Biology subjects

Gao, S.

Publications and source records attributed to Gao, S..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Rapid production of modified cattle and sheep from spermatid-like stem cells

Genome-modified ruminants, such as cattle and sheep, are important germplasm for agricultural applications. Haploid androgenetic stem cells (haSCs) can support the full-term development of embryos upon intracytoplasmic haSCs injection (iCHI) into intact oocytes. Thus, haSCs are invaluable resources for studying economic traits and significantly impact livestock breeding; however, ruminant haSCs have yet to be obtained. Here, we report the derivation of cattle and sheep haSCs using a recombinant FACE medium. These cells display characteristics of formative-state pluripotency and can differentiate into three germ layers, both in vitro and in vivo. Interestingly, the ectopic expression of protamine in haSCs converts their nuclei into a spermatid-like structure and synergistic enhancement of full-term development of iCHI embryos, named as Pro-iCHI approach. Furthermore, gene-modified cattle and sheep can be efficiently produced through the combinatorial use of the CRISPR and Pro-iCHI approach. Overall, Pro-iCHI provides an easy-to-manipulate agrobiotechnology tool for rapidly producing genetically modified livestock.

bioengineering↗

bioRxiv2024

ElixirSeeker: A Machine Learning Framework Utilizing Attention-Driven Fusion of Molecular Fingerprints for the Discovery of Anti-Aging Compounds

Despite the growing interest in anti-aging drug development, high cost and low success rate pose a significant challenge. We present ElixirSeeker, a new machine-learning framework designed to help speed up the discovery of potential anti-aging compounds by utilizing the attention-driven fusion of molecular fingerprints. Our approach integrates molecular fingerprints generated by different algorithms and utilizes XGBoost to select optimal fingerprint lengths. Subsequently, we assign weights to the molecular fingerprints and employ Kernel Principal Component Analysis (KPCA) to reduce dimensionality, integrating different attention-driven methods. We trained the algorithm using DrugAge database. Our comprehensive analyses demonstrate that 64-bit Attention-ElixirFP maintains high predictive accuracy and F1 score while minimizing computational cost. Using ElixirSeeker to screen external compound databases, we identified a number of promising candidate anti-aging drugs. We tested top 6 hits and found that 4 of these compounds extend the lifespan of Caenorhabditis elegans, including Polyphyllin , Medrysone, Thymoquinone and Medrysone. This study illustrates that attention-driven fusion of fingerprints maximizes the learning of molecular activity features, providing a novel approach for high-throughput machine learning discovery of anti-aging molecules.

systems biology↗

bioRxiv2024

Ethylene Modulates the Phenylpropanoid Pathway by Enhancing VvMYB14 Expression via the ERF5-Melatonin-ERF104 Pathway in Grape Seeds

Ethylene plays a crucial role in regulating polyphenol metabolism, however the underlying mechanism remains largely unknown. This work demonstrated that ethylene release occurred earlier than melatonin during seed ripening. Ethylene treatment increased the VvASMT expression and melatonin content. VvERF5 was elucidated to bind to the ERE element in the VvASMT promoter. VvERF5 overexpression increased ASMT expression and melatonin content while its suppression generated the opposite results in grape seeds, calli and/or Arabidopsis seeds. Using the promoter of VvMYB14, which was strongly induced by melatonin, a melatonin responsive element (MTRE) was identified. VvERF104 was revealed not only to be strongly induced by melatonin but to bind to the MTRE of the VvMYB14. VvERF104 overexpression and suppression largely increased and decreased the MYB14 expression, respectively, in grape seeds, calli and/or Arabidopsis seeds. VvMYB14 overexpression widely modified the expression of genes in phenylpropanoid pathway and phenolic compound content in grape seeds. DAP-seq revealed that the MEME-1 motif was the most likely binding sites of VvMYB14. VvPAL, VvC4H and VvCHS were verified to be the target genes of VvMYB14. Additionally, the roles of VvERF5, VvASMT and VvERF104 in mediating ethylene-induced changes in phenylpropanoid pathway were elucidated using their suppressing seeds. Collectively, ethylene increased the VvMYB14 expression via the pathway of ERF5-melatonin-ERF104 and thereby modified phenylpropanoid pathway.

plant biology↗

bioRxiv2024

SIRT5-mediated GLS and GDH desuccinylation attenuates autophagy in MAC-T cells induced by ammonia

