Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 397 records · Page 22Linked to original sources

bioRxiv2024

LAPTM4B Alleviates Pulmonary Fibrosis by Enhancing NEDD4L-Mediated TGF-beta Signaling Suppression

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with fatal outcome and a poorly understood pathogenesis. The lysosomal protein transmembrane 4 beta (LAPTM4B), a multi-transmembrane endo-lysosomal membrane protein, has been implicated in the pathogenesis of several diseases. However, its involvement in IPF remains unexplored. This study aimed to investigate the role of LAPTM4B in lung fibrosis and elucidate its underlying mechanisms. The results showed that LAPTM4B was significantly reduced in IPF and mouse fibrotic lungs. In vivo studies showed that the deficiency of LAPTM4B exacerbated bleomycin-induced lung fibrosis, while the restoration of LAPTM4B alleviated fibrosis. Mechanistically, LAPTM4B recruits the NEDD4 like E3 ubiquitin protein ligase (NEDD4L) to endosomes, leading to increased ubiquitin-mediated proteasomal degradation of TGFRB2 and active SMAD2/3, thereby blocking the TGF-{beta}/SMAD signaling pathway. Overall, our data provided a novel insight for a deeper understanding of the pathogenesis of IPF, supporting the therapeutic potential of restoration of LAPTM4B as a promising therapeutic approach for the treatment of pulmonary fibrosis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/610429v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@1272d12org.highwire.dtl.DTLVardef@10030baorg.highwire.dtl.DTLVardef@17f1756org.highwire.dtl.DTLVardef@d54f78_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Accurate antibody loop structure prediction enables zero-shot design of target-specific antibodies

Protein loops, characterized by their versatile structures with varying sizes and shapes, can recognize a wide range of targets with high specificity and affinity. The variable loops of the antibody complementarity-determining region (CDR) are particularly crucial for immune responses and therapeutic applications due to their effective target recognition capabilities. Accurate structure prediction of these antibody loops is essential for the efficient in silico design of target-binding antibodies for therapeutic or industrial use. However, predicting antibody loop structures is challenging due to the lack of evolutionary information from related proteins. Thus, a successful ab initio structure prediction method, which operates without structural templates or related sequences, is crucial for the effective design of antibody loop-mediated interactions. This study demonstrates that highly accurate antibody loop structure prediction enables the effective zero-shot design of target-binding antibody loops. The performance of loop design has been shown to depend on the accuracy of ab initio loop structure prediction, as tested with two versions of our design model. The high affinity, diversity, novelty, and specificity of the antibody loops designed with these new methods were validated experimentally on four target proteins.

bioengineering↗

bioRxiv2024

Inflammatory Signatures of Microglia in the Mouse Model of Corticosterone-Induced Depression

Microglia-mediated inflammation has been recognized as a key feature of major depressive disorder. Although hypercortisolemia commonly occurs in depressed patients and can be predictive of treatment response, how chronic exposure to this stress hormone influences microglia is incompletely characterized. Here, we exploited a standard mouse model of depressive-like behaviors induced by peripheral administration of corticosterone. Microglia in the prefrontal cortex of mice were profiled by bulk RNA sequencing, which exhibited the up-regulation of inflammatory markers. In addition, single-cell RNA sequencing identified distinct molecular patterns of microglial responses. Moreover, we revealed the elevation of Pu.1 and Irf8, the two central transcription factors governing microglia-mediated inflammation, in the prefrontal cortex and hippocampus of corticosterone-treated mice, which was similarly observed in the single-nucleus RNA sequencing dataset of depressed patients microglia. These results have established inflammatory signatures of microglia in the mouse model recapitulating hypercortisolemia-related depression, providing new insights into diagnostic and therapeutic strategies.

neuroscience↗

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

Phased chromosome-level genome assembly provides insight into the origin of hexaploid sweetpotato

