Biology subjects

Deng, L.

Publications and source records attributed to Deng, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Flu Virus Infection in Juvenile Mice Leads to Lifelong Multi-Organ Damage and Parkinsonian Pathological Changes in Aging

The widespread prevalence of Long COVID underscores the potential for viral infections to exert prolonged effects on hosts long after initial recovery. Despite this recognition, the long-term and even lifelong consequences of viral infections remain poorly understood. In this study, we infected juvenile mice with influenza viruses and systematically examined the lifelong effects (from 4 to 450 days post-infection) of these infections. Pathological analysis revealed persistent lifelong damage in multiple organs, including chronic lung inflammation and fibrosis, along with significant cardiac and renal pathology. Viral infection led to substantial neuronal loss in key brain regions of mice (hippocampal CA1, CA3, and striatum) during middle and old age. Strikingly, we identified two hallmark pathological features of Parkinsons disease - dopaminergic neuron degeneration and Lewy body-like -synuclein inclusions - in middle and aged infected mice. Transcriptomic profiling demonstrated sustained upregulation of inflammation-related genes in both lung and blood tissues, correlating with observed pathological changes. Lung-derived secreted proteins, encoded by differentially expressed genes, may mediate cross-organ communication affecting cardiac, renal, and neurological function. Brain transcriptome analysis at three months post-infection revealed downregulation of neurodevelopmental genes, potentially contributing to subsequent neuronal loss and Parkinsonian pathology. These findings collectively suggest that pulmonary influenza infection can induce systemic multi-organ effects through both secretory pathways and chronic inflammatory responses. The study offers crucial insights for developing more effective strategies to prevent and manage infectious diseases and their long-term sequelae.

microbiology↗

bioRxiv2025

Rapid ecosystem collapse and biofilter formation following seabed methane leakage

Globally, vast amounts of methane are trapped within subseafloor gas hydrates. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release, yet the response of deep-sea ecosystems to these changes remains poorly understood. Here we show multi-year in situ monitoring of seabed ecosystem following methane leakage induced by hydrate exploration activities. Within just two years, benthic microbial and eukaryotic diversity in the affected areas declined significantly, while microbial and macrofaunal abundance increased. Integrated geochemical and omics analyses reveal the rapid successional shift of seabed ecosystem to a novel chemosynthetic system. Aerobic methanotrophs (Methyloprofundus) co-established with unexpectedly fast growing anaerobic methanotrophic archaea (ANME-3), accompanied by a rapid recruitment of opportunistic polychaetes that bioirrigated the seabed to >50 cm depths. The active animal-microbe interactions sustained exceptionally high rates of methane oxidation that utilized diverse electron acceptors. We demonstrate that methane hydrate destabilization can trigger rapid collapse of native seabed ecosystem while driving the formation of an effective methane biofilter consuming this potent greenhouse gas much faster than previously estimated. Understanding seabed ecosystem response and feedback is critical for predicting benthic methane cycling under ongoing global change and for developing sustainable strategies for methane hydrate resource management.

ecology↗

bioRxiv2025

TXNDC5 Governs Extracellular Matrix Homeostasis in Pulmonary Hypertension

BACKGROUNDPulmonary hypertension (PH) is characterized by vascular remodeling without effective treatments. Thioredoxin domain containing 5 (TXNDC5), a member of the protein disulfide isomerases (PDI) family, regulates protein folding and vascular homeostasis, yet its role in PH remains unknown. METHODSLabel-free proteomics profiled protein expression in lungs from PH patients. TXNDC5 was analyzed by single-cell RNA sequencing, immunofluorescence, and Western blot. Endothelial gain- and loss-of-function approaches were applied in Sugen5416/hypoxia (SuHx)-induced rodent PH models. RNA sequencing and protein-protein interaction analysis were used to investigate underlying mechanisms. RESULTSTXNDC5 was significantly upregulated in the lungs of patients with PH and in experimental PH models, with predominant localization in endothelial cells (ECs) of remodeled distal pulmonary arteries. Endothelial TXNDC5 overexpression exacerbated pulmonary vascular remodeling, elevated right ventricular systolic pressure, and promoted right ventricular hypertrophy, whereas global or endothelial-specific TXNDC5 deficiency conferred protection against SuHx-induced PH. Hypoxia-induced factor (HIF)-2 transcriptionally activated TXNDC5 to drive PH development. Single-cell RNA sequencing identified a distinct subpopulation characterized by TXNDC5high extracellular matrix (ECM)-producing ECs. Bulk RNA sequencing combined with protein-protein interaction analysis revealed that TXNDC5 regulated ECM homeostasis through biglycan (BGN). Pharmacological inhibition of TXNDC5 with E64FC26 and endothelial-targeted TXNDC5 gene therapy significantly attenuated PH severity in rats. CONCLUSIONSOur study reveals that TXNDC5 is a main modulator to regulate ECM homeostasis and may serve as a promising target for the treatment of PH.