Our previous research revealed that NH3 regulated autophagy dependent on SIRT5 in MAC-T cells. Interestingly, SIRT5 reduced the content of NH3 and glutamate by inhibiting GLS activity, ADP/ATP value also declined. In this study, SIRT5 interacted with endogenous GLS and GDH, and had no effect on endogenous GLS and GDH expression. SIRT5 declined significantly the succinylation levels of GLS and GDH, and further reduced the enzymatic activity of GLS and GDH. SIRT5 declined the glutamine metabolism, which attenuated ammonia release in MAC-T cells, accompanying with cellular autophagy decline, reducing the formation of autophagosome. Deletion of SIRT5 increased the content of NH3 and glutamate, as well as promotes autophagy, which could be alleviated by SIRT5 overexpression. SIRT5 KO was associated with increased succinylation and activity of GLS and GDH, as well as autophagy response in MAC-T cells. Furthermore, SIRT5 promoted the maintenance of mitochondria homeostasis. Mechanistically, SIRT5 modulated the succinylation levels and enzymatic activities of GLS and GDH in mitochondria and promoted the maintenance of mitochondria homeostasis, further attenuating ammonia-stimulated autophagy in MAC-T cells. HighlightsO_LISIRT5 catalyzed lysine desuccinylation of GLS and GDH. C_LIO_LIGLS and GDH enzymatic activity were enhanced by lysine succinylation. C_LIO_LIGLS and GDH were required for SIRT5 to regulate ammonia-induced cellular autophagy. C_LIO_LISIRT5 promoted the maintenance of mitochondrial homeostasis C_LI

physiology↗

bioRxiv2024

Therapeutic targeting of Syndecan-1 axis overcomes acquired resistance to KRAS-targeted therapy in gastrointestinal cancers

The therapeutic benefit of recently developed mutant KRAS (mKRAS) inhibitors has been limited by the rapid onset of resistance. Here, we aimed to delineate the mechanisms underlying acquired resistance to mKRAS inhibition and identify actionable targets for overcoming this clinical challenge. Previously, we identified Syndecan-1 (SDC1) as a key effector for pancreatic cancer progression whose surface expression is driven by mKRAS. By leveraging both pancreatic and colorectal cancer models, we found that surface SDC1 expression was initially diminished upon mKRAS inhibition, but recovered in tumor cells that bypass mKRAS dependency. Functional studies showed that these tumors depended on SDC1 for survival, further establishing SDC1 as a driver for the acquired resistance to mKRAS inhibition. Mechanistically, we revealed that the YAP1-SDC1 axis was the major driving force for bypassing mKRAS dependency to sustain nutrient salvage machinery and tumor maintenance. Specifically, YAP1 activation mediated the recovery of SDC1 localization on cell surface that sustained macropinocytosis and enhanced the activation of multiple RTKs, promoting resistance to KRAS-targeted therapy. Overall, our study has provided the rationale for targeting the YAP-SDC1 axis to overcome resistance to mKRAS inhibition, thereby revealing new therapeutic opportunities for improving the clinical outcome of patients with KRAS-mutated cancers.

cancer biology↗

bioRxiv2024

Identifying Causal Relations between Gut Microbiome, Metabolic Dysfunction-Associated Fatty Liver Disease and the Novel Mediators of Blood Metabolites

BackgroundResearch has established connection between gut microbiome and the risk of metabolic dysfunction-associated fatty liver disease (MAFLD). However, the causal relationships and the roles of potential mediating factors, such as blood metabolites, remain unclear. MethodsWe conducted a bidirectional and mediation Mendelian randomization (MR) study using the genome-wide summary statistics of gut microbial taxa (Dutch Microbiome Project, n = 7,738), blood lipids (UK Biobank, n =8,299), and the largest MAFLD GWAS data (1,483 cases and 17,781 controls). We used the inverse-variance weighted estimation method as our primary approach. The multivariable Mendelian randomization (MVMR) and two-step MR approaches were used to prioritize the most likely causal metabolites as mediators. Additionally, we conducted linkage disequilibrium score regression (LDSC) analyses to assess genetic correlations, and downstream gene-based analyses to investigate the shared biological mechanism. ResultsBy testing the causal effects of 205 bacterial pathways and 207 taxa on MAFLD, we identified 5 microbial taxa causally associated with MAFLD, notably the species Parabacteroides merdae (OR [95%CI] = 1.191[1.022-1.388], p = 0.025). Among 1,399 blood metabolites, 53 showed causal associations with MAFLD, with pregnenetriol sulfate identified as a mediator for genus Parabacteroides on MAFLD (proportion mediated = 16.30%). LDSC analysis also provided suggestive evidence for a potential genetic correlation between them (rg= 2.124, p=0.009). ConclusionsThe study suggested a novel causal relationship between gut microbial taxa and MAFLD, especially the genus Parabacteroides merdae and blood metabolite pregnenetriol sulfate might mediate this relationship. ImportanceOur study reveals novel insights into how the intersection of microorganisms living in the human gut, known as the gut microbiome, influences the development of Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD), a condition increasingly recognized as a major global health concern. By identifying specific gut microbiome taxa and metabolites that contribute to the onset and progression of MAFLD, our findings enhance comprehension of this prevalent condition and unveil promising prospects for its prevention and intervention. We discovered that certain gut bacteria can affect the levels of blood metabolites, which in turn impact the livers health. This work carries significant implications for novel strategies for MAFLD prevention and treatment, including interventions aimed at modifying the gut microbiome. Our research underscores the gut-liver connection and its implications for metabolic diseases, contributing to future therapeutic developments that could improve public health worldwide. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/606637v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1b16347org.highwire.dtl.DTLVardef@ecf53eorg.highwire.dtl.DTLVardef@d8cb5borg.highwire.dtl.DTLVardef@10efe44_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Dual modes of DNA N6-methyladenine maintenance by distinct methyltransferase complexes