The hexaploid sweetpotato (Ipomoea batatas [L.] Lam.) is a globally important stable crop and plays a significant role in biofortification. The high resilience and adaptability of sweetpotato provide it with advantages in addressing food security and climate change issues. Here we report a haplotype-resolved chromosome-level genome assembly of an African cultivar, Tanzania, which enables ancestry inference along the haplotype-phased chromosomes. Our analyses reveal that the wild tetraploid I. aequatoriensis, currently found in coastal Ecuador, is the closest known relative of sweetpotato and likely a direct descendant of one of the sweetpotato progenitors. The other unknown progenitor(s) of sweetpotato have a closer genetic relationship to the wild tetraploid I. batatas 4x, distributed in Central America, than to I. aequatoriensis. The different ancestral sequences are not distributed in typical subgenomes but are intertwined on the same chromosomes, possibly due to the known non-preferential recombination among haplotypes. Although I. batatas 4x was not involved in the hexaploidization event, introgression from I. batatas 4x to the hexaploid sweetpotato is evident. Our study improves our understanding of sweetpotato origin and provides valuable genomic resources to accelerate sweetpotato breeding.

plant biology↗

bioRxiv2024

Transcriptomic signatures of mouse ovarian aging and estropausal transition at single cell resolution

Female reproductive aging affects fertility and overall health. Functional decline in mouse ovary during reproductive aging is accompanied by estrous cycle prolongation and cessation. However, the molecular mechanism underlying reproductive aging concomitant with such cycle changes remains unclear. Using single-cell transcriptomics, we characterized aging signatures in mouse ovaries across the reproductive lifespan ranging from reproductively young (regular cycle) through peri-estropause (regular vs. irregular cycles) to post-estropause age (acyclic). Reproductive aging significantly remodeled cell compositions and increased transcriptional heterogeneity, with more pronounced changes post-estropause, exhibiting coordinated alterations across cell types in the ovary. Genes undergoing monotonic changes during reproductive aging across cell types were consistently enriched in the conserved pathways of aging, including oxidative phosphorylation, stress responses, and proteostasis. Additionally, cell type-specific changes were identified including dysregulation of hormone synthesis in granulosa cells, alterations in collagen and hyaluronan metabolism in stromal and early theca cells, and functional decline of a unique phagocytosis-associated macrophage. Aging also led to a significant decrease in cell-cell communications, particularly between stromal and granulosa cells, and an increase in extracellular vesicle secretion. Furthermore, we found increased expression of the senescence marker Cdkn1a and senescence-associated secretory phenotype (SASP) factors during ovarian aging, especially in granulosa cells. Notably, most of these aging-associated changes were more pronounced in irregular cycling ovaries compared to the regular cycling counterparts at the same age during the peri-estropause stage, suggesting that aging-related molecular changes in the ovary drive the estropausal transition in mice.

bioinformatics↗

bioRxiv2024

FACT-(H3-H4) complex stimulates Pol activity to coordinate DNA synthesis with nucleosome assembly

Deficiencies in replication-coupled (RC) nucleosome assembly often lead to reduced DNA replication rate, but the precise mechanism underlying this process remains unsolved. Here, we discovered that H3-H4, but not H2A-H2B, mediates the interaction between FACT and the primase-polymerase complex DNA Pol . This interaction stimulates the DNA polymerase activity of Pol , and is indispensable for Okazaki fragment synthesis and replication fork progression. Moreover, the Pol1-N domain of Pol provides a specific binding site for FACT and H3-H4. Furthermore, CAF-1 and Rtt106-mediated replication-coupled nucleosome assembly pathways regulate this interaction. Together, we propose that the FACT-(H3-H4)-Pol interaction acts as a "Pre-Warning System" that regulates DNA replication, ensuring proper coordination between DNA synthesis and nucleosome assembly.

molecular biology↗

bioRxiv2024

A modified decision tree improves generalization across multiple brains proteomic data sets and reveals the role of ferroptosis in Alzheimer disease

