Biology subjects

Cao, C.

Publications and source records attributed to Cao, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Landscape of Differentiation Potentials as a "Hallmark" in Oral-derived MSCs

BackgroundMesenchymal stem cells (MSCs) offer clinical promise for use in cell therapy approaches for regenerative medicine. A therapeutic challenge is that MSCs from different tissues are phenotypically and functionally distinct. Therefore, this study aims to molecularly characterize oral-derived MSCs by defining one of the three hallmarks of MSCs, differentiation potential, to discern their true molecular identities. MethodsThree different populations of oral tissue MSCs (from alveolar bone-aBMSCs; from dental pulp-DPSCs; and from gingiva-GMSCs) from three different patients were isolated and cultured. These MSCs were characterized for their stemness by flow cytometry and multi-differentiation potential, and their RNA was also isolated and analyzed quantitatively with RNA sequencing. Total mRNA-seq was performed and differentially expressed genes (DEGs) were identified in pairwise (DPSCs vs. aBMSCs, GMSCs vs. aBMSCs, and GMSCs vs. DPSCs) and tissue-specific comparisons (aBMSCs vs. Others, DPSCs vs. Others, GMSCs vs. Others) (FDR, p<0.05). Further, these DEGs, either common between MSC populations or unique to a specific MSC population, were evaluated for pathways and biological processes ResultsaBMSCs, DPSCs, and GMSCs were successfully isolated and characterized. The tissue-specific comparison revealed that DEGs were most numerous in DPSCs (693 genes) as compared to aBMSCs (103 genes) or DPSCs (232 genes). Statistically significant DEGs through pairwise comparisons present higher numbers in GMSCs vs. DPSCs (627) as compared to either DPSCs vs aBMSCs (286) or GMSCs vs. aBMSCs (82). Further analysis found that RUNX2, IBSP, SOX6, ACAN, and VCAM1 were significantly upregulated in aBMSCs. In DPSCs, BMP4 and IL6 were significantly downregulated, whereas AXL and NES were significantly upregulated. In GMSCs, AGPT1, SEMA4D, and PGDFA were significantly downregulated. Additionally, MAPK, PI3-AKT, and RAS signaling pathways were significantly regulated in GMSCs. Interestingly, aBMSCs and DPSCs revealed positive regulation of osteoblast differentiation, whereas GMSCs revealed negative regulation of osteoblast differentiation. DPSCs also revealed negative regulation of angiogenesis. ConclusionsOral-derived MSCs have an inherent "landscape" of differentiation defined by their tissue of origin; yet this differentiation potential can be modulated by their microenvironment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/606413v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@60aeceorg.highwire.dtl.DTLVardef@17480a2org.highwire.dtl.DTLVardef@1a9315aorg.highwire.dtl.DTLVardef@e74d30_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

TurboID-mediated surface protein biotinylation to inhibit the growth of Staphylococcus aureus

Staphylococcus aureus (S. aureus) infection is major cause of nosocomial infections. Antibiotic treatment for S. aureus remains the primary solution for managing S. aureus infections, which, however, increases the risk of antibiotic resistance. To broaden the resolutions on S. aureus infection, here we report TurboID-mediated protein proximity technologies to inhibit the growth of S. aureus. To achieve this goal, we utilized synthetic biology techniques to create a fusion protein named N-AgrD-TurboID (Agr-ID). The N-AgrD domain includes auto-inducer peptide (AIP) which combined to the surface AgrC protein on S. aureus. As such, TurboID then catalyzed the production of biotinoyl-5-AMP anhydride, triggering the biotinylation of surface proteins on S. aureus 25923 which were visualized by using fluorescence microscopy after incubating with Alexa Fluor 647-conjugated streptavidin. The biotinylation of surface protein on S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA) also resulted in growth inhibition and impaired colonization. Moreover, the biotinylation on surface protein further inhibited virulence protein production in S. aureus 25923, as indicated by reduced apoptosis of HEK 293T cells after treatment with S. aureus 25923 lysates. Overall, our work reveals that the biotinylation of surface proteins can inhibit the growth and toxicity of S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA), indicating therapeutic potential in clinical treatment.

