Biology subjects

Lin, X.

Publications and source records attributed to Lin, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Mapping AAV capsid sequences to functions through function-guided in silico evolution

Artificial intelligence (AI) offers significant potential to accelerate the functional engineering of adeno-associated virus (AAV) capsids in a time- and cost-efficient manner. However, existing approaches lack the ability to systematically map capsid sequences to multifunctional properties. To address this challenge, we developed ALICE, a knowledge-driven platform for in silico AAV capsid engineering that directly maps sequence to multiple functions. Our method incorporating a heuristic algorithm with contrastive learning principles, termed function-guided evolution (FE), to iteratively optimize high-performing capsid sequences generated by a naive language model toward desired functions. We elucidate FEs evolutionary mechanism, demonstrating its ability to navigate a function-guided landscape and generate capsids with tailored properties. After validating ALICEs ability to design murine-specific AAV capsids targeting Ly6a/Ly6c1 with limited training data, we developed ALICE-X by integrating a curriculum learning strategy. This upgrade facilitated exploration of sequence space beyond existing wet-lab datasets, enabling successful targeting of the human transferrin receptor 1 (hTfR1). The resulting engineered AAV variant, AAV.ALICE-H3, demonstrated improved viability, specific receptor targeting, and [~] 251-fold enhanced CNS tropism in human TFRC knock-in (hTFRC KI) mice compared to wildtype controls. This interpretable, knowledge-driven framework advances in silico AAV capsid design, offering broad applicability for translational gene therapy.

bioengineering↗

bioRxiv2024

Genomic and epigenomic maps of mouse centromeres and pericentromeres

Satellite DNA makes up [~]11% of the mouse genome, predominantly located in centromeric and pericentric regions, which are crucial for chromosome segregation. While comprehensive assemblies of these regions have been established in the human genome, they are still lacking in the mouse genome. In this study, we used PacBio long-read sequencing, CUT&RUN sequencing, DNA methylation analysis, and RNA sequencing to generate genomic and epigenomic maps of these regions. We find that centromeric regions are primarily occupied by 120-mer Minor satellites, with other Minor Satellite length variants, 112-mers and 112-64-dimers, localized at centromere-pericentric junctions. Pericentromeric regions are mainly composed of homogeneous Major satellites, while pericentric-chromosomal junctions contain a higher density of divergent satellites. Additionally, the density of non-satellite repeats increases progressively from centromeres to pericentromeres, and further toward chromosomal arm junctions. We found that 120-mer Minor satellites in the core centromere are highly enriched with CENP-A, while the 112-mers and 112-64-dimers show lower CENP-A levels. Homogeneous Major satellites are more enriched with H3K9me3 heterochromatin, whereas divergent Major satellites are preferentially associated with H3K27me3. Furthermore, DNA methylation levels are lower in centromeres compared to pericentric regions. We also observed that only a small subset of satellites is transcribed into RNA, particularly regions exhibiting lower DNA methylation density. Our comprehensive assembly and characterization of the genomic and epigenomic landscape of mouse centromeric and pericentric regions have major implications for satellite biology and ongoing mouse telomere-to-telomere (T2T) assembly efforts.

genomics↗

bioRxiv2024

Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Whole-genome duplication (WGD) events are widespread across the Web of Life (WoL). Given the prevalence of WGDs in the polyploid Prunus (Rosaceae), this economically- and agriculturally-important angiosperm lineage provides an excellent model for exploring this mode of reticulation. We used the polyploid Prunus to demonstrate a progressive strategy for analyzing Deep Genome Skimming (DGS) data in the presence of WGDs. Phylogenomic discordance analyses indicated that allopolyploidization, rather than Incomplete Lineage Sorting (ILS), played a dominant role in the origin and dynamics of polyploid Prunus. This study underscores how a progressive strategy to identify WGD events at different depths in a phylogenetic tree reveals the nuances of evolutionary mechanisms driving allopolyploidization. We inferred that the continued uplift of the Himalayas from the Middle to Late Miocene drove the rapid diversification of the Eastern Asia endemic Maddenia clade, by facilitating frequent hybridization and allopolyploidization, specifically introgression between the Himalayas-Hengduan and the Central-Eastern China clades.

systems biology↗

bioRxiv2024

Inhibition of Ribosome Biogenesis in vivo Causes p53-Dependent Death and p53-Independent Dysfunction