Low generalization to the patient cohort and variety of experimental conditions in the proteomic search for disease biomarkers are among the main reasons for the bumpy road of quantitative proteomics from discovery stage to clinical validation. Only a small fraction of biomarkers discovered so far by proteomic analysis reaches clinical trials. Here, we presented a machine learning-based workflow for proteomics data analysis, which partially solves some of these issues. In particular, we used a customized decision tree model, which was regulated using a newly introduced parameter, min_cohorts_leaf, that resulted in better generalization of trained models. Further, we analyzed the trend of feature importances curve as a function of min_cohorts_leaf parameter and found that it could be used for accurate feature selection to obtain a list of proteins with significantly improved generalization. Finally, we demonstrated that the recently introduced DirectMS1 search algorithm for protein identification and quantitation provides a simple, yet, a highly efficient solution for the problem of combining multiple data sets obtained using different experimental settings. The developed workflow was tested using five published LC-MS/MS data sets obtained in the large consortia studies of Alzheimers disease brain samples. The selected data sets consist of 535 files in total analyzed using label-free single-shot data-dependent or data-independent acquisitions. Using the proposed modified ExtraTrees model we found that the expressions of two proteins involved in ferroptosis Serotransferrin TRFE and DNA repair nuclease/redox regulator APEX1, are important for explaining a lack of dementia for patients with the presence of neuritic plaques and neurofibrillary tangles.

molecular biology↗

bioRxiv2024

VSTM2L protects prostate cancer cells against ferroptosis via inhibiting VDAC1 oligomerization and maintaining mitochondria homeostasis

Mitochondria play a critical role in initiating and amplifying ferroptosis. VDAC1 embedded in the mitochondrial outer membrane, exerts a crucial role in regulation of ferroptosis. However, the mechanisms of VDAC1 oligomerization in regulating ferroptosis are not well elucidated. Here, we identified that VSTM2L, a novel VDAC1 binding protein, is positively associated with prostate cancer (PCa) progression, and a key regulator of ferroptosis. Moreover, VSTM2L knockdown in PCa cells enhanced the sensibility of RSL3-induced ferroptosis. Mechanistically, VSTM2L forms complex with VDAC1 and HK2, enhancing their binding affinity and preventing VDAC1 oligomerization, thereby inhibiting ferroptosis and maintaining mitochondria homeostasis in vitro and in vivo. Collectively, our findings reveal a pivotal role for VSTM2L in driving ferroptosis resistance and highlight its potential as a ferroptosis-inducing therapeutic target for the treatment of PCa.

cancer biology↗

bioRxiv2024

Loss of RREB1 reduces adipogenesis and improves insulin sensitivity in mouse and human adipocytes

There are multiple independent genetic signals at the Ras-responsive element binding protein 1 (RREB1) locus associated with type 2 diabetes risk, fasting glucose, ectopic fat, height, and bone mineral density. We have previously shown that loss of RREB1 in pancreatic beta cells reduces insulin content and impairs islet cell development and function. However, RREB1 is a widely expressed transcription factor and the metabolic impact of RREB1 loss in vivo remains unknown. Here, we show that male and female global heterozygous knockout (Rreb1+/-) mice have reduced body length, weight, and fat mass on high-fat diet. Rreb1+/- mice have sex- and diet-specific decreases in adipose tissue and adipocyte size; male mice on high-fat diet had larger gonadal adipocytes, while males on standard chow and females on high-fat diet had smaller, more insulin sensitive subcutaneous adipocytes. Mouse and human precursor cells lacking RREB1 have decreased adipogenic gene expression and activated transcription of genes associated with osteoblast differentiation, which was associated with Rreb1+/- mice having increased bone mineral density in vivo. Finally, human carriers of RREB1 T2D protective alleles have smaller adipocytes, consistent with RREB1 loss-of-function reducing diabetes risk.

physiology↗

bioRxiv2024

The connectional diaschisis and normalization of cortical language network dynamics after basal ganglia and thalamus stroke

Stroke affecting the basal ganglia and thalamus can lead to language deficits. In addition to the lesions direct impact on language processing, connectional diaschisis involving cortical-subcortical interactions also plays a critical role. This study investigated connectional diaschisis using the "dynamic meta-networking framework of language" in patients with basal ganglia and thalamus stroke, analyzing longitudinal resting-state fMRI data collected at 2 weeks (n = 32), 3 months (n = 19), and one year post-stroke (n = 23). As expected, we observed dynamic cortico-subcortical interactions between cortical language regions and subcortical regions in healthy controls (HC, n = 25). The cortical language network exhibited dynamic domain-segregation patterns in HCs, severely disrupted in the acute phase following stroke. The connectional diaschisis manifested as dual effects characterized by both hypo- and hyper-connectivity, which positively and negatively correlated with language deficits, respectively. State-specific changes in nodal and topological properties were also identified. Throughout language recovery, cortical language network dynamics gradually normalized toward sub-optimal domain-segregation patterns, accompanied by the normalization of nodal and topological properties. These findings underscore the crucial role of cortico-subcortical interactions in language processing.