microbiology↗

bioRxiv2024

Multi-omic Landscape of Extracellular Vesicles in Human Carotid Atherosclerotic Plaque Reveals Endothelial Communication Networks

Background: Carotid atherosclerosis is orchestrated by cell-cell communication that drives progression along a clinical continuum (asymptomatic to symptomatic). Extracellular vesicles (EVs) are cell-derived nanoparticles representing a new paradigm in cellular communication. Little is known about their biological cargo, cellular origin/destination, and functional roles in human atherosclerotic plaque. Methods: EVs were enriched via size exclusion chromatography from human carotid endarterectomy samples dissected into paired plaque and marginal zones (symptomatic n=16, asymptomatic n=13). EV cargos were assessed via whole transcriptome miRNA sequencing and mass spectrometry-based proteomics. EV multi-omics were integrated with bulk and single cell RNA-sequencing (scRNA-seq) datasets to predict EV cellular origin and ligand-receptor interactions, and multi-modal biological network integration of EV-cargo was completed. EV functional impact was assessed with endothelial angiogenesis assays. Results: Carotid plaques contained more EVs than adjacent marginal zones, with differential enrichment for EV-miRNAs and EV-proteins in key atherogenic pathways. EV cellular origin analysis suggested that tissue EV signatures originated from endothelial cells (EC), smooth muscle cells (SMC), and immune cells. Integrated tissue vesiculomics and scRNA-seq indicated complex EV-vascular cell communication that changed with disease progression and plaque vulnerability (i.e., symptomatic disease). Plaques from symptomatic patients, but not asymptomatic patients, were characterized by increased involvement of endothelial pathways and more complex ligand-receptor interactions, relative to their marginal zones. Plaque-EVs were predicted to mediate communication with ECs. Pathway enrichment analysis delineated an endothelial signature with roles in angiogenesis and neovascularization - well-known indices of plaque instability. This was validated functionally, wherein human carotid symptomatic plaque EVs induced sprouting angiogenesis in comparison to their matched marginal zones. Conclusion: Our findings indicate that EVs may drive dynamic changes in plaques through EV- vascular cell communication and effector functions that typify vulnerability to rupture, precipitating symptomatic disease. The discovery of endothelial-directed angiogenic processes mediated by EVs creates new therapeutic avenues for atherosclerosis.

cell biology↗

bioRxiv2024

Generators of the frequency-following response in the subthalamic nucleus: implications for non-invasive deep brain stimulation

While Deep Brain Stimulation (DBS) is effective treatment for several movement disorders, non-invasive stimulation modes have major clinical relevance. We report on a novel method holding potential for non-invasive subthalamic nucleus (STN) stimulation. We used an auditory frequency-following response task (FFR), a popular tool for studying the auditory brainstem as the neural response in the cortical and midbrain generator, as it precisely reflects the ongoing dynamics of a speech or non-speech sound. We recorded EEG and DBS electrodes from 5 patients, in 4 from the STN, and one from the anterior thalamus and a number of cortical and subcortical areas located in the hippocampus and frontal regions, during an FFR at a frequency higher than the upper limit of phase-locking in the cortex (333Hz). Our results revealed a neural response local to the STN, but not other structures. This finding is novel. Auditory perception in the basal ganglia is rather unexplored, and the STN generator of the FFR has likely gone unseen due to the limitations of our tools and research focus. The potential clinical implications are far-reaching. Future research should investigate whether auditory stimuli at common electrical stimulation frequencies and waveforms of electrical DBS stimulation can induce clinical improvement.

