Biology subjects

Dai, Z.

Publications and source records attributed to Dai, Z..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Engineering novel AAV capsids by global de-targeting and subsequent muscle-specific tropism in mice and NHPs

Recombinant adeno-associated viral (rAAV) vectors are a potent tool, but their clinical application is restricted by insufficient target tissue transduction and liver toxicity. We employed a novel two-step engineering strategy to create novel rAAV capsids with global tissue de-targeting, then produced strong tissue-specific expression by adding a peptide sequence. We created a novel capsid, AAV.Zero1, with globally de-targeted transduction by loop swapping domains from AAV9 into AAV2. Making an R585A substitution (AAV.Zero2) re-targeted tissues but deleting residues 585-587 (AAV.Zero3) abrogated transduction. Inserting a myogenic peptide into AAV.Zero3 produced a novel capsid (AAV.eM) with strong muscle-specific transgene expression while maintaining minimal off-target expression, including in liver, which was conserved in two mouse strains and non-human primates. AAV.eM showed similar expression as the leading myotropic vector MyoAAV.4A but had a more favorable safety profile. Importantly, AAV.eM was able to functionally rescue a mouse model of Duchenne Muscular Dystrophy following systemic delivery of a micro-dystrophin gene. Thus, AAV.eM is an improved myotropic rAAV capsid that de-targets other tissues, especially the liver, and proof-of-concept for a platform to create capsids with specific properties that translate across species by addition of peptides onto low transduction backbones.

bioengineering↗

bioRxiv2025

LOSS OF ROR2 TYROSINE KINASE RECEPTOR IS ASSOCIATED WITH ENDOTHELIAL DYSFUNCTION IN PAH VIA INAPPROPRIATE INTEGRIN BETA 1 ACTIVATION

RationaleEndothelial dysfunction is a key feature of pulmonary arterial hypertension (PAH). We previously identified Wnt7a, a ligand of the Wnt planar cell polarity (PCP) pathway, as essential for pulmonary angiogenesis, with its loss linked to PAH. Given the importance of Wnt/PCP to lung endothelial function and angiogenesis, our goal is to elucidate how Wnt/PCP regulates angiogenic responses in pulmonary microvascular endothelial cells (PMVECs). ROR2, a tyrosine kinase receptor specific to Wnt/PCP, is crucial for cardiovascular development, but its role in PAH is unclear. We hypothesized that ROR2 supports endothelial homeostasis, and its loss would impair angiogenesis, contributing to PAH. MethodsEndothelial-specific ROR2 knockout (ROR2 ECKO) and wild-type (WT) mice were studied under normoxia and chronic hypoxia using echocardiography, hemodynamics, and lung morphometry. PMVECs from healthy and PAH lungs were transfected with ROR2 siRNA/constructs for functional and molecular studies. Focal adhesion (FA) activation and force generation were assessed via FRET-based methods. Bulk and single-cell transcriptomic analyses were performed on siROR2 PMVECs and ROR2 ECKO lungs. ResultsROR2 ECKO mice exhibited worsened pulmonary hypertension, right ventricular remodeling, microvascular loss, and muscularization in hypoxia. Single-cell RNA sequencing of lung endothelial cells showed dysregulation of pathways involved in barrier formation and angiogenesis. Evans blue dye extravasation confirmed reduced endothelial barrier integrity in ROR2 ECKO mice. ROR2-deficient PAH PMVECs displayed increased adhesion, permeability, and FA numbers, with reduced VE-cadherin at cell junctions. Confocal imaging revealed ROR2 localization in FAs, interacting with integrin {beta}1 (ITGB1). FRET analysis showed that ITGB1 remained in an active, adhesion-promoting state in ROR2-deficient cells. Restoring ROR2 in PAH PMVECs normalized adhesion, barrier function, and FA abundance. Transcriptomic analysis identified Rab12 as a key mediator of ROR2-ITGB1 crosstalk, with Rab12 knockdown mimicking ROR2 deficiency in PMVECs. ConclusionsROR2 regulates pulmonary angiogenesis by maintaining endothelial barrier integrity and facilitating integrin recycling. Restoring ROR2 signaling could be a potential therapeutic approach for PAH.