neuroscience↗

bioRxiv2024

Active Learning-Assisted Directed Evolution

Directed evolution (DE) is a powerful tool to optimize protein fitness for a specific application. However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior. Here, we present Active Learning-assisted Directed Evolution (ALDE), an iterative machine learning-assisted DE workflow that leverages uncertainty quantification to explore the search space of proteins more efficiently than current DE methods. We apply ALDE to an engineering landscape that is challenging for DE: optimization of five epistatic residues in the active site of an enzyme. In three rounds of wet-lab experimentation, we improve the yield of a desired product of a non-native cyclopropanation reaction from 12% to 93%. We also perform computational simulations on existing protein sequence-fitness datasets to support our argument that ALDE can be more effective than DE. Overall, ALDE is a practical and broadly applicable strategy to unlock improved protein engineering outcomes.

bioengineering↗

bioRxiv2024

Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH

Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report on structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early-stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.

biochemistry↗

bioRxiv2024

Nuclear FAK aggravates CD8+ T cell exhaustion via the SP1-IL-6 axis in colorectal cancer

Nuclear abnormalities such as nuclear deformation are hallmarks of many diseases, including cancer. Accumulating evidence suggests that the dense and mechanically stiff tumor microenvironment promotes nuclear deformation in cancer cells. However, little is known about how nuclear deformation in neoplastic cells regulates immune exhaustion in the tumor microenvironment. Here, we found that lamin A/C-mediated nuclear stiffening in neoplastic cells promotes the nuclear translocation of phosphorylated focal adhesion kinase (pFAK), which is strongly correlated with the heterogeneity and exhaustion of CD8+ T cells within the spatial context of the tumor microenvironment in human colorectal cancer. Mechanistically, we revealed that increased nuclear tension within tumor cells promotes pFAK nuclear translocation, where nuclear pFAK was found to regulate SP1/IL-6-mediated T-cell exhaustion and the transcription of proinflammatory cytokines/chemokines. Pharmacological inhibition or disruption of pFAK nuclear translocation enhanced antitumor immune responses and synergistically potentiated PD-1 and TIM-3 immunotherapy by increasing CD8+ T-cell cytotoxicity and restoring exhaustion in preclinical models of colorectal cancer. These findings highlight the pivotal role of nuclear tension-mediated pFAK translocation into the tumor cell nucleus in regulating CD8+ T-cell exhaustion, suggesting that pFAK is a promising target for advancing cancer immunotherapy.

immunology↗

bioRxiv2024

Freestanding rGO electrodes with tunable porous structures for improved neural recording

Invasive neural electrodes prepared from materials with miniaturized geometrical size could improve the longevity of implants by reducing the chronic inflammatory response. Graphene-based microfibers with tunable porous structures have a large electrochemical surface area (ESA)/geometrical surface area (GSA) ratio that has been reported to possess low impedance and high charge injection capacity (CIC), yet the control of the porous structure remains to be fully investigated. In this study, we introduce wet-spun graphene-based electrodes with pores tuned by sucrose concentrations in the coagulation bath. The electrochemical properties of thermally reduced rGO were optimized by adjusting the ratio of rGO to sucrose, resulting in significantly lower impedance, higher CIC, and higher charge storage capacity (CSC) than platinum microwires. Tensile and insertion tests confirmed that optimized electrodes had sufficient strength to ensure a 100% insertion success rate with low angle shift, thus allowing precise implantation without the need for additional mechanical enhancement. Acute in-vivo recordings from the auditory cortex found low impedance benefits from the recorded amplitude of spikes, leading to an increase in the signal-to-noise ratio (SNR). Ex-vivo recordings from hippocampal brain slices demonstrate that it is possible to record and/or stimulate with graphene-based electrodes with good fidelity compared with conventional electrodes.