neuroscience↗

bioRxiv2024

Exploring new nanopore sensors from the aerolysin family

Aerolysin-like proteins are a family of {beta}-pore-forming toxins which are widely present in all kingdoms of life. Recently, this family of proteins is gaining attention because of their biotechnological application as nanopore sensors for sensing and sequencing of biomolecules. Here, we explore the possibilities of using the knowledge of the sequence and structure of proteins to screen and explore new potential nanopore candidates. However, in spite of the conserved structural fold, the sequence identity in this family is very low. This complicates their sequence alignment, hindering the understanding of their pore structure and properties, therefore limiting further biotechnological applications. In an attempt to further understand the properties of aerolysin-like pores, we analyzed the pore structure of three family members, Clostridium perfringens epsilon toxin (ETX), Laetiporus sulphureus lectin (LSL) and Bacillus thuringiensis parasporin-2, comparing it to aerolysin. Their structure and sensing capabilities for ssDNA were first assessed by in silico methods. Moreover, ETX was characterized experimentally in planar lipid membranes for the detection of biomolecules. We found that ETX can form three distinct pore conformations, each presenting a specific open pore current, and only one of them being able to translocate ssDNA. When the ssDNA translocate through ETX, the depth of current blockage is higher compared to aerolysin which indicates a higher sensitivity for molecular sensing. Our findings open a new venue for improving and diversifying nanopore capabilities for molecular sensing.

biophysics↗

bioRxiv2024

Long non-coding RNAs direct the SWI/SNF complex to cell-specific enhancers

The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control1. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a central role in cell type- and context-dependent gene expression2. Despite the absence of a defined DNA recognition motif, SWI/SNF binds lineage specific enhancers genome-wide where it actively maintains open chromatin state2-5. It does so while retaining the ability to respond dynamically to cellular signals4. However, the mechanisms that guide SWI/SNF to specific genomic targets have remained elusive. Here we demonstrate that trans-acting long non-coding RNAs (lncRNAs) direct the SWI/SNF complex to cell type-specific enhancers. SWI/SNF preferentially binds lncRNAs and these predominantly bind DNA targets in trans. Together they localize to enhancers, many of which are cell type-specific. Knockdown of SWI/SNF- and enhancer-bound lncRNAs causes the genome-wide redistribution of SWI/SNF away from enhancers and a concomitant differential expression of spatially connected target genes. These lncRNA-SWI/SNF-enhancer networks support an enhancer hub model of SWI/SNF genomic targeting. Our findings reveal a competitive recruitment of SWI/SNF by lncRNAs which provide a specific and dynamic layer of control in chromatin accessibility and gene expression.

molecular biology↗

bioRxiv2024

Single-molecule evidence of Entropic Pulling by Hsp70 chaperones

Hsp70 chaperones are central components of the cellular network that ensure the structural quality of proteins. Despite their crucial roles in processes as diverse as the prevention of protein aggregation and protein translocation into organelles, their molecular mechanism of action has remained a hotly debated issue. Due to a lack of suitable methods, no experimental data has directly proven any of the models that have been proposed (Power Stroke, Brownian Ratchet, and Entropic Pulling). Recently, nanopores have emerged as a powerful tool to analyze the function of motor enzymes, as well as protein-protein interactions. Here, we used an in vitro single-molecule nanopore to mimic in vivo translocation of proteins, and to investigate the molecular mechanism of Hsp70. Our experiments demonstrate that Hsp70s forcefully extract polypeptide substrates that are trapped inside the pore. The forces they exert are strong at the molecular level, being equivalent to 46 pN over distances of 1 nm, and depend on the size of Hsp70. These findings provide unambiguous evidence supporting the Entropic Pulling mechanism of action of Hsp70s, thus solving a long-standing debate, and proposing a potentially universal principle governing diverse cellular processes. In addition, these results emphasize the utility of biological nanopores for studying protein function at the single-molecule level.

