Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 613 records · Page 34Linked to original sources

bioRxiv2024

N1-methylpseudouridine mRNA modification enhances efficiency and specificity of gene overexpression by preventing Prkra-mediated global translation repression

In vitro transcribed messenger RNA (IVT mRNA) has emerged as a pivotal tool in mRNA-based therapies and has been extensively employed in gene function studies and genetic tool applications. However, the IVT process generates double-stranded RNA (dsRNA) by-products that are recognized by dsRNA sensors, triggering innate immune responses. In this study, we comprehensively analyzed the detrimental effects of dsRNA by-products on early zebrafish embryos, revealing that these by-products induce cell necrosis and delay maternal-zygotic transition by reducing global translation efficiency via Prkra, a recently identified dsRNA sensor in pluripotent cells. Importantly, we demonstrate that N1-methylpseudouridine (m1{varphi}) modification of IVT mRNAs effectively mitigates these adverse effects, as m1{varphi}-modified dsRNAs exhibit significantly lower binding affinity to the Prkra dimer. Our findings underscore a previously overlooked challenge in the use of IVT mRNA in early embryos and offer a robust solution to enhance the fidelity of mRNA applications. Furthermore, we elucidate that m1{varphi} modification minimizes the dsRNA-induced stress response in pluripotent cells through a distinct mechanism.

developmental biology↗

bioRxiv2024

PathOmCLIP: Connecting tumor histology with spatial gene expression via locally enhanced contrastive learning of Pathology and Single-cell foundation model

Tumor morphological features from histology images are a cornerstone of clinical pathology, diagnostic biomarkers, and basic cancer biology research. Spatial transcriptomics, which provides spatially resolved gene expression profiles overlaid on histology images, offers a unique opportunity to integrate morphological and expression features, thereby deepening our understanding of tumor biology. However, spatial transcriptomics experiments with patient samples in either clinical trials or clinical care are costly and challenging, whereas histology images are generated routinely and available for many legacy prospective cohorts of disease progression and outcomes in well-annotated cohorts. Inferring spatial transcriptomics profiles computationally from these histology images would significantly expand our understanding of tumor biology, but paired data for training multi-modal spatial-histology models remains limited. Here, we tackle this challenge by incorporating performant foundation models pre-trained on massive datasets of pathology images and single-cell RNA-Seq, respectively, which provide useful embeddings to underpin multi-modal models. To this end, we developed PathOmCLIP, a model trained with contrastive loss to create a joint-embedding space between a histopathology foundation model and a single-cell RNA-seq foundation model. We incorporate a set transformer to gather localized neighborhood tumor architecture following contrastive training, which further enhances performance and is necessary to obtain robust results. We validate PathOmCLIP across five tumor types and achieve significant performance improvements in gene expression prediction tasks over other methods. PathOmCLIP can be applied to many archived histology images, unlocking valuable clinical information and facilitating new biomarker discoveries.

bioinformatics↗

bioRxiv2024

Enantioselective photoenzymatic C(sp3)-H functionalization via single-electron oxidation of carbanions

Established strategies for enantioselective hydroalkylation for C(sp3)-C(sp3) bond formation usually require pre-functionalized substrates as radical precursors in both transition-metal and photoenzymatic catalysis. Based on a sequential proton transfer/electron transfer (PT/ET) strategy, here we show a cooperative photoenzymatic system consisting of a flavin-dependent ene-reductase (ER) and an organophotoredox catalyst fluorescein (FI) to achieve atom-economic enantiodivergent hydroalkylation of electron-deficient C(sp3)-H with olefins. Mechanistic studies revealed a pathway for radical intermediate formation via excited-state FI*-induced single-electron oxidation of carbanions under alkaline conditions. The overall catalytic efficiency is enhanced by the electron transfer (ET) between FMNox and FI-*, while the stereoselectivity is controlled by ERs through enantioselective hydrogen atom transfer (HAT). We anticipate that this mode of photoenzymatic catalysis will inspire new pathways for generating free radical intermediates and foster innovative strategies for achieving photoenzymatic new-to-nature reactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/627421v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@11b6c1eorg.highwire.dtl.DTLVardef@1575346org.highwire.dtl.DTLVardef@1c24a2org.highwire.dtl.DTLVardef@1a93c0d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Deep-learning-enabled generative prevalent mutation prediction through host-to-herd in silico virus evolution