cell biology↗

bioRxiv2025

Natural self-attenuation of pathogenic viruses by deleting the silencing suppressor coding sequence for long-term plant-virus coexistence

Potyviridae is the largest family of plant-infecting RNA viruses. All members of the family (potyvirids) have positive-sense single-stranded RNA genomes, with polyprotein processing as the main expression strategy. The 5-proximal regions of their genomes encode two types of leader proteases: the serine protease P1 and the cysteine protease HCPro. However, their arrangement and sequence composition vary greatly among genera or even species. The leader proteases play multiple important roles in different potyvirid-host combinations, including RNA silencing suppression and virus transmission. Here, we report that viruses in the genus Arepavirus, which encode two HCPro leader proteases in tandem (HCPro1-HCPro2), can naturally lose the coding sequences for these two proteins during infection. Notably, this loss is associated with a shift in foliage symptoms from severe necrosis to mild chlorosis or even asymptomatic infections. Further analysis revealed that the deleted region is flanked by two short repeated sequences in the parental isolates, suggesting that recombination during virus replication likely drives this genomic deletion. Reverse genetic approaches confirmed that the loss of leader proteases weakens RNA silencing suppression and other critical functions. A field survey of areca palm trees displaying varied symptom severity identified a transitional stage in which full-length viruses and deletion mutants coexist in the same tree. Based on these findings, we propose a scenario in which full-length isolates drive robust infections and facilitate plant-to-plant transmission, eventually giving rise to leader protease-less variants that mitigate excessive damage to host trees, allowing long-term coexistence with the perennial host. To our knowledge, this is the first report of potyvirid self-attenuation via coding sequence loss. Author summaryPlant viruses typically persist throughout the lifespan of their host plants, employing multiple strategies to ensure long-term survival. This study reveals an unusual self-attenuation mechanism in which potyvirids, likely through recombination, discard a large genomic fragment containing the RNA silencing suppressor coding sequence. This deletion reduces viral pathogenicity, enabling a peaceful long-term virus-plant coexistence. Meanwhile, the attenuated viruses may function as natural vaccines, protecting plants from reinfection by the full-length pathogenic strains or related variants. These findings highlight a direct link between viral evolution and long-term coexistence, suggesting that such adaptations may promote mutual benefits. Understanding these dynamics could provide valuable insights into virus-host interactions and inspire new approaches to plant disease management.

pathology↗

bioRxiv2024

Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate

Inorganic phosphate (Pi) is fundamental to life, and its intracellular concentration must be tightly regulated to prevent toxicity. XPR1, the only known phosphate exporter, plays a crucial role in maintaining this delicate balance. However, the mechanisms underlying the function and regulation of XPR1 remain elusive until now. Here we present cryo-electron microscopy structures of the human XPR1-KIDINS220 complex in both substrate-free closed states and substrate-bound outward-open states, as well as the structure of an XPR1 mutant alone in a substrate-bound inward-facing state. In the presence of inositol hexaphosphate (InsP6) and phosphate, the XPR1-KIDINS220 complex adopts an outward-open conformation. InsP6 binds both the SPX domain and the peripheral juxtamembrane regions of XPR1, indicative of an active phosphate-export state. Conversely, in the absence of either phosphate or InsP6, the complex assumes a closed state, where the extracellular half of transmembrane 9 occupies the outward cavity, and a C-terminal plug-in loop blocks the intracellular cavity. Notably, XPR1 without KIDINS220 adopts a closed state despite the presence of phosphate and InsP6. The functional mutagenesis experiments further demonstrate that InsP6, whose concentrations fluctuate in response to Pi availability, functions synergistically with KIDINS220 to regulate the phosphate export activity of XPR1. These findings not only elucidate the intricate mechanisms of cellular phosphate regulation but also hold promise for the development of targeted therapies for ovarian cancer, where XPR1 plays a significant role.