biophysics↗

bioRxiv2024

Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe

Aerolysin is a bacterial pore-forming toxin able to form transmembrane pores at the host plasma membrane of narrow internal diameter and great stability. These assets make it a highly promising nanopore for the detection of biopolymers such as nucleic acids and peptides. While much is known about aerolysin from a microbiological and structural side, its membrane association and pore-formation mechanism are not yet fully disclosed. Here, we studied the interaction of femtomolar concentrations of aerolysin and its mutants with liposomes in aqueous solution using angle-resolved second harmonic scattering (AR-SHS), in combination with single-channel current measurements. The measurements were so sensitive to detect electrostatic changes on the membrane-bound aerolysin induced by pH variation induced by the changes in the hydration shell of aerolysin. We reported for the first time the membrane binding affinity of aerolysin at different stages of the pore formation mechanism: while wt aerolysin has a binding affinity as high as 20 fM, the quasi-pore state and the prepore state show gradually decreasing membrane affinities, incomplete insertion and pore opening signature. Moreover, we quantitatively characterized the membrane affinity of mutants relevant for applications to nanopore sensing. This approach opens new possibilities to efficiently screen biological pores suitable for conducting molecular sensing and sequencing measurements, as well as to probe pore forming processes.

biophysics↗

bioRxiv2023

Accelerating protein engineering with fitness landscape modeling and reinforcement learning

Protein engineering holds significant promise for designing proteins with customized functions, yet the vast landscape of potential mutations versus limited lab capacity constrains the discovery of optimal sequences. To address this, we present the {micro}Protein framework, which accelerates protein engineering by combining {micro}Former, a deep learning model for accurate mutational effect prediction, with {micro}Search, a reinforcement learning algorithm designed to efficiently navigate the protein fitness landscape using {micro}Former as an oracle. {micro}Protein leverages single mutation data to predict optimal sequences with complex, multi-amino acid mutations through its modeling of epistatic interactions and a multi-step search strategy. Except from state-of-the-art performance on benchmark datasets, {micro}Protein identified high-gain-of-function multi-point mutants for the enzyme {beta}-lactamase, surpassing the highest known activity level, in wet-lab, trained solely on single mutation data. These results demonstrate {micro}Proteins capability to discover impactful mutations across vast protein sequence space, offering a robust, efficient approach for protein optimization.

synthetic biology↗

bioRxiv2023

In vivo silencing of regulatory elements using a single AAV-CRISPRi vector

CRISPR-Cas9 based transcriptional repressors (CRISPRi) have emerged as specific and robust tools for functional epigenetic silencing of regulatory elements. Adeno-associated viruses (AAVs) are promising CRISPRi delivery vectors for cardiovascular research and therapy. However, compact vectors enabling codelivery of all CRISPRi components by a single AAV are needed for an enhanced and consistent performance. We engineered a 4.7kb all-in-one CRISPRi construct compatible with AAV-mediated delivery and produced cardiotropic AAVi 6 and 9 particles for in vitro and in vivo application, respectively. AAVi vectors targeting the Nppa promoter (AAViNppa) reduced gene expression in cultivated cardiomyocytes (HL-1 cells) in a dose-dependent manner. The maximum effect was a >95% reduction as measured by qPCR and RNA-seq. This effect was orchestrated by loss of chromatin accessibility (ATAC-seq) and establishment of heterochromatin (H3K9me3 ChIP-seq) specifically at the target promoter region. We confirmed the broad applicability of AAVi to different cardiomyocyte cell culture systems by silencing several genes in primary neonatal rat ventricular cardiomyocytes (NRVMs), human iPSC-derived cardioids and iPSC-CMs. To demonstrate the efficacy of AAVi in vivo we injected 8-week-old C57Bl/6 WT mice with a single dose of AAViNppa and implanted osmotic minipumps releasing Phenylephrine (50 mg/kg/d) and Angiotensin II (0.45 mg/kg/d) to induce Nppa transcription. AAViNppa silenced Nppa transcription as revealed by qPCR and single nuclei RNA-seq even under stress conditions. On the epigenome layer AAViNppa induced closed chromatin at the Nppa promoter site comparable to the in vitro effect. Here, we present an efficient AAV-based method for CRISPRi-mediated epigenetic silencing of gene expression in cardiac myocytes in vivo and in vitro. This functional epigenetic approach provides an efficient way to modulate gene expression in the heart and could become a standard method for cardiovascular disease modelling and translational research.