Ribosomes are critical for cell function; their synthesis (known as ribosome biogenesis; "RiBi") is complex and energy-intensive. Surprisingly little is known about RiBi in differentiated cells in vivo in adult tissue. Here, we generated mice with conditional deletion of Nat10, an essential gene for RiBi and translation, to investigate effects of RiBi blockade in vivo. We focused on RiBi in a long-lived, ribosome-rich cell population, pancreatic acinar cells, during homeostasis and tumorigenesis. We observed a surprising latency of several weeks between Nat10 deletion and onset of structural and functional abnormalities and p53-dependent acinar cell death, which was associated with translocation of ribosomal proteins RPL5 and RPL11 into acinar cell nucleoplasm. Indeed, deletion of Trp53 could rescue acinar cells from apoptotic cell death; however, Nat10{Delta}/{Delta}; Trp53{Delta}/{Delta} acinar cells remained morphologically and functionally abnormal. Moreover, the deletion of Trp53 did not rescue the lethality of inducible, globally deleted Nat10 in adult mice nor did it rescue embryonic lethality of global Nat10 deletion, emphasizing p53-independent consequences of RiBi inhibition. Deletion of Nat10 in acinar cells blocked Kras-oncogene-driven pancreatic intraepithelial neoplasia and subsequent pancreatic ductal adenocarcinoma, regardless of Trp53 mutation status. Together, our results provide initial insights into how cells respond to defects in RiBi and translation in vivo.

cell biology↗

bioRxiv2024

Exploring the Biological Mechanisms of Severe COVID-19 in the Elderly: Insights from an Aged Mouse Model

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in a global health crisis, particularly affecting the elderly, who are more susceptible to severe outcomes. However, definitive parameters or mechanisms underlying the severity of COVID-19 in elderly people remain confused. Thus, this study seeks to elucidate the mechanism behind the increased vulnerability of elderly individuals to severe COVID-19. We employed an aged mouse model with a mouse-adapted SARS-CoV-2 strain to mimic the severe symptoms observed in elderly patients with COVID-19. Comprehensive analyses of the whole lung were performed using transcriptome and proteome sequencing, comparing data from aged and young mice. For transcriptome analysis, bulk RNA sequencing was conducted using an Illumina sequencing platform. Proteomic analysis was performed using mass spectrometry following protein extraction, digestion, and peptide labeling. We analyzed the transcriptome and proteome profiles of young and aged mice and discovered that aged mice exhibited elevated baseline levels of inflammation and tissue damage repair. After SARS-CoV-2 infection, aged mice showed increased antiviral and inflammatory responses; however, these responses were weaker than those in young mice, with significant complement and coagulation cascade responses. In summary, our study demonstrates that the increased vulnerability of the elderly to severe COVID-19 can be attributed to an attenuated antiviral response and the overactivation of complement and coagulation cascades.

immunology↗

bioRxiv2024

Photochemical processes drive thermal responses of dissolved organic matter in the dark ocean

How dissolved organic matter (DOM) responds to climate warming is critical for understanding its role in future ocean carbon cycling. Here, we use a highly resolved dataset of over 800 DOM samples covering the surface waters to the deep Atlantic, Southern, and Pacific oceans to examine the changes in DOM molecular composition in response to warming water temperatures, referred to as DOM thermal responses. Towards the deep waters, the strength (i.e., overall magnitude) and diversity (i.e., variation among molecules) of these thermal responses both decline. However, these responses show opposite trends with the concentration of more recalcitrant molecules, decreasing and increasing, respectively. These contrasting trends concur with the observation that, compared to the strength of thermal responses, their diversity is more strongly explained by photochemical processes of DOM. By projecting global ocean thermal responses from 1950 to 2020 using environmental temperature, salinity and radiation, we predict that increases in the diversity of thermal responses are unexpectedly largest at deeper depths (> 1,000 m). Such increases could elevate the recalcitrant deep-ocean carbon sink by approximately 10 Tg C yr-1, which accounts for > 5% of the carbon flux reaching and persisting in the deep ocean. Our findings highlight the role of photochemical processes in imprinting DOM thermal responses, offering new insights into the future capacity of the oceanic carbon sink under global climate change.