molecular biology↗

bioRxiv2025

Human pancreatic organoids derived from pluripotent stem cells recapitulate pancreatic organogenesis

Pancreas organogenesis relies on sequential interactions between the pancreatic epithelium and surrounding mesodermal cell types that initiate epithelial budding and branching to form a complex ductal network with terminal acini. Despite recent advances with pluripotent stem cell-based approaches, there are no models that robustly recapitulate pancreas morphogenesis or the spatial organization of ductal, exocrine, endocrine and mesenchymal cells seen in the native organ. Here, we introduce a new pluripotent stem cell-based pancreatic organoid that captures the complexity seen during pancreatic development, with budding and stratification of multipotent progenitors followed by formation of a ductal network that give rise to peripheral acini. We identify a critical role for mesenchyme-derived factors to robustly promote pancreatic organoid formation and morphogenesis. Human pancreatic organoids are correctly patterned, with functional exocrine acini secreting digestive enzymes into a ductal network. Comparative analysis confirms that the pancreatic organoids are similar to early second trimester human pancreas, with potential to further mature upon transplantation in mice. Finally, we show that endocrinogenesis can be reproduced in organoids, generating functional islet-like clusters interspersed within the ductal network. Together, this represents an exciting new platform to study human pancreas development and a broad array of pancreatic diseases.

developmental biology↗

bioRxiv2025

Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans

The bacterial microbiome influences many aspects of animal health and disease. Some bacteria have beneficial functions, for example providing nutrients, whereas others act as pathogens. These bacteria are sensed by host cells to induce adaptive changes in physiology and behavior. While immune and intestinal cells detect bacterial signals through well-characterized mechanisms, recent studies indicate that neurons can also directly sense bacterial signals. However, the bacterial sensory mechanisms in neurons are less well understood. In the nematode Caenorhabditis elegans, the enteric sensory neuron NSM innervates the pharyngeal lumen and is directly activated by bacterial food ingestion; in turn, NSM releases serotonin to induce feeding-related behaviors. However, the molecular identities of the bacterial signals that activate NSM are unknown. To identify these signals, we systematically probed bacterial macromolecules from nutritive bacteria using biochemical approaches and GC-MS identification. We find that polysaccharides from gram-positive and gram-negative bacteria are sufficient to activate NSM. We further identify peptidoglycan from gram-positive bacteria as a specific component capable of activating NSM. NSM responses to polysaccharides require the acid-sensing ion channels DEL-3 and DEL-7, which localize to its sensory dendrite in the pharyngeal lumen. Ingestion of bacterial polysaccharides enhances feeding rates and reduces locomotion, matching the known effects of NSM on behavior. We also examine bacterial signals from pathogenic bacteria that can infect and kill C. elegans. This approach identifies prodigiosin, a metabolite from pathogenic Serratia marcescens, as a bacterial cue that prevents NSM activation by nutritive bacterial signals. This study identifies molecular signals that underlie neuronal recognition of nutritive bacteria in the alimentary canal and competing signals from a pathogenic bacterial strain that mask this form of recognition.

neuroscience↗

bioRxiv2025

Retrospective metabolomics via dual-dimensional deconvolution using ZT Scan DIA 2.0

We present a scanning data-independent acquisition (DIA) strategy, ZT Scan DIA, combined with dual-dimensional tandem mass spectrometry spectral filtering and deconvolution along both the quadrupole and retention time axes to reconstruct compound-specific MS2 spectra from complex mixtures. This approach is particularly effective for hydrophilic metabolomics data, where spectral similarity-based annotation is widely used, increasing annotation rates by 119-193% compared with conventional data-dependent acquisition (DDA) and window-based DIA methods. In lipidomics, deconvolution improved annotation precision by removing contaminant product ions and enabled separate quantification of co-eluting isomers using MS2 chromatograms, although common diagnostic ions could also be erroneously removed. Nevertheless, optimization of analysis parameters minimized this negative effect. Furthermore, we developed a practical data processing pipeline in which raw ZT Scan DIA-MS2 chromatograms are directly used for isomer separation and MS2-based quantification, covering 1,393 and 3,020 molecules for human plasma and mouse liver tissues, respectively. All data processing steps, including direct import of vendor raw data, are supported in MS-DIAL.