biophysics↗

bioRxiv2024

Structural insights into cholesterol sensing by the LYCHOS-mTORC1 pathway

The mechanistic target of rapamycin complex 1 (mTORC1) pathway regulates cellular metabolism and growth by coordinating nutrient resources, including cholesterol, and its aberrant activation is linked to various age-related diseases. LYCHOS is a cholesterol sensor on the lysosome and bound to the GATOR1 complex, a GTPase-activating protein for the Rag GTPase, at high cholesterol concentrations, thereby activating the protein kinase mTORC1. However, how LYCHOS senses cholesterol and transduces signal to GATOR1 remain largely unknown. Here we report six cryo-electron microscopy structures of human LYCHOS, depicting five distinct states. These are categorized into a contracted state when complexed with a sufficient amount of the cholesterol analogue cholesteryl hemisuccinate (CHS), and an expanded state when CHS is deficient. The structure forms a homodimer, within each monomer the transmembrane region is divided into a permease-like domain (PLD) and a GPCR-like domain (GLD) with two clearly defined adjacent cholesterol binding sites between them. The PLD shares a conserved Na+/H+ antiporter (NhaA) fold, which much resembles plant auxin transporter PINs. Cholesterol locates between PLD and GLD and cholesterol binding induces a translation of GLD towards PLD and exposes the cytosolic extension of transmembrane 15, which mediates the interaction between LYCHOS and GATOR1. Strikingly, structure-guided mutations of Gly702 in GLD of LYCHOS increase its affinity for cholesterol, leading to sustained mTORC1 activation in cells. This indicates that LYCHOSs moderate affinity for cholesterol is crucial as a cholesterol sensor. Our results not only showed a solute carrier mechanistically coordinates a GPCR domain, elucidating the structural mechanism of cholesterol sensing by the mTORC1 pathway on the lysosome; but also provides a structural basis for developing inhibitors that selectively target to mTORC1 pathway to treat age-related diseases by blocking LYCHOS in its expanded state.

biochemistry↗

bioRxiv2024

A telosma mosaic virus-based vector for foreign gene expression and virus-induced gene silencing in the perennial woody vine, passion fruit (Passiflora edulis)

Passion fruit (Passiflora edulis) is a perennial, woody, tropical vine crop. It produces edible round to oval fruit that has been increasingly favored for its unique aroma and taste, and richness in antioxidants, vitamins and minerals. However, the functional genomic study of passion fruit lags far behind due to a lack of simple and efficient genetic tools. Here, we report the development of virus-mediated protein overexpression (VOX) and virus-induced gene silencing (VIGS) vector based on telosma mosaic virus (TelMV), an emerging potyvirus infecting passion fruit plants worldwide. This vector, designated pTelMV-GW, incorporates the Gateway-compatible recombination sites for rapid gene cloning. We show that this vector allows for the systemic stable expression of two heterologous proteins, green fluorescent protein (GFP) and bacterial phytoene synthase (crtB) in passion fruit plants, and pTelMV-GW containing different fragments of GFP can also induce systemic gene silencing on the GFP-transgenic N. benthamiana plants. Moreover, we demonstrated that in passion fruit plants, this vector can trigger gene silencing of endogenous phytoene desaturase (PDS) to a limited extent. Furthermore, we upgraded the vector by using a mild TelMV strain that does not induce noticeable symptoms in plants. We show that the upgraded vector (pTelMV-R181K-GW) containing PDS or ChlI fragments induces the robust silencing of the corresponding endogenous gene in passion fruit plants. Together, we reported the first development of VIGS and VOX vectors in passion fruit plants, as the first step in our endeavor to discover horticulturally important genes for improving passion fruit production and quality.

plant biology↗

bioRxiv2024

CRISPR-Cas9/Cas12a Systems for efficient genome editing and large genomic fragment deletions in Aspergillus niger