ecology↗

bioRxiv2024

Deciphering the Cell Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish

Cell fate determination during early embryonic development is a complex process modulated by gene expression. The intricate interplay of transcriptional and post-transcriptional regulation is integral to the developmental trajectory of embryogenesis, yet how RNA processing may contribute to early development programming is largely elusive. Leveraging recent technological advances in single-molecule nanopore sequencing, we developed a single-cell long-read transcriptome sequencing technology, allowing a clear view of transcript diversity during zebrafish embryogenesis during pre- and post-zygotic genome activation (ZGA). A closer examination of the dynamic transcript usage and potential alternative splicing revealed that abundant stage-specific transcripts with differential coding potentials are involved in distinct biological functions. Specifically, we identified two cell populations at the onset of ZGA based on isoform diversity instead of gene profiling, which followed divergent developmental trajectories toward the ectoderm and the presumptive ectoderm. These two populations of cells were characterized by divergent splicing regulations linked to differential RNA-binding proteins, including SNRPA and SFPQ. Altogether, using the single-cell long-read transcriptome sequencing strategy, we work has revealed the cell-specific transcriptome dynamics contributing to the cell fate determination during embryogenesis.

developmental biology↗

bioRxiv2024

Sociability genetically separable from social hierarchy in amniotes

The emergence of social structure and organization is essential for the evolution of amniotes, including human beings. Sociability and social hierarchy are two key features to form a social group. However, it remains unknown whether sociability and social hierarchy are genetically separable. In this study, we examined the social hierarchy, social and social novelty preference of PAS1 (placental-accelerated sequence 1) knock-out and knock-in mice. PAS1 is a social enhancer that modulates social hierarchy. We found that PAS1 knock-out mice lack social hierarchy while wallaby/chicken PAS1 knock-in mice establish stable social ranks. Moreover, social and social novelty preference was observed in all PAS1-mutated mice. PAS1 knock-in mice have stronger preference to interact with other mice than wild-type mice (C57BL/6). No aggressive alteration was found in PAS1-mutated mice. Overall, our results showed that PAS1 is an indispensable regulatory element in the formation of social hierarchy while PAS1 regulates one of pathways modulating sociability. Therefore, sociability is genetically separable from social hierarchy in amniotes, providing insights into how social structure and organization evolved. HighlightsPAS1, a social enhancer, is indispensable for amniotes to establish social hierarchy. PAS1 modulates sociability in amniotes. Sociability and social hierarchy are regulated differently in amniotes. The frequency of PAS1 allele was not rare when social hierarchy first appeared.

animal behavior and cognition↗

bioRxiv2024

Spatial Heterogeneity of Climate Fluctuations Shapes Ecological Processes and Community Dynamics in Riverine Invertebrates Across a Landscape

The environment and its variability exhibit spatial heterogeneity in influencing ecological processes and community dynamics across landscapes. However, the mechanisms remain unexplored. This study investigates relative significance of temporal ecological processes that shape invertebrate community dynamics across 15 rivers in the European Iberian Peninsula over 21 years. Spatial asymmetry in community dynamics was driven by a combination of temporal deterministic and stochastic processes (i.e., environmental filtering and temporal distance within the same locations, respectively). It is noteworthy that the relative importance of deterministic versus stochastic processes diminishes with increasing elevation. The analysis of community dynamics in diverse landscapes offers a foundation for anticipating and mitigating the consequences of prospective environmental transformation on biodiversity, thereby directing efficacious conservation strategies.

ecology↗

bioRxiv2024

A single-molecule nanopore sequencing platform

Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield (>50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0%. Preliminary findings on human whole-genome de novo assembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQs potential across different areas of genomics.

genomics↗

bioRxiv2024

Human Replication Protein A complex is a Telomerase Processivity Factor Essential for Telomere Maintenance

Telomerase is crucial for maintaining telomere length and safeguarding genome stability. In this study, we identified Replication Protein A (RPA) as a novel telomerase processivity factor, functioning alongside the telomerase recruitment factor TPP1-POT1. AlphaFold2 predictions revealed that RPA and TPP1 interact with telomerase at distinct binding sites. Using separation- of-function mutants, we discovered that RPA-mediated telomerase stimulation is indispensable for telomere elongation, while TPP1-POT1 primarily functions in recruiting telomerase to telomeres. Furthermore, we demonstrated that short telomere disease-associated telomerase mutations compromise RPAs ability to stimulate telomerase, establishing a link between impaired RPA-dependent processivity and telomeropathies. Our findings redefine human telomerase regulation by establishing RPA as a critical regulator and provide new insights into the molecular basis of telomere-related diseases.

molecular biology↗

bioRxiv2024

Dual-Targeted Microbubbles Promote Apoptosis of M1 Macrophages by Inhibiting Telomerase Activity for Atherosclerosis Therapy

