of HSV-1 contributing to AD pathophysiology.

PMID:39751344 | DOI:10.1002/alz.093497

Alzheimers Dement. 2024 Dec;20 Suppl 1:e086464. doi: 10.1002/alz.086464.

ABSTRACT

BACKGROUND: Alzheimer's disease (AD) is complex and multifactorial. Precision medicine approaches are needed to capture the basis of heterogeneity in AD pathogenesis, clinical presentation and neuropathology. Large-scale molecular, deep phenotypic and exposomal data necessary to enable precision medicine research requires team-based, interdisciplinary programs. Accelerating Medicines Partnership in Alzheimer's Disease (AMP-AD) was launched in 2014 with the goals to characterize disease heterogeneity and discover precision-medicine therapeutic targets and biomarkers for AD and related disorders (ADRD).

METHOD: AMP-AD consortium, comprising eight teams addresses the barriers that historically limited therapeutic target and biomarker discovery in ADRD by characterizing the molecular disease complexity in deeply phenotyped human biospecimens and experimental disease models. Over the past decade, AMP-AD teams generated multi-omics data in ∼2,000 human brain samples from largely non-Hispanic white donors and from >600 African American and Latin American donors. AMP-AD datasets, including bulk and single cell molecular profiles from brain and peripheral tissues are analyzed using innovative analytic approaches generated and applied by these teams. Findings are validated with a broad array of cross-species experimental platforms including human iPSC, fly and rodent models. These outcomes are integrated with deep phenotypic and exposomal measures for precision medicine discoveries and broadly shared.

RESULT: AMP-AD generates high-dimensional molecular data and applies novel systems biology approaches bringing new insights into ADRD. AMP-AD teams discovered molecular subtypes of AD and characterized the cell-type specificity of these molecular changes. Discovery of disease signatures in brain and peripheral tissues enabled nominations of precision medicine therapeutic targets and biomarkers. Over 600 targets, annotated with human and cross-species data, are shared with the research community on the Agora Platform of AD Knowledge portal that also houses all research data and outputs for rapid and responsible dissemination in a centralized manner.

CONCLUSION: First decade of AMP-AD led to unprecedented data and knowledge for rigorous and reproducible ADRD research, accelerated the delivery of many new disease insights, and expanded the target and biomarker landscape. Future directions include discovery of subtypes for disease specificity and progression, contextualized by multi-ethnic, molecular, exposomal data and validation platforms well-integrated into therapeutic development pipelines to deliver new cures to ADRD.

PMID:39751281 | DOI:10.1002/alz.086464

Physiol Genomics. 2025 Jan 3. doi: 10.1152/physiolgenomics.00059.2024. Online ahead of print.

ABSTRACT

We examined the effects of a 20-week exercise intervention on whole-blood genome-wide DNA methylation signature and its association with the exercise-induced changes in gene expression profiles in boys and girls with overweight/obesity (OW/OB). Twenty-three children (10.05 ± 1.39 years, 56% girls) with OW/OB, were randomized to either a 20-week exercise intervention (exercise group [EG]; n=10; 4 boys/ 6 girls), or to usual lifestyle (control group [CG] (n=13; 6 boys/ 7 girls). Whole-blood genome-wide methylome (CpG sites) analysis using Infinium Methylation EPIC array and transcriptome analysis using RNA-seq (STRT2 protocol) were performed. Exercise induced modifications in DNA methylation at 485 and 386 CpGs sites in boys and girls respectively. These CpG sites mapped to loci enriched in distinct gene pathways related to metabolic diseases, fatty acid metabolism, and immune function. In boys, changes in the DNA methylation of 87 CpG sites (18% of the 485 CpGs sites altered by exercise) were associated with changes in the gene expression levels of 51 genes also regulated by exercise. Among girls, changes in DNA methylation at 46 CpG sites (12% of the initial 386 significant CpGs) were associated with changes in the expression levels of 30 exercise-affected genes. Genes affected by exercise that were associated with DNA methylation are related to obesity, metabolic syndrome, and inflammation. Multi-omics analysis of whole-blood samples from children with OW/OB, suggests that gene expression response to exercise may be modulated by DNA methylation and involve gene pathways related to metabolism and immune functions.