bioengineering↗

bioRxiv2025

Dendritic computation for rule-based flexible categorization

A hallmark of intelligent behavior is the ability to flexibly respond to external sensory inputs based on dynamically changing rules. A central question is how neurons in the brain implement computations underlying intelligent behaviors. The neocortical pyramidal neurons use their elaborated dendritic arbors to segregate a plethora of inputs and dynamically integrate them--a process known as dendritic computation--which may play important roles in rule-dependent sensory processing. However, evidence directly linking dendritic computation with intelligent cognitive behaviors has been absent. Here we combine two-photon imaging and a rule-switching flexible categorization task in mice to show that a projectome-defined extratelencephalic (ET) cortical layer 5 (L5) neurons in the auditory cortex integrate dendritic rule information and somatic sensory input to enable rule-dependent flexible categorization. The apical dendrite and soma within the same ET neurons exhibit distinct compartmental representations for sensory and rule information, with the soma predominantly encoding sensory information and the dendrites representing inferred task rule. Simultaneous optogenetic dendritic inhibition and two-photon imaging revealed that dendritic rule coding is essential for somatic output of flexible categorization. Our findings indicate that nonlinear dendritic integration of rule and sensory information constitutes a neuronal computational mechanism underlying rule-switching flexible decision-making.

neuroscience↗

bioRxiv2025

Hepatitis C virus NS3/4A protease cleaves SPG20, a key regulator of lipid droplet turnover, to promote lipid droplet formation

ABSTRACTSHepatitis C virus (HCV) assembles in close proximity to lipid droplets (LDs), which play important roles in HCV RNA replication. HCV infection often causes the accumulation of large LDs in hepatocytes. However, the molecular mechanism underlying HCV-induced large LD formation is poorly understood. It has been reported that the SPG20/Spartin protein associates with the LD surface and plays a crucial role in LD turnover by recruiting the ubiquitin ligase Itch to promote the ubiquitin-dependent degradation of adipophilin (ADRP), which protects LDs from lipase-mediated degradation. To elucidate the mechanism underlying HCV-induced large LD formation, we investigated the SPG20 proteins role in LD formation in HCV J6/JFH1-infected Huh-7.5 cells. Immunoblot analysis revealed that HCV infection promoted SPG20 protein cleavage. Transfection of increasing amounts of NS3/4A, but not the inactive NS3/4A mutant, resulted in SPG20 cleavage, implicating the NS3/4A protease in this cleavage. Site-directed mutagenesis suggested that the NS3/4A protease cleaves SPG20 at Cys504 and Cys562. The SPG20 protein was co-immunoprecipitated with the LD-attached protein TIP47. Increasing amounts of NS3/4A protease, but not inactive NS3/4A, decreased the co-precipitation of SPG20 with TIP47. The siRNA-mediated knockdown of Itch in Huh-7.5 cells restored ADRP levels, suggesting that Itch mediates ubiquitylation-dependent ADRP degradation. Immunofluorescence staining of HCV-infected cells revealed that ADRP was localized mainly around LDs in HCV-infected cells, whereas cytosolic ADRP was decreased. We propose that the HCV NS3/4A protease specifically cleaves SPG20 and inhibits Itch-mediated ubiquitin-dependent degradation of LD-associated ADRP, thereby promoting the formation of large LDs. IMPORTANCEHCV infection often promotes the formation of large LDs in HCV-infected cells. However, the molecular mechanism underlying large LD formation is poorly understood. LD turnover is regulated by SPG20, Itch E3 ligase, and ADRP. To elucidate the mechanism underlying the formation of large LDs induced by HCV infection, we investigated the roles of SPG20, Itch, and ADRP in large LD formation. The HCV NS3/4A protease specifically cleaves SPG20 and disrupts Itch recruitment to LD-associated ADRP. Therefore, LD-associated ADRP can escape and protects LDs from lipase-mediated degradation, thereby promoting LD growth. We propose that HCV NS3/4A protease-mediated cleavage of SPG20 contributes to a previously uncharacterized mechanism underlying the formation of large LDs in HCV-infected cells. These findings may lead to a better understanding of how the virus forms large LDs in infected cells.