CRISPR technology has revolutionized fungal genetic engineering by accelerating the pace and expanding the feasible scope of experiments in this field. Among various CRISPR-Cas systems, Cas9 and Cas12a are widely used in genetic and metabolic engineering. In filamentous fungi, both Cas9 and Cas12a have been utilized as CRISPR nucleases. In this work we first compared efficacies and types of genetic edits for CRISPR-Cas9 and -Cas12a systems at the polyketide synthase (albA) gene locus in Aspergillus niger. By employing a tRNA-based gRNA polycistronic cassette, both Cas9 and Cas12a have demonstrated remarkable editing efficacy. Cas12a demonstrated superiority over Cas9 protein when one gRNA was used for targeting, achieving an editing efficiency of 89.5% compared to 15% for Cas9. Moreover, when employing two gRNAs for targeting, both systems achieved up to 100% editing efficiency for single gene editing. In addition, the CRISPR-Cas9 system has been reported to induce large genomic deletions in various species. However, its use for engineering large chromosomal segments deletions in filamentous fungi still requires optimization. Here, we engineered Cas9 and - Cas12a-induced large genomic fragment deletions by targeting various genomic regions of A. niger ranging from 3.5 kb to 40 kb. Our findings demonstrate that targeted engineering of large chromosomal segments can be achieved, with deletions of up to 66.7% efficiency. Furthermore, by targeting a secondary metabolite gene cluster, we show that fragments over 100 kb can be efficiently and specifically deleted using the CRISPR-Cas9 or -Cas12a system. Overall, in this paper, we present an efficient multi-gRNA genome editing system utilizing Cas9 or Cas12a that enables highly efficient targeted editing of genes and large chromosomal regions in A. niger.

microbiology↗

bioRxiv2024

New drinking water genome catalog identifies a globally distributed bacterial genus adapted to disinfected drinking water systems.

Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from non-disinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomevar) within this genus is detected in >82% of drinking water systems included in this study. We propose a provisional name for this uncultured bacterium as "Raskinella chlorumaquaticus" and describe the genus as "Raskinella" (pending SeqCode approval). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, able to metabolize halogenated compounds, proliferates in a biofilm-based environment and shows clear indications of disinfection-mediated selection. SynopsisCreation and analysis of a new curated drinking water genome catalog identifies uncharacterized bacterial species that is widely distributed in disinfected drinking water systems.

microbiology↗

bioRxiv2024

A conserved lysine/arginine-rich motif in potyviral 6K1 protein is key in engaging autophagy-mediated self-degradation for completing pepper veinal mottle virus infection

Potyviruses possess one positive-sense single-stranded RNA genome mainly with polyprotein processing as their gene expression strategy. The resulting polyproteins are proteolytically processed by three virus-encoded proteases into 11 or 12 mature proteins. One of such, 6-kDa peptide 1 (6K1), is an understudied viral factor. Its function in viral infection remains largely mysterious. This study is to reveal part of its roles by using pepper veinal mottle virus (PVMV) as a model virus. Alanine substitution screening analysis revealed that 15 out of 17 conserved residues across potyviral 6K1 sequences are essential for PVMV infection. However, 6K1 protein is less accumulated in virus-infected cells, even though P3-6K1 junction is efficiently processed by NIa-Pro for its release, indicating that 6K1 undergoes a self-degradation event. Mutating the cleavage site to prevent NIa-Pro processing abolishes viral infection, suggesting that the generation of 6K1 along with its degradation might be important for viral multiplication. We corroborated that cellular autophagy is engaged in 6K1s degradation. Individual engineering of the 15 6K1 variants into PVMV was performed to allow for their expression along with viral infection. Five of such variants, D30A, V32A, K34A, L36A, and L39A, significantly interfere with viral infection. The five residues are enclosed in a conserved lysine/arginine-rich motif; four of them appear to be crucial in engaging autophagy-mediated self-degradation. Based on these data, we envisaged a scenario that potyviral 6K1s interact with an unknown anti-viral component to be co-degraded by autophagy to promote viral infection. IMPORTANCEPotyvirus is the largest genus of plant-infecting RNA viruses, which encompasses socio-economically important virus species, such as Potato virus Y, Plum pox virus, and Soybean mosaic virus. Like all picorna-like viruses, potyviruses express their factors mainly via polyprotein processing. Theoretically, viral factors P3 through CP, including 6K1, should share an equivalent number of molecules. The 6K1 is small in size ([~]6 kDa) and conserved across potyviruses, but less accumulated in virus-infected cells. This study demonstrates that cellular autophagy is engaged in the degradation of 6K1 to promote viral infection. In particular, we found a conserved lysine/arginine-rich motif in 6K1s across potyviruses that is engaged in this degradation event. This finding reveals one facet of a small protein that help understand the pro-viral role of cellular autophagy in viral infection.