PMID:39751206 | DOI:10.1152/physiolgenomics.00059.2024

Alzheimers Dement. 2024 Dec;20 Suppl 1:e087010. doi: 10.1002/alz.087010.

ABSTRACT

BACKGROUND: Alzheimer's Disease (AD) presents a significant challenge in understanding its complex pathophysiology, owing to its multifaceted genetic and environmental factors. Despite extensive research, the translatability of findings from animal models to human conditions remains a critical hurdle. This study addresses the need to uncover shared molecular changes in AD by comparing human and mouse models, thereby enhancing our understanding of the disease's underlying mechanisms and improving the prospects for effective treatments.

METHOD: The study employed a comprehensive multi-omic approach, integrating spatial transcriptomics (ST) and single-nucleus RNA-sequencing (snRNA-seq) data from postmortem human prefrontal cortical tissue and 5xFAD mouse brains across various stages of AD pathology, including AD in Down Syndrome (DS). An unbiased clustering algorithm, BayesSpace, was used to identify distinct clusters in both human and mouse datasets. Cross-species differential expression analysis and multi-scale co-expression network analysis using hdWGCNA were conducted. These analyses were complemented with fluorescent amyloid imaging to correlate gene expression changes with amyloid pathology.

RESULT: The analysis revealed evolutionary-conserved AD transcriptional changes, particularly in genes associated with amyloid-beta response and microglial activation. The study identified upregulated genes with age in the mouse model, with variances across different brain regions. Co-expression network analysis exposed amyloid-associated gene modules that were consistent across species. Additionally, the integration of spatial and single-cell data elucidated cellular diversity and transcriptomic alterations within the AD brain, providing a spatial context to the observed molecular changes.

CONCLUSION: This study successfully decodes shared multi-omic changes in human and mouse models of Alzheimer's Disease, highlighting key molecular similarities and differences across species. The findings underscore the significance of a multi-faceted, integrated omic approach in understanding AD pathogenesis. This cross-species analysis not only advances our knowledge of the molecular underpinnings of AD but also opens avenues for developing more accurate and translatable AD models, ultimately guiding the discovery of potential therapeutic targets.

PMID:39750969 | DOI:10.1002/alz.087010

Alzheimers Dement. 2024 Dec;20 Suppl 1:e092897. doi: 10.1002/alz.092897.

ABSTRACT

BACKGROUND: Microglial processing and recycling of debris is implicated in AD. AD GWAS loci are enriched for genes in efferocytosis, phagocytosis, endosomal trafficking and cholesterol efflux. Acting as a buffer, lipid droplets increase as a consequence of an imbalance between lipid debris influx and efflux rates. We hypothesize that a pivotal point in disease progression occurs when this buffering saturates, resulting in expanded lipid-droplet accumulating microglia (LDAM). We anticipate a positive-feedback effect where saturation accelerates neurodegeneration via inflammation and lipid processing via astrocytes. Susceptibility to this saturation may be connected to microglial AD GWAS loci-and would be reflected in progression rates. To explore this hypothesis, we analyzed lipidomic, proteomic, cognitive and genetic ADNI data to identify a signature indicative of this inflection point.

METHOD: We identified ADNI individuals in comparable states of disease progression, grouping them into ADAS13 (cognitive score) quartiles, then examined blood lipidomic and CSF proteomic data. This resulted in a cross-sectional dataset of 608 subjects spanning from cognitively normal to demented. We examined protein/lipid correlations across each quartile, identifying and characterizing inflection points.

RESULT: We observed a stark and unique pattern of correlations in individuals with an ADAS13 score range from 13 to 19. We observed two subpopulations that differed in their rate of disease progression. CSF proteins in the rapid progressors point to microglial lipid droplet signaling and the lactate shuttle. We observed key changes in plasmalogens and cholesterol esters with DHA fatty acid tails, both indicative of neuronal debris processing and reverse cholesterol transport, as well as changes in acylcarnitines-indicative of reduced lipid hydrolysis. We also found differential enrichment of specific AD GWAS loci between the fast and slow progressors.

CONCLUSION: Our analysis provides evidence for the importance of lipid droplet saturation coinciding with correlational changes in CSF proteins and plasma lipids, occurring in individuals transitioning from cognitively normal to MCI. We connected microglial AD GWAS loci to differences in the progression rates at this transition. These results have potential clinical relevance for predicting progression rate at MCI diagnosis, and inform our understanding of the role of GWAS loci in key transitions.