microbiology↗

bioRxiv2025

HCV infection induces ubiquitin-dependent degradation of LATS1, inactivating the Hippo pathway and upregulating transcription of the CYR61 and CTGF genes

Hepatitis C virus (HCV) is often associated with chronic liver diseases and significant alterations in host cellular signaling. However, the molecular mechanisms underlying HCV- related liver pathogenesis remain to be elucidated. The Hippo signaling pathway, a key regulator of cell proliferation and survival, plays a critical role in maintaining liver homeostasis. Here we investigated the role of the Hippo pathway in HCV-related pathogenesis. We demonstrated that HCV infection induces degradation of LATS1, a key regulator of the Hippo pathway. Degradation of LATS1 protein was restored by a proteasomal inhibitor, but not a lysosome inhibitor, indicating that HCV promotes proteasomal degradation of LATS1 protein. HCV-induced degradation of LATS1 protein was suppressed in si-Itch-transfected Huh-7.5 cells. These results suggest that Itch ubiquitin ligase is involved in ubiquitin-dependent degradation of LATS1 protein. Cell fractionation assays and immunofluorescence staining revealed that HCV infection promoted nuclear translocation of YAP1 protein, suggesting that HCV infection suppresses the Hippo pathway. Furthermore, the transcription of YAP1 target genes, CYR61 and CTGF, that are involved in tissue remodeling and proliferation, was upregulated in HCV-infected Huh-7.5 cells and in HCV-infected patients. Taken together, we propose that HCV promotes the ubiquitin-dependent proteasomal degradation of LATS1 protein, leading to suppression of the Hippo pathway, thereby upregulating transcription of CYR61 and CTGF genes. DATA SUMMARYAll data are presented in the main figures. Raw sequencing data, microscopy images, materials, and sequence information are available upon request. Correspondence and requests for materials should be addressed to Professor Ikuo Shoji. The data that support the findings of this study is available at bioRxiv (https://www.biorxiv.org/). IMPACT STATEMENTWe demonstrate evidence suggesting that HCV infection promotes the Itch-mediated ubiquitin-dependent degradation of LATS1 protein, a key factor for the Hippo pathway. HCV-induced ubiquitin-dependent degradation of LATS1 protein promotes inactivation of the Hippo pathway and nuclear translocation of YAP1 protein, thereby upregulating transcription of CYR61 and CTGF genes. We propose a novel molecular mechanism in which HCV infection promotes degradation of LATS1 protein, leading to inactivation of the Hippo pathway. Understanding HCV-induced inactivation of the Hippo pathway may lead to developing new strategies for preventing or treating HCV-related pathogenesis.

microbiology↗

bioRxiv2025

Intrinsic fluctuations in global connectivity reflect transitions between states of high and low prediction error

While numerous researchers claim that the minimization of prediction error (PE) is a general force underlying most brain functions, others argue instead that PE minimization drives low-level, sensory-related neuronal computations but not high-order, abstract cognitive operations. We investigated this issue using behavioral, fMRI, and EEG data. Studies 1A/1B examined semantic- and reward-processing PE using task-fMRI, yielding converging evidence of PEs global effects on large-scale connectivity: high-PE states broadly upregulated ventral-dorsal connectivity, and low-PE states upregulated posterior-anterior connectivity. Investigating whether these global patterns characterize cognition generally, Studies 2A/2B used resting-state fMRI and showed that individuals continuously fluctuate between ventral-dorsal (high-PE) and posterior-anterior (low-PE) dynamic connectivity states. Additionally, individual differences in PE task responses track differences in resting-state fluctuations, further endorsing that these fluctuations represent PE minimization at rest. Finally, Study 3 combined fMRI and EEG data, and the study found that the fMRI fluctuation amplitude correlates most strongly with EEG power at 3-6 Hz, consistent with the PE network fluctuations occurring at Delta/Theta oscillation speeds. This whole-brain layout and timeline together are consistent with high/low-PE fluctuations playing a role in integrative and general sub-second cognitive operations.