It is known that M1 macrophages are the dominant phenotype in progressive atherosclerosis (AS). Studies have shown that telomerase in macrophages can be activated during the atherosclerosis formation, but how to regulate the telomerase activity of M1 macrophages is the focus of treatment of AS. Herein, we report a dual-targeted microbubbles delivery system encapsulating the telomerase inhibitor BIBR1532 (Ab-MMB1532), designed for precise targeted therapy of AS. The Ab-MMB1532 exhibits excellent biocompatibility and remarkable targeting capability towards M1 macrophages with its targeting advantage notably accentuated under high shear forces. Furthermore, it significantly downregulates telomerase activity. Metabolomics analysis indicates that the decrease in telomerase activity upregulates the expression of aspartic acid, a key protein in the Caspase pathway of apotosis. In vivo, Ab-MMB1532 efficiently targeted and accumulated within AS lesions, leading to significantly delay of the AS progression by inhibiting telomerase activity and promoting apoptosis of M1 macrophages after 4-week treatment. In summary, Ab-MMB1532 provides a new approach for potentially safer and more effective treatment of AS in the future.

bioengineering↗

bioRxiv2024

Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

In contrast to the traditional Tree of Life (ToL) paradigm, the Web of Life (WoL) model provides a more nuanced and precise depiction of organismal phylogeny, particularly considering the prevalent incongruence observed among gene/species trees. The lack of a generalized pipeline for teasing apart potential evolutionary mechanisms--such as Incomplete Lineage Sorting (ILS), hybridization, introgression, polyploidization, and Whole-Genome Duplication--poses significant challenges to the delineation of the WoL. The pear genus Pyrus, characterized by extensive hybridization events, serves as an excellent model for investigating the WoL. This study introduces a novel Step-by-Step Exclusion (SSE) approach to deciphering the complexities inherent in the WoL. Our findings indicate: 1) ILS, rather than polyploidization, is identified as the primary driver behind the origin of Pyrus from the arid regions of the Himalayas-Central Asia; 2) the two subgenera of Pyrus have independent evolutionary trajectories, facilitated by the geographical barriers that arose via the uplift of the Tibetan Plateau and increased aridity in Central Asia; 3) ILS and hybridization have facilitated the diversification of Oriental pears, while hybridization alone has driven the reticulate evolution of Occidental pears; 4) the establishment of the Silk Road during the Han Dynasty acted as a conduit for genetic exchange between Occidental and Oriental pears. The novel SSE approach provides a universally applicable framework for investigating evolutionary mechanisms defining the WoL paradigm.

systems biology↗

bioRxiv2024

Intraperitoneal programming of tailored CAR macrophages via mRNA-LNP to boost cancer immunotherapy

Therapeutic strategies for peritoneal metastasis in solid tumors are urgently needed in the clinic. Programming chimeric antigen receptor macrophages (CAR-Ms) in situ offers opportunities for an unmet demand. However, potential intracellular domains (ICDs) for CAR design and their antitumor mechanisms for macrophage empowerment remain to be explored systematically. By developing a targeted mRNA-LNP delivery system for macrophages, we have investigated 36 CAR combinations to determine the impact of CAR-Ms on immune regulation in vitro and in vivo. In two solid tumor mouse models, intraperitoneal programming of CAR-Ms was shown to elicit robust adaptive immune activation and significantly synergize with PD-1/L1 therapy. Single-cell RNA sequencing (scRNA-seq) analysis revealed that CAR-Ms could reshape the immunosuppressive tumor microenvironment (TME) and boost the TCF1+PD-1+ progenitor- exhausted CD8+ T cells (Tpex) population. Meanwhile, we found that tailored CAR-M with CD3{zeta}/TLR4 ICDs could favorably maintain proinflammatory phenotype and simultaneously upregulate MHC I and PD-L1 expression by perturbing NF-{kappa}B pathways. Moreover, the synergism between macrophage PD-L1 knockdown and CAR-M therapy highlighted the need to block the PD-1/L1 axis in antigen cross-presentation. In short, we developed an mRNA-LNP delivery system for intraperitoneal programming of tailored CAR-Ms in vivo and broadened understanding of both regulatory and feedback mechanisms for CAR-M therapies against solid tumors.

bioengineering↗

bioRxiv2024

Overcrowding Drives Tumor Invasion by Inducing Nanotopographical Transition of Plasma Membrane