PMID:39750930 | DOI:10.1002/alz.092897

Alzheimers Dement. 2024 Dec;20 Suppl 1:e093129. doi: 10.1002/alz.093129.

ABSTRACT

BACKGROUND: Previously, we developed a co-calibrated and harmonized brain pathology score (BPS) across prospective cohort studies with research brain donation that incorporates multiple forms of postmortem neuropathology, using confirmatory factor analysis. We sought to identify genetic loci associated with BPS using a systems-biology approach, combining data from participants in the Adult Changes in Thought (ACT), the Religious Orders Study, and Rush Memory and Aging Project (ROSMAP) autopsy cohorts.

METHOD: We used PLINK in each cohort separately for genome-wide association studies (GWAS) of BPS using HRC imputed data from European ancestry participants, adjusting for age at death, sex, and population substructure. We performed meta-analysis using the adaptively weighted Fisher's approach in METAL. We performed gene-wide analysis using the meta-analyzed results which we then integrated into the human protein-protein interaction (PPI) network using a dense module searching (DMS) method to identify network hub genes for BPS. We interrogated the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) dataset on the middle temporal gyrus to determine which cell types both hub genes were expressed in and how they differed across donors with higher degrees of AD pathology (i.e. along AD pseudo-progression).

RESULT: The sample size consisted of 1,848 brain donors (Table 1). The quantile-quantile plot and genomic inflation (λ = 1.005) for GWAS meta-analyses showed no bias (Figure 1a), with the Manhattan plot in Figure 1b. Apart from significant SNPs around the APOE region, we identified two candidate loci a) (Chr 9: rs1332179; MAF = 0.1; P_meta = 8.7 × 10-8) and b) (Chr 17: rs11078196; MAF = 0.34; P_meta = 1.9 × 10-7). Regional association plots for these two loci are shown in Figure 1c. The PPI network analysis identified VCP and IQCB1 as hub genes (Figure 2a). While both hub genes were expressed broadly across cell types, IQCB1 was specifically higher with higher degrees of AD pathology in Microglia and VCP was lower with higher degrees of AD pathology in several neuronal populations (Figure 2b).

CONCLUSION: We identified two potentially useful candidate loci associated with BPS using a systems-biology approach. Further functional enrichment analysis is needed to determine whether these novel loci may identify targets for interventions to ameliorate AD.

PMID:39750880 | DOI:10.1002/alz.093129

Phys Rev Lett. 2024 Dec 13;133(24):248402. doi: 10.1103/PhysRevLett.133.248402.

ABSTRACT

Influenza A viruses (IAVs) must navigate through a dense extracellular mucus to infect airway epithelial cells. The mucous layer, composed of glycosylated biopolymers (mucins), presents sialic acid that binds to ligands on the viral envelope and can be irreversibly cleaved by viral enzymes. It was recently discovered that filamentous IAVs exhibit directed persistent motion along their long axis on sialic acid-coated surfaces. This Letter demonstrates through stochastic simulations and mean-field theory, how IAVs harness a "burnt-bridge" Brownian ratchet mechanism for directed persistent translational motion. Importantly, our analysis reveals that equilibrium features of the system primarily control the dynamics, even out of equilibrium, and that asymmetric distribution of ligands on the virus allows for more robust directed transport. We show viruses occupy the optimal parameter range ("Goldilocks zone") for efficient mucous transport, possibly due to the evolutionary adaptation of enzyme kinetics. Our findings suggest novel therapeutic targets and provide insight into possible mechanisms of zoonotic transmission.

PMID:39750332 | DOI:10.1103/PhysRevLett.133.248402

Brief Bioinform. 2024 Nov 22;26(1):bbae694. doi: 10.1093/bib/bbae694.