microbiology↗

bioRxiv2024

5'-S-(3-aminophenyl)-5'-thioadenosine, a novel chemoprotective agent for reducing toxic side effects of fluorouracil in treatment of MTAP-deficient cancers

BackgroundNucleobase analogue (NBA) drugs are effective chemotherapeutics, but their clinical use is limited by severe side effects. Compelling evidence suggests the use of S-methyl-5-thioadenosine (MTA) can selectively reduce NBA toxicity on normal tissues while maintaining the efficacy of NBAs on methylthioadenosine phosphorylase (MTAP)-deficient cancers. However, we found that MTA induced hypothermia at its effective dose, limiting its translational potential. We intended to find an MTA analogue that can exert MTA function while minimize the undesired side effects of MTA. Thus, such an analogue can be used in combination with NBAs in selectively targeting MTAP-deficient cancers. MethodsWe screened a library of MTA analogues for the following criteria: 1) being substrates of MTAP; 2) selectively protection on MTAP-expressing cells from NBA toxicity using MTAP-isogenic cell lines; 3) ability to protect the host from NBA toxicity without hypothermic effect; and 4) lack of interference on the tumor-suppressive effect of NBA in mice bearing MTAP-deficient tumors. ResultsWe identified 5-S-(3-aminophenyl)-5-thioadenosine (m-APTA) that did not induce hypothermia at the effective doses. We demonstrated that m-APTA could be converted to adenine by MTAP. Consequently, m-APTA selectively protected mouse hosts from 5-FU-induced toxicity (i.e. anemia); yet it did not interfere with the drug efficacy on MTAP-deficient bladder cancers. In silico docking studies revealed that, unlike MTA, m-APTA interact inefficiently with adenosine A1 receptor, providing a plausible explanation of the superior safety profile of m-APTA. Conclusionm-APTA can significantly improve the translational potential of the NBA toxicity reduction strategy in selectively targeting MTAP-deficient cancers.

cancer biology↗

bioRxiv2024

Mutating the arginine residue within the FRNK motif of HC-Pro yield highly attenuated strains that confer complete cross protection against telosma mosaic virus (TelMV) in passion fruit (Passiflora edulis)

Telosma mosaic virus (TelMV, Potyvirus, Potyviridae) is an emerging viral pathogen causing a major global threat to passion fruit plantations. However, an efficient strategy for controlling such viruses is not yet available. Cross protection is a phenomenon in which pre-infection of a plant with one virus prevents or delays superinfection with the same or closely related virus. HC-Pro is the potyviral encoded multifunctional protein involved in several steps of viral infection, including multiplication, movement, transmission and RNA silencing suppression. The main hypothesis we tested in this study was whether it is possible to generate attenuated viral strains capable of conferring protection against severe TelMV infection by manipulating the HC-Pro gene. By introducing point mutation into the potyviral conserved motif FRNK of HC-Pro, we have successfully obtained three highly attenuated mutants of TelMV (R181K, R181D and R181E, respectively) that can systemically infect passion fruit plants without any noticeable symptoms. Importantly, these mutants confer complete protection against subsequent infection of severe recombinant virus TelMV-GFP, evidenced by no detection of viral RNA or protein of the superinfection virus in the systemic leaves of passion fruit plants in both early and late stages. Lastly, we demonstrated that the HC-Pros harbored by the highly attenuated mutants exhibited reduced RNA silencing suppression activity in Nicotiana benthamiana leaves. Altogether, this study provides the first demonstration of the generation of highly attenuated strains for TelMV and highlights key amino acid residue involved in complete cross protection against TelMV, opening a new avenue to fight TelMV in the field.

pathology↗

bioRxiv2024

General Capillary Endothelial Cells Undergo Reprogramming into Arterial Endothelial Cells in Pulmonary Hypertension through HIF-2a/Notch4 Pathway