genomics↗

bioRxiv2023

Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore

Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both the spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish -synuclein-derived peptides bearing single or multiple PTMs, namely phosphorylation, nitration and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the -synuclein peptide and its PTM variants could be confidently identified using a deep learning model for signal processing. We further demonstrate that this framework can quantify -synuclein peptides at picomolar concentration and detect the C-terminal peptides generated by digestion of full-length -synuclein. Collectively, our work highlights the unique advantage of using nanopore as a tool for simultaneous detection of multiple PTMs and paves the way for their use in biomarker discovery and diagnostics.

biophysics↗

bioRxiv2023

A humoral stress response protects Drosophila tissues from antimicrobial peptides

The immune response against an invading pathogen is generally associated with collateral tissue damage caused by the immune system itself. Consequently, several resilience mechanisms have evolved to attenuate the negative impacts of immune effectors. Antimicrobial peptides (AMPs) are small, cationic peptides that contribute to innate defenses by targeting negatively charged membranes of microbes1, 2. While being protective against pathogens, AMPs can be cytotoxic to host cells1, 3. Little is known of mechanisms that protect host tissues from AMP-induced immunopathology. Here, we reveal that a family of stress-induced proteins, the Turandots4, 5, protect Drosophila host tissues from AMPs, increasing resilience to stress. Deletion of several Turandot genes increases fly susceptibility to environmental stresses due to trachea apoptosis and poor oxygen supply. Tracheal cell membranes expose high levels of phosphatidylserine, a negatively charged phospholipid, sensitizing them to the action of AMPs. Turandots are secreted from the fat body upon stress and bind to tracheal cells to protect them against AMPs. In vitro, Turandot A binds to phosphatidylserine on membranes and inhibits the pore-forming activity of Drosophila and human AMPs on eukaryotic cells without affecting their microbicidal activity. Collectively, these data demonstrate that Turandot stress proteins mitigate AMP cytotoxicity to host tissues and therefore improve their efficacy. This provides a first example of a humoral mechanism used by animals limiting host-encoded AMP collateral damages.

immunology↗

bioRxiv2023

Targeting CD301+ macrophage inhibits endometrial fibrosis and improves pregnancy outcome

Macrophages are a key and heterogeneous cell population involved in endometrial repair and regeneration during the menstrual cycle, but their role in the development of intrauterine adhesion (IUA) and sequential endometrial fibrosis remains unclear. Here, we reported that CD301+ macrophages were significantly increased and showed their most active interaction with profibrotic cells in the endometria of IUA patients compared with the normal endometria by single-cell RNA sequencing, bulk RNA sequencing and experimental verification. Increasing CD301+ macrophages promoted the differentiation of endometrial stromal cells into myofibroblasts and resulted in extracellular matrix accumulation, which destroyed the physiological architecture of endometrial tissue, drove endometrial fibrosis and ultimately led to female infertility or adverse pregnancy outcomes. Mechanistically, CD301+ macrophages secreted GAS6 to activate the AXL/NF-{kappa}B pathway, up-regulating the profibrotic protein synthesis. Targeted deletion of CD301+ macrophages or inhibition of AXL by Bemcentinib blunted the pathology and improved the outcomes of pregnancy in mice, supporting the therapeutic potential of targeting CD301+ macrophages for treating endometrial fibrosis.

immunology↗

bioRxiv2023

Longitudinal analysis of memory T follicular helper cells and antibody response following CoronaVac vaccination

The inactivated vaccine CoronaVac is one of the most widely used COVID-19 vaccines globally. However, the longitudinal evolution of the immune response induced by CoronaVac remains elusive compared to other vaccine platforms. Here, we recruited 88 healthy individuals that received 3 doses of CoronaVac vaccine. We longitudinally evaluated their polyclonal and antigen-specific CD4+ T cells and neutralizing antibody response after receiving each dose of vaccine for over 300 days. Both the 2nd and 3rd dose of vaccination induced robust spike-specific neutralizing antibodies, with a 3rd vaccine further increased the overall magnitude of antibody response, and neutralization against Omicron sub-lineages B.1.1.529, BA.2, BA.4/BA.5 and BA.2.75.2. Spike-specific CD4+ T cell and circulating T follicular helper (cTFH) cells were markedly increased by the 2nd and 3rd dose of CoronaVac vaccine, accompanied with altered composition of functional cTFH cell subsets with distinct effector and memory potential. Additionally, cTFH cells are positively correlated with neutralizing antibody titers. Our results suggest that CoronaVac vaccine-induced spike-specific T cells are capable of supporting humoral immunity for long-term immune protection.