ABSTRACT

Protein phosphorylation is dynamically and reversibly regulated by protein kinases and protein phosphatases, and plays an essential role in orchestrating a wide range of biological processes. Although a number of tools have been developed for predicting kinase-specific phosphorylation sites (p-sites), computational prediction of phosphatase-specific dephosphorylation sites remains to be a great challenge. In this study, we manually curated 4393 experimentally identified site-specific phosphatase-substrate relationships for 3463 dephosphorylation sites occurring on phosphoserine, phosphothreonine, and/or phosphotyrosine residues, from the literature and public databases. Then, we developed a hybrid learning framework, the group-based prediction system for the prediction of phosphatase-specific dephosphorylation sites (GPSD). For model training, we integrated 10 types of sequence features and utilized three types of machine learning methods, including penalized logistic regression, deep neural networks, and transformer neural networks. First, a pretrained model was constructed using 561 416 nonredundant p-sites and then fine-tuned to generate computational models for predicting general dephosphorylation sites. In addition, 103 individual phosphatase-specific predictors were constructed via transfer learning and meta-learning. For site prediction, one or multiple protein sequences in FASTA format could be inputted, and the prediction results will be shown together with additional annotations, such as protein-protein interactions, structural information, and disorder propensity. The online service of GPSD is freely available at https://gpsd.biocuckoo.cn/. We believe that GPSD can serve as a valuable tool for further analysis of dephosphorylation.

PMID:39749667 | DOI:10.1093/bib/bbae694

FEBS Lett. 2025 Jan 2. doi: 10.1002/1873-3468.15096. Online ahead of print.

ABSTRACT

Lipid nanodiscs have become a widely used approach for studying membrane proteins thanks to several advantages they offer. They have been especially useful for studying ABC transporters, despite the growing concern about the possible restriction of the conformational changes of the transporters due to the small size of the discs. Here, we performed a systematic study to determine the effect of the nanodisc size on the ATPase activity of model ABC transporters from human, plant, and bacteria. Our data confirm that the activity of the transporters and their response to regulatory molecules is affected by the nanodisc size. Our findings suggest the use of larger membrane scaffold proteins (MSPs), such as MSP2N2 nanodiscs, to minimize alterations caused by the commonly used small MSP1D1.

PMID:39748569 | DOI:10.1002/1873-3468.15096

Mol Syst Biol. 2025 Jan 2. doi: 10.1038/s44320-024-00084-z. Online ahead of print.

ABSTRACT

Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.

PMID:39748127 | DOI:10.1038/s44320-024-00084-z

Nat Commun. 2025 Jan 2;16(1):107. doi: 10.1038/s41467-024-55740-7.

ABSTRACT

Caves are primary sites for studying human and animal subsistence patterns and genetic ancestry throughout the Palaeolithic. Iberia served as a critical human and animal refugium in Europe during the Last Glacial Maximum (LGM), 26.5 to 19 thousand years before the present (cal kya). Therefore, it is a key location for understanding human and animal population dynamics during this event. We recover and analyse sedimentary ancient DNA (sedaDNA) data from the lower archaeological stratigraphic sequence of El Mirón Cave (Cantabria, Spain), encompassing the (1) Late Mousterian period, associated with Neanderthals, and (2) the Gravettian (c. 31.5 cal kya), Solutrean (c. 24.5-22 cal kya), and Initial Magdalenian (d. 21-20.5 cal kya) periods, associated with anatomically modern humans. We identify 28 animal taxa including humans. Fifteen of these taxa had not been identified from the archaeozoological (i.e., faunal) record, including the presence of hyenas in the Magdalenian. Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. Finally, we recover three human mtDNA sequences from the Solutrean levels. These sequences, along with published data, suggest mtDNA haplogroup continuity in Iberia throughout the Solutrean/Last Glacial Maximum period.

PMID:39747910 | DOI:10.1038/s41467-024-55740-7

Nat Microbiol. 2025 Jan 2. doi: 10.1038/s41564-024-01879-4. Online ahead of print.

ABSTRACT

Cross-species transmission of animal viruses poses a threat to human health. However, systematic experimental assessments of these risks remain scarce. A critical step in viral infection is cellular internalization mediated by viral receptor-binding proteins (RBPs). Here we constructed viral pseudotypes bearing the RBPs of 102 enveloped RNA viruses and assayed their infectivity across 5,202 RBP-cell combinations. This showed that most of the tested viruses have the potential to enter human cells. Pseudotype infectivity varied widely among the 14 viral families examined and was influenced by RBP characteristics, host of origin and target cell type. Cellular gene expression data revealed that the availability of specific cell-surface receptors is not necessarily the main factor limiting viral entry and that additional host factors must be considered. Altogether, these results suggest weak interspecies barriers in the early stages of infection and advance our understanding of the molecular interactions driving viral zoonosis.