Predicting the mutation prevalence trends of emerging viruses in the real world is an efficient means to update vaccines or drugs in advance. It is crucial to develop a computational method for the prediction of real-world prevalent SARS-CoV-2 mutations considering the impact of multiple selective pressures within and between hosts. Here, a deep-learning generative framework for real-world prevalent SARS-CoV-2 mutation prediction, named ViralForesight, is developed on top of protein language models and in silico virus evolution. Through the paradigm of host-to-herd in silico virus evolution, ViralForesight reproduced previous real-world prevalent SARS-CoV-2 mutations for multiple lineages with superior performance. More importantly, ViralForesight correctly predicted the future prevalent mutations that dominate the COVID-19 pandemic in the real world more than half a year in advance with in vitro experimental validation. Overall, ViralForesight demonstrates a proactive approach to the prevention of emerging viral infections, accelerating the process of discovering future prevalent mutations with the power of generative deep learning.

evolutionary biology↗

bioRxiv2024

A non-muscle α-actinin is an intrinsic component of the cardiac Z-disc and regulates sarcomere turnover, contractility, and heart remodeling

Cardiac sarcomeres generate the fundamental forces behind each heartbeat and are thought to contain only muscle-specific cytoskeletal proteins. We show that a widely expressed actin cross-linking protein, -actinin 4 (ACTN4), is a sarcomere component of the human and zebrafish heart in vivo and in human iPSC-derived cardiac myocytes (CMs) in vitro. A confluence of biochemical experiments, immunofluorescence, and AI modeling suggest ACTN4 forms a heterodimeric complex with muscle-specific ACTN2 at the cardiac Z-disc, the cardiac sarcomere border. ACTN4 depletion from human iPSC-CMs stabilizes canonical sarcomere proteins and drives contractility-dependent cellular hypertrophy while ACTN4 overexpression destabilizes sarcomeres. ACTN4 depletion from zebrafish embryos specifically increases ventricular contractility which drives atrial enlargement, suggesting biomechanically driven atrial remodeling. ACTN4-associated phenotypes in both model systems lack hallmarks of cardiac disease models and an ACTN4 variant in humans is associated with reduced risk for disease. Our findings suggest a "non-muscle" actinin regulates heart contractility and influences clinical outcomes related to heart failure.

cell biology↗

bioRxiv2024

Successful establishment of an exogenous gene expression system in Chlamydomnas chloroplast based on viral replication elements

Currently, transformation in unicellular green alga (Chlamydomonas reinhardtii) chloroplast is hindered by a low yield of target products, possibly due to the heterogeneity of the chloroplast genome. In this study, an expression platform was established in C. reinhardtii by leveraging replicative elements from beet curly top geminivirus, which led to a high level of heterologous gene expression, as previously reported in Nicotiana tabacum. Platform performance was verified by the successful expression of a linearized mvenus cassette, achieving a higher expression level than that obtained using the homologous-recombination-based approach. This study provides a new strategy in microalgae synthetic biology and opens new avenue for accumulating valuable bioproducts at high concentrations.

synthetic biology↗

bioRxiv2024

Intraspecific and intraindividual trait variability decrease with tree species richness in a subtropical tree biodiversity experiment

Phenotypic variability within tree species responds to local tree species richness. However, we lack evidence on how different sources of trait variation shape tree-tree interactions. Along a diversity gradient from one to eight tree species, we sampled 4,568 leaves from 381 trees to study changes in intraspecific and intraindividual leaf trait variability and assessed their contribution to community functional diversity. Intraspecific variability decreased with tree species richness, while intraindividual variability barely responded. Functional overlap between conspecific trees increased with tree species richness and through intraindividual variation, but was reduced through intraspecific variability, meaning that intraspecific variability may reduce intraspecific competitive interactions while intraindividual variability could arise due to varying microenvironmental conditions within the canopy. Last, intraspecific and intraindividual variability explained high community functional richness and divergence, respectively, especially in mixtures. Our findings emphasize that fine-scale variability influences tree-tree interactions and can be a driver of local functional diversity. TeaserTrait variability within tree species decreases with diversity and explains high forest functional diversity.