Pulmonary arterial hypertension (PAH) is characterized by a progressive increase of pulmonary vascular resistance and obliterative pulmonary vascular remodeling that result in right heart hypertrophy, failure, and premature death. The underlying mechanisms of loss of distal capillary endothelial cells (ECs) and obliterative vascular lesion formation remain unclear. Our recent single-cell RNA sequencing, spatial transcriptomics analysis, RNASCOPE, and immunostaining analysis showed that arterial ECs accumulation and loss of capillary ECs were evident in human PAH patients and pulmonary hypertension (PH) rodents. Pseudotime trajectory analysis of the single-cell RNA sequencing data suggest that lung capillary ECs transit to arterial ECs during the development of PH. Our study also identified CXCL12 as the marker for arterial ECs in PH. Capillary EC lineage tracing approach using capillary specific-Dre;Tdtomato reporter mice demonstrated that capillary ECs gave rise to arterial ECs during PH development. Genetic deletion of HIF-2a or pharmacological inhibition of Notch4 normalized the arterial programming in PH. In conclusion, our study demonstrates that capillary endothelium transits to arterial endothelium through the HIF-2a-Notch4 pathway during the development of PAH. Thus, targeting arterial EC transition might be a novel approach for treating PAH patients.

physiology↗

bioRxiv2024

Endothelial fatty acid-binding proteins contribute to the pathogenesis of pulmonary hypertension

Pulmonary arterial hypertension (PAH) is a devastating disease characterized by obliterative vascular remodeling and persistent increase of vascular resistance, leading to right heart failure and premature death. Understanding the cellular and molecular mechanisms will help develop novel therapeutic approaches for PAH patients. Single-cell RNA sequencing (scRNAseq) analysis found that both FABP4 and FABP5 were highly induced in endothelial cells (ECs) of Egln1Tie2Cre (CKO) mice, which was also observed in pulmonary arterial ECs (PAECs) from idiopathic PAH (IPAH) patients, and in whole lungs of pulmonary hypertension (PH) rats. Plasma levels of FABP4/5 were upregulated in IPAH patients and directly correlated with severity of hemodynamics and biochemical parameters using plasma proteome analysis. Genetic deletion of both Fabp4 and 5 in CKO mice (Egln1Tie2Cre/Fabp4-5-/-, TKO) caused a reduction of right ventricular systolic pressure (RVSP) and RV hypertrophy, attenuated pulmonary vascular remodeling and prevented the right heart failure assessed by echocardiography, hemodynamic and histological analysis. Employing bulk RNA-seq and scRNA-seq, and spatial transcriptomic analysis, we showed that Fabp4/5 deletion also inhibited EC glycolysis and distal arterial programming, reduced ROS and HIF-2 expression in PH lungs. Thus, PH causes aberrant expression of FABP4/5 in pulmonary ECs which leads to enhanced ECs glycolysis and distal arterial programming, contributing to the accumulation of arterial ECs and vascular remodeling and exacerbating the disease.

molecular biology↗

bioRxiv2024

Unraveling principles of thermodynamics for genome-scale metabolic networks using graph neural networks

The fundamental laws of thermodynamics determine the feasibility of all natural processes including metabolism. Although several algorithms have been developed to predict the most important thermodynamic parameter, the standard Gibbs free energy, for metabolic reactions and metabolites, their application to genome-scale metabolic networks (GEMs) with thousands of metabolites and reactions is still limited. Here, we develop a graph neural network (GNN)- based model dGbyG for predicting Gibbs energy for metabolites and metabolic reactions which outperforms all existing methods in accuracy, versatility, robustness, and generalization ability. By applying dGbyG to the human GEM, Recon3D, we identify a critical subset of reactions with substantial negative values of the standard Gibbs free energy change, which we name thermodynamic driver reactions. These reactions exhibit distinctive network topological characteristics akin to driver nodes defined in control theory and remarkable heterogeneity in enzyme abundance, implying evolutionary constraints on the selection of thermodynamic parameters of metabolic networks. We also develop a thermodynamics-based flux balance analysis (TFBA) approach to integrate reaction thermodynamics with GEMs to curate these models. Our work not only transcends the augmentation of accessible thermodynamic data to facilitate an enriched understanding of metabolism, but also enables refinement of metabolic reconstructions from a thermodynamic perspective, thereby underscoring the critical role of thermodynamics in the accurate modeling of biological systems.