During the progression from epithelial neoplasms to invasive carcinoma, cells are subjected to prolonged confinement. However, the response of cancer cells to such mild yet sustained compressive pressure during the initial stages of tumor invasion remain poorly understood. Here, using a spontaneous crowding model to recapitulate the progressive compressive stress caused by cell proliferation, we demonstrated that prolonged crowding alone is sufficient to induce the acquisition of an invasive phenotype and associated gene expression patterns in cancer cells. This invasiveness persisted even after cells were removed from the crowded environment, a phenomenon mediated by mechanomemory. By combining genetic manipulations, mechanical modeling, and biophysical measurements, we revealed that the disaggregation of membrane domains--driven by a nanoscale smooth-corrugated topography transition of plasma membranes induced by Laplace pressure under crowded conditions--is essential for initiating cancer cell invasion. Inhibiting membrane domains disaggregation through membrane-to-cortex-attachment effectively suppresses cancer cell invasion in both cellular crowding models and mouse xenograft models. This study underscores the critical role of tissue-scale mechanics in regulating the biophysics of mechanosensitive membrane domains during the early stages of tumor invasion.

cancer biology↗

bioRxiv2024

Olfactory cortical outputs recruit and shape distinct brain-wide spatiotemporal networks

Odor information is transmitted from the olfactory bulb to several primary olfactory cortical regions in parallel, including the anterior olfactory nucleus (AON) and piriform cortex (Pir). However, the specific roles of the olfactory bulb and cortical outputs in wider interactions with other interconnected regions throughout the brain remain unclear due to the lack of suitable in vivo techniques. Furthermore, emerging associations between olfactory-related dysfunctions and neurological disorders underscore the need for examining olfactory networks at the systems level. Using optogenetics, fMRI, and computational modeling, we interrogated the spatiotemporal properties of brain-wide neural interactions in olfactory networks. We observed distinct downstream recruitment patterns. Specifically, stimulation of excitatory projection neurons in OB predominantly activates primary olfactory network regions, while stimulation of OB afferents in AON and Pir primarily orthodromically activates hippocampal/striatal and limbic networks, respectively. Temporally, repeated OB or AON stimulation diminishes neural activity propagation brain-wide in contrast to Pir stimulation. Dynamic causal modeling analysis reveals a robust inhibitory effect of AON outputs on striatal and limbic network regions. In addition, experiments in aged rat models show decreased brain-wide activation following OB stimulation, particularly in the primary olfactory and limbic networks. Modeling analysis identifies a dysfunctional AON to Pir connection, indicating the impairment of this primary olfactory cortical circuit that disrupts the downstream long-range propagation. Our study delineates the spatiotemporal properties of olfactory neural activity propagation in brain-wide networks for the first time and distinguishes the roles of primary olfactory cortical, AON and Pir, outputs in shaping neural interactions at the systems level.

neuroscience↗

bioRxiv2024

Dynamic regulation of H2A.Zub and H3K27me3 by ambient temperature in plant cell fate determination

Crucial to plant development, ambient temperature triggers intricate mechanisms enabling adaptive responses to temperature variations. The precise coordination of chromatin modifications in shaping cell fate under diverse temperatures remains elusive. Our study, integrating comprehensive transcriptome, epigenome profiling and genetics, unveils that lower ambient temperature (16{degrees}C) restores developmental defects caused by H3K27me3 loss in PRC2 mutants by specifically depositing H2A.Zub at ectopically expressed embryonic genes, such as ABI3 and LEC1. This deposition leads to re-silencing of these genes and compensates for H3K27me3 depletion. PRC1-mediated H2A.Zub and PRC2-catalyzed H3K27me3 play roles in silencing transcription of these embryonic genes for post-germination development. Low temperature decelerates H2A.Z turnover at specific loci likely by attenuating the interaction between TOE1 and H2A.Z chaperone, sustaining repression of embryonic genes and alleviating requirement for PRC2-H3K27me3 at post-germination stage. Our findings offer mechanistic insights into the cooperative epigenetic layers facilitating plants adaptation to varying environmental temperatures.

plant biology↗

bioRxiv2024

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron

T492I, a mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, causing potential evolutionary impacts. Through comprehensive comparative analyses based on evolve-and-resequence experiments of SARS-CoV-2 wild-type and Delta strains with or without T492I, we demonstrate that NSP4 T492I not only increases the mutation rate, but also accelerates the emergence of many mutations characteristic for Omicron variants. Accordingly, viral populations that evolved from ancestors with T492I, show Omicron-biased selective forces and increases in viral replication, infectivity, immune evasion capacity, potentials for cross-species transmission and receptor-binding affinity. Aside from enhanced replication, we observed stronger epistasis regarding viral replication and infectivity in T492I than in S N501Y and NSP6 {Delta}SGF; this facilitates the regulation of mutation types, which can drive fast evolution of Omicron specific mutations. Our results highlight the role of an important replication-enhancing mutation in regulating the evolutionary rates and mutational trends of SARS-CoV-2.

evolutionary biology↗