neuroscience↗

bioRxiv2024

How do we imagine a speech? A triple network model for situationally simulated inner speech

Inner speech is a silent verbal experience and plays central roles in human consciousness and cognition. Despite impressive studies over the past decades, the neural mechanisms of inner speech remain largely unknown. In this study, we adopted an ecological paradigm called situationally simulated inner speech. Unlike mere imaging speech of words, situationally simulated inner speech involves the dynamic integration of contextual background, episodic and semantic memories, and external events into a coherent structure. We conducted dynamic activation and network analyses on fMRI data, where participants were instructed to engage in inner speech prompted by cue words across 10 different contextual backgrounds. Our seed-based co-activation pattern analyses revealed dynamic involvement of the language network, sensorimotor network, and default mode network in situationally simulated inner speech. Additionally, frame-wise dynamic conditional correlation analysis uncovered four temporal-reoccurring states with distinct functional connectivity patterns among these networks. We proposed a triple network model for deliberate inner speech, including language network for a truncated form of overt speech, sensorimotor network for perceptual simulation and monitoring, and default model network for integration and sense-making processing. HighlightsO_LIIn ten contextual backgrounds, subjects were instructed to perform situationally simulated inner speech based on cue words. C_LIO_LIThe ventral parts of the bilateral somatosensory areas and middle superior temporal gyrus were as centers for seed-based co-activation pattern analyses. C_LIO_LIA triple network model of language network, sensorimotor network, and default mode network was proposed for deliberate inner speech. C_LI

neuroscience↗

bioRxiv2024

Elevational constraints on flight efficiency shape global gradients in avian wing morphology

Wings with elongated shape or larger surface area are associated with increased flight efficiency and dispersal ability in a wide range of animals from insects to birds 1-4. Inter- and intraspecific variation in these attributes of wing shape is determined by a range of factors - including foraging ecology, migration and climatic seasonality 5-8 - all of which may drive latitudinal gradients in wing morphology 9,10. A separate hypothesis predicts that wing shape should also follow an elevational gradient because air density and oxygen supply decline with altitude 11, altering the aerodynamics of flight, and driving the evolution of more efficient wings in high-elevation species to compensate for reduced lift 12,13. However, previous analyses have found only mixed support for the thin-air hypothesis 14-18, and we currently lack a global synthesis of elevational gradients in wing design for any taxonomic group. In this study, we use phylogenetic comparative models to explore elevational effects on wing morphology in 9986 bird species, while accounting for multiple climatic and ecological attributes, including latitude, temperature seasonality, body mass, aerial lifestyle and migration. We found that relative wing elongation (hand-wing index) and wing area increase with elevation, particularly in the upper montane zone (>4 km above sea level). These results confirm a pervasive elevational gradient in avian wing morphology, highlighting the role of aerodynamic constraints as key mechanisms shaping global patterns of trait evolution in flying animals.

evolutionary biology↗

bioRxiv2024

Single-cell resolved differentiation of pre-Kranz anatomy in maize leaf primordia

Typical C4 plants such as maize possess highly optimized Kranz-type leaf anatomy, whereby concentric wreaths of mesophyll and bundle sheath cells surround closely spaced veins. The veins and the cells that surround them are derived from the middle ground meristem (mGM) through processes that are as yet undefined. Here we distinguished the active zone of vascular development within early leaf primordia, and used comparative transcriptomics of sub-sectioned maize and rice primordia to identify cohorts of genes likely involved in early Kranz development. Leveraging single-nucleus RNA sequencing (snRNA-seq) we then explored the cell heterogeneity and developmental trajectories within single maize leaf primordia. Assisted by in situ hybridization, cell clusters of mGM and procambium were identified, with candidate marker genes showing different yet inter-related expression patterns. Localization of the vascular marker ZmSHR1 was preceded by that of ZmEREB161 and ZmEREB114 in terms of procambium initiation. Potential subclusters of bundle sheath cells and different layer of mesophyll cells were depicted from developing cells toward the tip of sub-sectioned maize primordia. Collectively our results identify potential mGM derived or procambium localized Kranz regulators and provide resources for investigating leaf vein development in maize and rice, at sub-primordium and single-cell resolution.

plant biology↗