PMID:39747691 | DOI:10.1038/s41564-024-01879-4

EMBO Rep. 2025 Jan 2. doi: 10.1038/s44319-024-00356-7. Online ahead of print.

ABSTRACT

Ductular reaction (DR) is the hallmark of cholestatic diseases manifested in the proliferation of bile ductules lined by biliary epithelial cells (BECs). It is commonly associated with an increased risk of fibrosis and liver failure. The receptor for advanced glycation end products (RAGE) was identified as a critical mediator of DR during chronic injury. Yet, the direct link between RAGE-mediated DR and fibrosis as well as the mode of interaction between BECs and hepatic stellate cells (HSCs) to drive fibrosis remain elusive. Here, we delineate the specific function of RAGE on BECs during DR and its potential association with fibrosis in the context of cholestasis. Employing a biliary lineage tracing cholestatic liver injury mouse model, combined with whole transcriptome sequencing and in vitro analyses, we reveal a role for BEC-specific Rage activity in fostering a pro-fibrotic milieu. RAGE is predominantly expressed in BECs and contributes to DR. Notch ligand Jagged1 is secreted from activated BECs in a Rage-dependent manner and signals HSCs in trans, eventually enhancing fibrosis during cholestasis.

PMID:39747668 | DOI:10.1038/s44319-024-00356-7

EMBO Rep. 2025 Jan 2. doi: 10.1038/s44319-024-00286-4. Online ahead of print.

ABSTRACT

Neuroligins are postsynaptic cell-adhesion molecules that regulate synaptic function with a remarkable isoform specificity. Although Nlgn1 and Nlgn2 are highly homologous and biochemically interact with the same extra- and intracellular proteins, Nlgn1 selectively functions in excitatory synapses whereas Nlgn2 functions in inhibitory synapses. How this excitatory/inhibitory (E/I) specificity arises is unknown. Using a comprehensive structure-function analysis, we here expressed wild-type and mutant neuroligins in functional rescue experiments in cultured hippocampal neurons lacking all endogenous neuroligins. Electrophysiology confirmed that Nlgn1 and Nlgn2 selectively restored excitatory and inhibitory synaptic transmission, respectively, in neuroligin-deficient neurons, aligned with their synaptic localizations. Chimeric Nlgn1-Nlgn2 constructs reveal that the extracellular neuroligin domains confer synapse specificity, whereas their intracellular sequences are exchangeable. However, the cytoplasmic sequences of Nlgn2, including its Gephyrin-binding motif that is identically present in the Nlgn1, is essential for its synaptic function whereas they are dispensable for Nlgn1. These results demonstrate that although the excitatory vs. inhibitory synapse specificity of Nlgn1 and Nlgn2 are both determined by their extracellular sequences, these neuroligins enable normal synaptic connections via distinct intracellular mechanisms.

PMID:39747663 | DOI:10.1038/s44319-024-00286-4

Nat Commun. 2025 Jan 2;16(1):45. doi: 10.1038/s41467-024-55545-8.

ABSTRACT

Lilies are economically important monocots known for their ornamental flowers, bulbs, and large genomes. The absence of their genomic information has impeded evolutionary studies and genome-based breeding efforts. Here, we present reference genomes for Lilium sargentiae (lily, 35.66 Gb) and Gloriosa superba (flame lily, 5.09 Gb). The giant lily genome is shaped by recent long terminal repeat retroelements. Phylogenetic analysis reveals diverse, independent origins of lily cultivars. Gene families involved in sucrose and starch metabolism are significantly expanded in the lily genome. Key homologs of XTH22, SOC1, and AP1/FUL-like genes regulate the development, bud growth transition, and floral bud growth transition of lily bulbs. Colchicine biosynthetic gene clusters are identified in G. superba but are absent in L. sargentiae, highlighting independent colchicine evolution in Colchicaceae. These genomic insights enhance understanding of Liliales evolution, providing a foundation for future breeding and molecular research.

PMID:39747119 | DOI:10.1038/s41467-024-55545-8