immunology↗

bioRxiv2023

Ebola Virus Sequesters IRF3 in Viral Inclusion Bodies to Evade Host Antiviral Immunity

Viral inclusion bodies (IBs) commonly form during the replication of Ebola virus (EBOV) in infected cells, but their role in viral immune evasion has rarely been explored. Here, we found that interferon regulatory factor 3 (IRF3), but not TANK-binding kinase 1 (TBK-1) or I{kappa}B kinase epsilon (IKK{varepsilon}), was recruited and sequestered in viral IBs when the cells were infected by EBOV transcription- and replication-competent virus-like particles (trVLPs). NP/VP35-induced IBs formation was critical for IRF3 recruitment and sequestration, probably through interaction with STING. Consequently, the association of TBK1 and IRF3, which plays a vital role in type I interferon (IFN-I) induction, was blocked by EBOV trVLPs infection. Additionally, IRF3 phosphorylation and nuclear translocation induced by Sendai virus (SeV) or poly(I:C) stimulation were suppressed by EBOV trVLPs. Furthermore, downregulation of STING significantly attenuated VP35-induced IRF3 accumulation in IBs. Coexpression of the viral proteins by which IBs-like structures formed was much more potent in antagonizing IFN-I than expression of the IFN-I antagonist VP35 alone. These results suggested a novel immune evasion mechanism by which EBOV evades host innate immunity. Impact statementEbola virus VP35 protein evades host antiviral immunity by interacting with STING to sequester IRF3 into inclusion bodies and inhibit type-I interferon production.

microbiology↗

bioRxiv2023

Host and transmission route of Enterocytozoon hepatopenaei (EHP) from dragonfly to shrimp

Enterocytozoon hepatopenaei (EHP) is a shrimp pathogen that causes huge economic losses. In the present study, the hosts of EHP were investigated using polymerase chain reaction (PCR) in an aquaculture farm located in Maoming, China. EHP was detected in Litopenaeus vannamei, Penaeus monodon, crab, false mussel, and three dragonfly species (Anax parthenope, Pantala flavescens, and Ischnura senegalensis). In the histopathological examination using hematoxylin-eosin staining, EHP spores were found in nymphs and adult dragonflies naturally infected with EHP that were collected from the shrimp farm. Fluorescence in situ hybridization results showed a positive signal for EHP infection in the fat body of dragonfly nymphs. Immature and mature microsporidian spores and late sporogonial plasmodium were observed in the cytoplasm of dragonfly nymphs using transmission electron microscopy. The transmission of EHP from shrimp to dragonfly nymphs was confirmed via cohabitation challenge experiments in which EHP-free dragonfly nymphs were cohabited with EHP-infected shrimp, and the transmission of EHP from dragonfly nymphs to shrimp was demonstrated via the cohabitation of EHP-infected dragonfly nymphs with EHP-free shrimp and oral administration challenge experiments. This study confirms that dragonflies can act as natural EHP hosts, and a novel EHP horizontal transmission route exists between dragonflies and shrimp. Author summaryTo the authors knowledge, this study presents the first report of microsporidia (EHP) infecting both crustaceans and insects (A. parthenope, P. flavescens, and I. senegalensis). The horizontal transmission of EHP between dragonfly nymphs and shrimp was confirmed through cohabitation and oral administration challenge experiments. EHP has become a globally significant threat to shrimp aquaculture. The findings of the present study will help to design prevention strategies, such as the use of nets to prevent dragonflies from entering shrimp ponds.