ecology↗

bioRxiv2024

A pair of congenic mice for imaging of transplants by positron emission tomography using anti-transferrin receptor nanobodies

Two anti-transferrin receptor (TfR) nanobodies, VHH123 specific for mouse TfR and VHH188 specific for human TfR (huTfR) were used to track transplants non-invasively by PET/CT in mouse models, without the need for genetic modification of the transferred cells. We provide a comparison of the specificity and kinetics of the PET signals acquired when using nanobodies radiolabeled with 89Zr, 64Cu and 18F, and find that the chelation of the 89Zr and 64Cu radioisotopes to anti-TfR nanobodies results in radioisotope release upon endocytosis of the radiolabeled nanobodies. We used a knock-in mouse that expresses a TfR with a human ectodomain (huTfR +/+) as a source of bone marrow for transplants into C57BL/6 recipients and show that VHH188 detects such transplants by PET/CT. Conversely, C57BL/6 bone marrow and B16.F10 melanoma cell-line transplanted into huTfR +/+ recipients can be imaged with VHH123. In C57BL/6 mice impregnated by huTfR+/+ males we saw an intense VHH188 signal in the placenta, showing that TfR-specific VHHs accumulate at the placental barrier but do not enter the fetal tissue. We were unable to observe accumulation of the anti-TfR radiotracers in the central nervous system (CNS) by PET/CT but show evidence of CNS accumulation by radiospectrometry. The model presented here can be used to track many transplanted cell types by PET/CT, provided cells express TfR, as is typically the case for proliferating cells such as tumor lines.

immunology↗

bioRxiv2024

Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities

Allele-sharing dissimilarity (ASD) statistics are measures of genetic differentiation for pairs of individuals or populations. Given the allele-frequency distributions of two populations--possibly the same population--the expected value of an ASD statistic is computed by evaluating the expectation of the pairwise dissimilarity between two individuals drawn at random, each from its associated allele-frequency distribution. For each of two ASD statistics, which we term [D]1 and [D]2, we investigate the extent to which the expected ASD is constrained by allele frequencies in the two populations; in other words, how is the magnitude of the measure bounded as a function of the frequency of the most frequent allelic type? We first consider dissimilarity of a population with itself, obtaining bounds on expected ASD in terms of the frequency of the most frequent allelic type in the population. We then examine pairs of populations that might or might not possess the same most frequent allelic type. Across the unit interval for the frequency of the most frequent allelic type, the expected allele-sharing dissimilarity has a range that is more restricted than the r0, 1s interval. The mathematical constraints on expected ASD assist in explaining a pattern observed empirically in human populations, namely that when averaging across loci, allele-sharing dissimilarities between pairs of individuals often tend to vary only within a relatively narrow range.

genetics↗

bioRxiv2024

Green Elegance T2T: An upgraded telomere-to-telomere genome assembly and annotation of looseleaf lettuce (Lactuca sativa var. crispa)

Lettuce (Lactuca sativa L.), a globally important vegetable crop, is cultivated in various horticultural varieties. Looseleaf lettuce is one of the main varieties that are consumed. Here, we report a telomere-to-telomere (T2T) genome assembly of looseleaf lettuce (L. sativa var. crispa cv. Green Elegance). By combining the sequencing data of previously reported Green Elegance v1.2, the 42.20 Gb clean ultra-long reads produced by Oxford Nanopore Technology were used to close the gaps and upgrade the genome assembly. After filling 11 gaps in Green Elegance v1.2, the final gapless telomere-to-telomere genome assembly is 2.58 Gb in length with a contig N50 of 282.47 Mb, containing nine centromeres and 18 telomeres. The genome contained 41,375 protein-coding genes, of which 99.10% were functionally annotated. This T2T genome of looseleaf lettuce will be valuable for the identification of genetic variation and the advancement of lettuce breeding.

genomics↗

bioRxiv2024

Oncogene-induced senescence and senescence-associated secretory phenotype (SASP) determine the efficacy of palbociclib in PIK3CA mutated colorectal cancer