neuroscience↗

bioRxiv2025

Phase separation drives SNARE complexes formation

BackgroundNeuronal exocytosis is mainly driven by the assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes. However, little is known about the organization principle of the SNARE complex. MethodsProtein condensates formed by SNARE complex were imaged by confocal microscope. Fluorescence recovery after photobleaching (FRAP) assay together with fusion and division assays at the cellular level and in vitro studies with purified proteins were performed to characterize the dynamic properties of protein condensates. The effect of SNARE complex phase separation on the recruitment of synaptic vesicles was detected by immunofluorescence. ResultsWe discover that phase separation drives SNARE complex formation and aggregation; in addition, nonintrinsically disordered regions (non-IDRs) of the syntaxin1 protein is necessary for the formation of these biological condensates. Functionally, phase separation of the SNARE complex can be regulated by the major cofactors of the fusion machinery and has the ability to recruit synaptic vesicles in neurons. ConclusionsOur study here establishes that phase separation is a promising way to mediate the formation and aggregation of the SNARE complex, and further identified that the non-IDRs of syntaxin1 is necessary for the phase separation of the SNARE complex. Our work answers an vital scientific question: does the SNARE complex function as multiple copies that are dispersed or clustered together to ensure sustained neurotransmitter release. In sum, phase separation provides an ideal working model for SNARE complex-mediated membrane fusion and neurotransmitter release.

neuroscience↗

bioRxiv2024

Drivers of methane-cycling archaeal abundances, community structure, and catabolic pathways in continental margin sediments

Marine sediments contain Earths largest reservoir of methane, with most of this methane being produced and consumed in situ by methane-cycling archaea. While numerous studies have investigated communities of methane-cycling archaea in hydrocarbon seeps and sulfate-methane transition zones, little is known about how these archaea change from the seafloor downward in the far more common diffusion-dominated marine sediments. Focusing on four continental margin sites of the North Sea-Baltic Sea transition, we here investigate the in situ drivers of methane-cycling archaeal community structure and metabolism based on geochemical and stable carbon-isotopic gradients, functional gene (mcrA) copy numbers and phylogenetic compositions, as well as thermodynamic calculations. We observe major vertical and lateral changes in community structure that largely follow changes in organic matter reactivity and content, sulfate concentration, and bioturbation activity. While methane-cycling archaeal communities in bioturbation and sulfate reduction zones are dominated by known methyl-dismutating taxa within the Methanosarcinaceae and putatively CO2-reducing Methanomicrobiaceae, the communities change toward dominance of known methane-oxidizing taxa (ANME-2a-b, ANME-2c, ANME-1a-b) in sulfate-methane transitions. Underlying methanogenesis zones were characterized by a change toward mainly physiologically uncharacterized groups, including ANME-1d and several new genus-level groups of putatively CO2-reducing Methanomicrobiaceae and methyl-reducing Methanomassiliicoccales. Notably, group-specific increases in mcrA copy numbers by 2 to 4 orders of magnitude from the sulfate reduction zone into the sulfate-methane transitions or methanogenesis zones indicate the thriving of several major methane-cycling archaeal taxa. Together our study provides insights into the community and pathway shifts vertically along the geochemical gradients and horizontally along the different sedimentary settings and their underlying drivers in continental margin sediments.

ecology↗

bioRxiv2024

Molecular epidemiology of carbapenem-resistant hypervirulent Klebsiella pneumoniae: Risk factors and resistance mechanism of ceftazidime/avibactam in China