microbiology↗

bioRxiv2023

CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization

Circular RNAs (circRNAs) play a significant role in some diseases by acting as transcription templates. Therefore, analyzing the interaction mechanism between circRNA and RNA-binding proteins (RBPs) has far-reaching implications for the prevention and treatment of diseases. Existing models for circRNA-RBP identification most adopt CNN, RNN, or their variants as feature extractors. Most of them have drawbacks such as poor parallelism, insufficient stability, and inability to capture long-term dependence. To address these issues, we designed a Seq_transformer module to extract deep semantic features and then propose a CircRNA-RBP identification model based on Sequence Self-attention with Pre-normalization. We test it on 37 circRNA datasets and 31 linear RNA datasets using the same set of hyperparameters, and the overall performance of the proposed model is highly competitive and, in some cases, significantly out-performs state-of-the-art methods. The experimental results indicate that the proposed model is scalable, transformable, and can be applied to a wide range of applications without the need for task-oriented fine-tuning of parameters. The code is available at https://github.com/cc646201081/CircSSNN. Author summaryIn this paper, we propose a new method completely using the self-attention mechanism to capture deep semantic features of RNA sequences. On this basis, we construct a CircSSNN model for the cirRNA-RBP identification. The proposed model constructs a feature scheme by fusing circRNA sequence representations with statistical distributions, static local context, and dynamic global context. With a stable and efficient network architecture, the distance between any two positions in a sequence is reduced to a constant, so CircSSNN can quickly capture the long-term dependence and extract the deep semantic features. Experiments on 37 circRNA datasets show that the proposed model has overall advantages in stability, parallelism, and prediction performance. Keeping the network structure and hyperparameters unchanged, we directly apply CircSSNN to linRNA datasets. The favorable results show that CircSSNN can be transformed simply and efficiently without task-oriented tuning. In conclusion, CircSSNN can serve as an appealing circRNA-RBP identification tool with good identification performance, excellent scalability, and wide application scope, which is expected to reduce the professional threshold required for hyperparameter tuning in bioinformatics analysis.

bioinformatics↗

bioRxiv2023

Increased Ca2+ signaling through CaV1.2 induces tendon hypertrophy with increased collagen fibrillogenesis and biomechanical properties

Tendons are tension-bearing tissues transmitting force from muscle to bone for body movement. This mechanical loading is essential for tendon development, homeostasis, and healing after injury. While Ca2+ signaling has been studied extensively for its roles in mechanotransduction, regulating muscle, bone and cartilage development and homeostasis, knowledge about Ca2+ signaling and the source of Ca2+ signals in tendon fibroblast biology are largely unknown. Here, we investigated the function of Ca2+ signaling through CaV1.2 voltage-gated Ca2+ channel in tendon formation. Using a reporter mouse, we found that CaV1.2 is highly expressed in tendon during development and downregulated in adult homeostasis. To assess its function, we generated ScxCre;CaV1.2TS mice that express a gain-of-function mutant CaV1.2 channel (CaV1.2TS) in tendon. We found that tendons in the mutant mice were approximately 2/3 larger and had more tendon fibroblasts, but the cell density of the mutant mice decreased by around 22%. TEM analyses demonstrated increased collagen fibrillogenesis in the hypertrophic tendon. Biomechanical testing revealed that the hypertrophic Achilles tendons display higher peak load and stiffness, with no changes in peak stress and elastic modulus. Proteomics analysis reveals no significant difference in the abundance of major extracellular matrix (ECM) type I and III collagens, but mutant mice had about 2-fold increase in other ECM proteins such as tenascin C, tenomodulin, periostin, type XIV and type VIII collagens, around 11-fold increase in the growth factor of TGF-{beta} family myostatin, and significant elevation of matrix remodeling proteins including Mmp14, Mmp2 and cathepsin K. Taken together, these data highlight roles for increased Ca2+ signaling through CaV1.2 on regulating expression of myostatin growth factor and ECM proteins for tendon collagen fibrillogenesis during tendon formation.

molecular biology↗