Palbociclib is an excellent CDK4/6 inhibitor, but its clinical application is mainly limited to the treatment of advanced ER+/HR+ and HER2- breast cancer. Its efficacy in colorectal cancer (CRC) is evaluated in multiple trials and so far remains undetermined. We found that the PIK3CA-mutant CRC cells were insensitive to palbociclib treatment compared with the PIK3CA wild-type counterparts, and they were in an OIS (oncogene-induced senescence) state which was predisposed to a strong senescence-associated secretory phenotype (SASP) upon treatment. These senescent cells excessively secreted various SASP factors LCN2, and ultimately caused palbociclib-resistance via upregulation of EGFR in the non-senescent CRC cells. Importantly, a drug combination screen identified that erlotinib could synergize with palbociclib to overcome the SASP-induced resistance. Overall, we found that PIK3CA mutation-induced senescence compromised the efficacy of palbociclib treatment in CRC but co-targeting EGFR could minimize the OIS-associated side effects while preserving the beneficial effects.

cancer biology↗

bioRxiv2024

Natural variations of TaMYB7-A1 regulate PHS resistance and specify wheat geographic adaptation

Crop domestication tended to select against seed dormancy for uniform germination--raising risks of undesirable pre-harvest sprouting (PHS) -- but regulation of seed dormancy and PHS in wheat are grossly under-characterized. Here, we identified wheat PHS resistance loci by GWAS. TaMYB7-A1 confers PHS resistance by elevating ABA signaling and seed dormancy in grains. Three TaMYB7-A1 haplotypes (Hap-1/2/3) contrast in PHS resistance, with Gly23 and Gly92 crucial for binding to and activating TaABI5 in Hap-1/3. A MITE transposon in the TaMYB7-A1Hap-1 promoter likely recruited the TaAZF1-TaABI4 module to boost expression, resulting in strong PHS resistance. TaMYB7-A1Hap-1 originated from wild einkorn and was integrated into hexaploid wheat through introgression into wild emmer. Different haplotypes of TaMYB7-A1, in conjunction with alleles of other major PHS resistance genes, is pivotal in shaping wheats adaptability to rainfall conditions in China, US and Europe during the harvest season. Introduction of TaMYB7-A1Hap-1 into elite cultivars confers PHS resistance without yield defects. Thus, artificial and natural selection across diverse climates regions have collectively shaped wheat adaptation and enabled rational delivery of improved lines tailored to local cropping needs.

plant biology↗

bioRxiv2024

Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps

Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum sensing is likely a key mechanism driving microbial interactions. However, the distribution, mechanisms, and ecological roles of quorum sensing in cold seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, and 18 metabolomes from 17 global cold seep sites. We identified 299,355 quorum sensing genes from the seep non-redundant gene catalog, representing 34 gene types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. These quorum sensing genes were present in 3,576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles of carbon, nitrogen, and sulfur. Phylogenetic analysis and protein domain identification highlighted the functional roles of key quorum sensing-related proteins (e.g., PDEs, CahR, RpfC/G and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression and metabolomic profiling further confirmed the activity of representative LuxI-R pairs and identified inhibitors of quorum sensing in cold seep sediments. Overall, these findings highlight complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere.

microbiology↗

bioRxiv2024

TopLib: Building and searching top-down mass spectral libraries for proteoform identification

Mass spectral library search is a widely used approach for spectral identification in mass spectrometry (MS)-based proteomics. While numerous methods exist for building and searching bottom-up mass spectral libraries, there is a lack of software tools for top-down mass spectral libraries. To fill the gap, we introduce TopLib, the first software package designed for building and searching top-down spectral libraries. TopLib utilizes an efficient spectral representation technique to reduce database size and improve query speed and performance. We systematically evaluated various spectral representation techniques and scoring functions for top-down spectral clustering and search. Our results demonstrated that TopLib is 140 times faster and achieves better reproducibility in proteoform identification compared with conventional database search methods in top-down MS.