systems biology↗

bioRxiv2024

RBM7 deficiency promotes breast cancer metastasis by coordinating MFGE8 splicing switch and NF-kB pathway

Aberrant alternative splicing is well-known to be closely associated with tumorigenesis of various cancers. However, the intricate mechanisms underlying breast cancer metastasis driven by deregulated splicing events remain largely unexplored. Here, we unveiled that RBM7 is decreased in lymph node and distant organ metastases of breast cancer as compared to primary lesions and low expression of RBM7 is correlated with the reduced disease-free survival of breast cancer patients. Breast cancer cells with RBM7 depletion exhibited an increased potential for lung metastasis compared to scramble control cells. The absence of RBM7 stimulated breast cancer cell migration, invasion, and angiogenesis. Mechanistically, RBM7 controlled the splicing switch of MFGE8, favoring the production of the predominant isoform of MFGE8, MFGE8-L. This resulted in the attenuation of STAT1 phosphorylation and alterations in cell adhesion molecules. MFGE8-L exerted an inhibitory effect on the migratory and invasive capability of breast cancer cells, while the truncated isoform MFGE8-S, which lack the second F5/8 type C domain had the opposite effect. In addition, RBM7 negatively regulates the NF-{kappa}B cascade and an NF-{kappa}B inhibitor could obstruct the increase in HUVEC tube formation caused by RBM7 silencing. Clinically, we noticed a positive correlation between RBM7 expression and MFGE8 exon7 inclusion in breast cancer tissues, providing new mechanistic insights for molecular-targeted therapy in combating breast cancer.

cancer biology↗

bioRxiv2023

LncPNdeep: A long non-coding RNA classifier based on Large Language Model with peptide and nucleotide embedding

Long non-coding RNA plays an important role in various gene transcription and peptide interactions. Classifying lncRNAs from coding RNA is a crucial step in bioinformatics analysis which seriously affects the post-analysis for transcriptome annotation. Although several machine learning-based methods were developed to classify lncRNAs, these methods were mainly focused on nucleotide features without considering the information from the peptide sequence. To integrate both nucleotide and peptide information in lncRNA classification, one efficient deep learning is desired. In this study, we developed one concatenated deep neural network named LncPNdeep to combine this information. LncPNdeep incorporates both peptide and nucleotide embedding from masked language modeling (MLM), being able to discover complex associations between sequence information and lncRNA classification. LncPNdeep achieves state-of-the-art performance in the human transcript database compared with other existing methods (Accuracy=97.1%). It also exhibits superior generalization ability in cross-species comparison, maintaining consistent accuracy and F1 scores compared to other methods. The combination of nucleotide and peptide information makes LncPNdeep able to facilitate the identification of novel lncRNA and gain high accuracy for classification. Our code is available at https://github.com/yatoka233/LncPNdeep

bioinformatics↗

bioRxiv2023

Virus-induced gene silencing (VIGS) as a tool for functional genetic analysis in passion fruit plants

Passion fruit (Passiflora edulis) is grown perennially in sub-tropical and tropical areas. Its fruits contain multiple vitamins and antioxidants, and thus are consumed increasingly in drinks and foods. However, the functions and regulations of genes that are engaged in the biosynthesis of the health-promoting compounds in passion fruits remain largely unknown. Its whole genome sequence has just been published recently. Virus-induced gene silencing (VIGS) is a reverse genetics tool for analyzing gene function. Here, we engineered telosma mosaic virus (TelMV), a potyvirus infecting passion fruit, into a VIGS vector by inserting the Gateway-compatible recombination sites. The newly constructed TelMV-VIGS virus successfully expressed foreign protein and induced systemic infection in both Nicotiana benthamiana and P. edulis plants. Intriguingly, TelMV-VIGS vector containing different fragments of green fluorescent protein (GFP) gene induced systemic gene silencing on the GFP-transgenic N. benthamiana plants (16c). When the phytoene desaturase (PDS) gene, an endogenous gene in passion fruit, was engineered into the vector, it triggered the silencing of PePDS, as evidenced by the reduced mRNA levels and photobleached phenotype. We reported the first development of VIGS vector in passion fruit, as the first step in our endeavor of discovering horticulturally important genes for improving passion fruit production and quality.

plant biology↗