The high morbidity and mortality rates associated with carbapenem-resistant hypervirulent Klebsiella pneumoniae have become a global public health problem. We analyzed the whole genome sequence and epidemiological data of 81 carbapenem-resistant Klebsiella pneumoniae strains and conducted sensitivity experiments to explore the optimal concentration of carbapenem-resistant Klebsiella pneumoniae. We verified the resistance and virulence genes of carbapenem-resistant Klebsiella pneumoniae using polymerase chain reaction and compared virulence between carbapenem-resistant hypervirulent Klebsiella pneumoniae a ndcarbapenem-resistant-non-hypervirulent Klebsiella pneumoniae through Galleria mellonella assays.The prevalent types of multilocus sequence typing in our carbapenem-resistant Klebsiella pneumoniae strains were ST11 (69.14%, 56/81). ST11-K64-O1/O2v1 has become an epidemic type in our hospital, with drug-resistance genes dominated by blaKPC-2 (90.12%, 73/81). Ceftazidime/avibactam has better antibacterial effects on carbapenem-resistant Klebsiella pneumoniae, and its resistance is mainly mediated by a resistance plasmid containing the blaKPC-2 gene. 52 carbapenem-resistant hypervirulent Klebsiella pneumoniae strains carry the blaKPC-2, with a high detection rate of siderophore. Further research has shown that the genetic environment of the blaKPC-2 contains TnpR_Tn3 and ISKpn27 upstream and ISKpn6 insertion sequences downstream. Galleria mellonella revealed that the survival rate of carbapenem-resistant hypervirulent Klebsiella pneumoniae was lower than that of carbapenem-resistant-non-hypervirulent Klebsiella pneumoniae, and the survival rate of carbapenem-resistant hypervirulent Klebsiella pneumoniae-K64 was lower than that of carbapenem-resistant hypervirulent Klebsiella pneumoniae-K47.The spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains is alarming, necessitating molecular monitoring of hypervirulent strains and strengthening the nosocomial infection prevention and control measures. Antibiotics should be used reasonably based on patients infection status and local epidemiological data. ImportanceCarbapenem-resistant Klebsiella pneumonia is a global public health concern. We conducted a molecular epidemiological analysis of 81 carbapenem-resistant hypervirulent Klebsiella pneumoniae strains from our hospital and explored the resistance mechanism of ceftazidime/avibactam. We identified the blaKPC-2 gene to be primarily responsible for carbapenem resistance in our hospital, and ST11-K64 was the dominant clone. A high-risk clone, ST307-K102, was detected, necessitating strengthened surveillance to prevent its spread. This studys findings contribute to the optimization of antimicrobial management and indicate that genomic research can assist with the tracking of hospital infection outbreaks and the improvement of infection-control measures.

microbiology↗

bioRxiv2024

Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs

Virus long non-coding RNAs (vlncRNAs) play crucial roles in viral infections, yet their identification and characterization remain limited. This study identified 5,053 novel vlncRNAs across 25 viral species using third-generation sequencing, with two from Influenza A virus and Vesicular stomatitis virus validated by RT-qPCR. Most vlncRNAs originated from dsDNA viruses. Only 1% having annotated RNA families, suggesting many novel RNA structures. Although only seven vlncRNAs shared sequence similarities with human lncRNAs (hlncRNAs), 772 vlncRNAs from 15 human viruses structurally mimicked hlncRNAs. These vlncRNA and hlncRNAs bound to similar miRNAs, potentially acting as miRNA sponges to promote essential life process. Splicing analysis showed vlncRNAs had a prevalence of alternative first exon. Finally, we developed vlncRNAbase (http://computationalbiology.cn/vlncRNAbase/#/) to store and organize the newly identified and known vlncRNAs. Overall, the study provides a valuable resource for further investigation into vlncRNAs and deepens our understanding of the diversity, structure and function of the molecule.

bioinformatics↗

bioRxiv2024

Abandoning the Quadrupole for Mass Spectrometry Fragmentation Analysis: Towards 1,000 Hz Speeds with 100% Ion Utilization Using High Resolution Ion Mobility Precursor Isolation

In todays fast-evolving landscape of omics research, tandem mass spectrometry has become a cornerstone for uncovering the complexities of biological systems. Yet, despite its essential role, the technology remains bound by the inherent limitations of quadrupole filters, which throw away up to 99% of the useful ion signal and caps the speed at which fragmentation data can be generated. These deficiencies often force compromises in data depth and accuracy, hindering breakthroughs that tie genomics, proteomics, and metabolomics together. A new technology is poised to break through these performance barriers, unlocking unprecedented capabilities in precision, sensitivity and throughput. This step-change in how mass spectrometry fragmentation analysis is performed will reshape the future of scientific discovery, pushing the boundaries of whats possible. The solution is high resolution ion mobility (HRIM), which offers a means to quickly and efficiently isolate ions prior to fragmentation and detection by a high resolution mass spectrometer (HRMS) while also resolving challenging isomeric and isobaric compounds that lead to chimeric MS/MS spectra. HRIM isolates ions in time as a result of a high speed separation rather than acting as a filter that discards ion signal like the pervasive quadrupole mass analyzer, allowing higher sensitivity analysis to be achieved. Also, since HRIM eliminates the need to hop or sweep electronics control parameters, as is the case with a quadrupole, fragmentation spectral generation can occur at a much faster rate, upwards of 500 Hz. This whitepaper describes an IM/MS methodology first contemplated over twenty years ago and today being positioned as the fastest method for high resolution fragmentation analysis. Revisiting this concept using the latest generation ion mobility technology based on structures for lossless ion manipulation (SLIM), which is the only HRIM technology that delivers similar resolution and range of analysis as a quadrupole, realizes the full potential of this approach to deliver benefits in both speed and sensitivity for high performance MS/MS measurements. This new way of achieving ion fragmentation in complex samples is set to revolutionize the mass spectrometry space, starting in the growing field of proteomics where all researchers are seeking faster methods to achieve more comprehensive proteomic coverage. Due to the advantages of HRIM physics, we predict this will set the bar for high throughput -omics within the coming years and will eventually be as ubiquitous as the quadrupole is today.