bioinformatics↗

bioRxiv2024

Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism

Human stem cell-derived {beta} (SC-{beta}) cells still exhibit limited glucose response required for insulin secretion due to glycolytic bottlenecks, yet how these metabolic abnormalities impact glucose response and functional maturation of SC-{beta} cells remains unclear. In this study, we identified a metabolic checkpoint located at PEP accumulation that impeded the functional maturation, which was rescued by restoration of pyruvate kinase 1 (PKM1). Glucose-tracing metabolomics in human stem cell-derived islets revealed abnormal glycolytic PEP accumulation at resting condition, resulting in impaired calcium response and insulin secretion upon high glucose or glycolytic metabolite stimulation. Mechanistically, elevated PEP significantly raised intracellular basal calcium levels, leading to downregulated expression of genes involved in TCA cycle elucidated by single cell transcriptomics. Furthermore, the activity of pyruvate kinase, which metabolizes PEP, was notably reduced due to low PKM1 expression. By overexpressing PKM1, the impairment of TCA-related genes caused by PEP accumulation was reversed via modulating PEP metabolism, resulting in enhanced calcium responses and insulin secretion upon high glucose stimulation. Together, we discovered a novel role of PKM1-regulated PEP metabolism in mediating the functional maturation of human SC-{beta} cells. This study highlights the importance of metabolic reprogramming in human SC-{beta} cell maturation, advancing cell therapy approaches for diabetes treatment.

cell biology↗

bioRxiv2024

Accurate prediction of CRISPR editing outcomes in somatic cell lines and zygote with few-shot learning

The CRISPR-Cas system has revolutionized gene editing, while its outcome prediction remains unsatisfactory, especially in new cell states due to their distinct DNA repair preferences. In this study, we introduce inDecay, a flexible system for predicting CRISPR editing outcomes from target sequence, returning probabilities of nearly the full spectrum of indel events. Uniquely, inDecay utilizes informative and parameter-efficient features for each indel event and incorporates cell-type-specific repair preferences through a multi-stage design. While both inDecay and existing methods achieve accurate results for prediction within cell lines, only inDecay with transfer learning can retain the high performance for cross-cell line prediction. We then applied inDecay to mouse embryo editing using our newly generated data and observed remarkable accuracy by including as few as 30 fine-tuning embryonic samples. Notably, inDecay is the first software to predict embryonic editing. Therefore, our few-shot learning-supported system may accelerate guide RNA prioritization in mouse model generation, mammal embryonic gene editing, and cellular therapeutics.

bioinformatics↗

bioRxiv2024

Preprints vs. Journal Articles: Citation Impact in COVID-19 Research

Focusing on article and citation count, this study examined 110 academic journals whose papers on COVID-19 were indexed in PubMed from 2020 to 2023. To analyze these journals characteristics, this study introduced the concepts of paper ratio, citation ratio, and citation impact. Journals with similar trends in paper and citation count were positioned near the diagonal on a two-dimensional graph (y=x) with paper ratio on the x-axis and citation ratio on the y-axis, indicating a slope close to 1. Conversely, the greater the disparity between paper ratio and citation ratio, the wider the angle between the journals position and the diagonal. Of the 110 journals in 2020, 83 were above the diagonal with a citation impact greater than 1, while 27 were below the diagonal with a citation impact of 1 or lower. Notably, nine journals--BMC Health Services Research, Genome Medicine, Nature, Annals of Epidemiology, BMC Bioinformatics, Nature Microbiology, PLoS Computational Biology, Medicine (Baltimore), and Journal of Clinical Investigation--showed high citation impact, with preprint-distributed papers being cited nearly five times more than directly submitted papers. This study demonstrates that articles initially distributed as preprints in these journals tend to receive substantially more citations than directly submitted ones.

scientific communication and education↗

bioRxiv2024

Biophysical Basis of Paracellular Barrier Modulation by a Pan-Claudin-Binding Molecule

Claudins are a 27-member protein family that form and fortify specialized cell contacts in endothelium and epithelium called tight junctions. Tight junctions restrict paracellular transport across tissues by forming molecular barriers between cells. Claudin-binding molecules thus hold promise for modulating tight junction permeability to deliver drugs or as therapeutics to treat tight junction-linked disease. The development of claudin-binding molecules, however, is hindered by their intractability and small targetable surfaces. Here, we determine that a synthetic antibody fragment (sFab) we developed binds directly to 10 claudin subtypes with nanomolar affinity by targeting claudins paracellular-exposed surface. Application of this sFab to cells that model intestinal epithelium show that it opens the paracellular barrier comparable to a known, but application limited, tight junction modulator. This novel pan-claudin-binding molecule can probe claudin or tight junction structure and holds potential as a broad modulator of tight junction permeability for basic or translational applications.

biophysics↗