biochemistry↗

bioRxiv2024

The Senescence-Associated-Secretory Phenotype constituting HIF-1α activation is independent of micronuclei induction and associated cGAS-mediated interferon response

The Senescence-Associated Secretory Phenotype (SASP), characterized by the upregulation of inflammatory cytokines, is triggered during senescence by anti-proliferation stresses, including replicative exhaustion, {gamma}-irradiation, Ras oncogene induction, and centrosome amplification. The elucidation of common signalling pathway(s) activated in SASP, induced by different anti-proliferation stresses, remains an important question. Indeed, micronuclei activation of the cGAS/Sting pathway, which has been thought to drive SASP(Kwon, Leibowitz, and Lee, 2020), remains controversial(Flynn, Koch, and Mitchison, 2021; Sato and Hayashi, 2024; Takaki et al., 2024). In this report, analyses of various cell lines induced to undergo senescence by diverse stressors revealed that HIF-1 is specifically induced in senescence but not in quiescence. Consistent with our previous findings(Wu et al., 2023a), we have further demonstrated how centrosome amplification induces a non-canonical SASP dominated by HIF-1 activation rather than the classical NF{kappa}B signaling. Lastly, we revealed that during SASP, centrosome amplification-generated micronuclei do not activate the cGAS/Sting-mediated interferon response. Together, our findings demonstrate that HIF-1-activation in SASP is a defining feature of the SASP induced by diverse stressors, acting independently of micronuclei generation and cGAS/Sting activation.

cell biology↗

bioRxiv2024

Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans

Immunotherapy leads to cancer eradication despite the tumors immunosuppressive environment. Here, we used extended long-term in-vivo imaging and high-resolution spatial transcriptomics of endogenous melanoma in zebrafish, and multiplex imaging of human melanoma, to identify domains that facilitate immune response during immunotherapy. We identified crater-shaped pockets at the margins of zebrafish and human melanoma, rich with beta-2 microglobulin (B2M) and antigen recognition molecules. The craters harbor the highest density of CD8+ T cells in the tumor. In zebrafish, CD8+ T cells formed prolonged interactions with melanoma cells within craters, characteristic of antigen recognition. Following immunostimulatory treatment, the craters enlarged and became the major site of activated CD8+ T cell accumulation and tumor killing that was B2M dependent. In humans, craters predicted immune response to ICB therapy, showing response better than high T cell infiltration. This marks craters as potential new diagnostic tool for immunotherapy success and targets to enhance ICB response.

cancer biology↗

bioRxiv2024

Cortico-hippocampal interactions underlie schema-supported memory encoding in older adults

Although episodic memory is typically impaired in older adults (OAs) compared to young adults (YAs), this deficit is attenuated when OAs can leverage their rich semantic knowledge, such as their knowledge of schemas. Memory is better for items consistent with pre-existing schemas and this effect is larger in OAs. Neuroimaging studies have associated schema use with the ventromedial prefrontal cortex (vmPFC) and hippocampus (HPC), but most of this research has been limited to YAs. This fMRI study investigated the neural mechanisms underlying how schemas boost episodic memory in OAs. Participants encoded scene-object pairs with varying congruency, and memory for the objects was tested the following day. Congruency with schemas enhanced object memory for YAs and, more substantially, for OAs. FMRI analyses examined how cortical modulation of HPC predicted subsequent memory. Congruency-related vmPFC modulation of left HPC enhanced subsequent memory in both age groups, while congruency-related modulation from angular gyrus (AG) boosted subsequent memory only in OAs. Individual differences in cortico-hippocampal modulations indicated that OAs preferentially used their semantic knowledge to facilitate encoding via an AG-HPC interaction, suggesting a compensatory mechanism. Collectively, our findings illustrate age-related differences in how schemas influence episodic memory encoding via distinct routes of cortico-hippocampal interactions.

neuroscience↗