Stable inheritance of DNA N6-methyladenine (6mA) is crucial for its biological functions in eukaryotes. Here, we identify two distinct methyltransferase (MTase) complexes, both sharing the catalytic subunit AMT1, but featuring AMT6 and AMT7 as their unique components, respectively. While the two complexes are jointly responsible for 6mA maintenance methylation, they exhibit distinct enzymology, DNA/chromatin affinity, genomic distribution, and knockout phenotypes. AMT7 complex, featuring high MTase activity and processivity, is connected to transcription-associated epigenetic marks, including H2A.Z and H3K4me3, and is required for the bulk of maintenance methylation. In contrast, AMT6 complex, with reduced activity and processivity, is recruited to initiate maintenance methylation immediately after DNA replication. These two complexes coordinate in maintenance methylation. By integrating signals from both replication and transcription, this mechanism ensures the faithful and efficient transmission of 6mA as an epigenetic mark in eukaryotes. Significance statementDNA N6-methyladenine (6mA) has recently been recognized as an epigenetic mark in eukaryotes. The stable inheritance of 6mA is essential for its biological functions. However, the precise mechanisms by which 6mA patterns are faithfully and efficiently transmitted remain largely unknown. Here, we have identified two distinct 6mA methyltransferase (MTase) complexes and elucidated their coordinated role in maintenance methylation. This dual- complex mechanism ensures rapid and accurate methylation at newly replicated loci with proper transcription-associated epigenetic marks.

molecular biology↗

bioRxiv2024

Biophysical Modeling and Experimental Analysis of the Dynamics of C. elegans Body-Wall Muscle Cells

This study combines experimental techniques and mathematical modeling to investigate the dynamics of C. elegans body-wall muscle cells. Specifically, by conducting voltage clamp and mutant experiments, we identify key ion channels, particularly the L-type voltage-gated calcium channel (EGL-19) and potassium channels (SHK-1, SLO-2), which are crucial for generating action potentials. We develop Hodgkin-Huxley-based models for these channels and integrate them to capture the cells electrical activity. To ensure the model accurately reflects cellular responses under depolarizing currents, we develop a parallel simulation-based inference method for determining the models free parameters. This method performs rapid parallel sampling across high-dimensional parameter spaces, fitting the model to the responses of muscle cells to specific stimuli and yielding accurate parameter estimates. We validate our model by comparing its predictions against cellular responses to various current stimuli in experiments and show that our approach effectively determines suitable parameters for accurately modeling the dynamics in mutant cases. Additionally, we discover an optimal response frequency in body-wall muscle cells, which corresponds to a burst firing mode rather than regular firing mode. Our work provides the first experimentally constrained and biophysically detailed muscle cell model of C. elegans, and our analytical framework combined with robust and efficient parametric estimation method can be extended to model construction in other species. Author summaryDespite the availability of many biophysical neuron models of C. elegans, a biologically detailed model of its muscle cell remains lacking, which hampers an integrated understanding of the motion control process. We conduct voltage clamp and mutant experiments to identify ion channels that influence the dynamics of body-wall muscle cells. Using these data, we establish Hodgkin-Huxley-based models for these ion channels and integrate them to simulate the electrical activity of the muscle cells. To determine the free parameters of the model, we develop a simulation-based inference method with parallel sampling that aligns the model with the muscle cells responses to specific stimuli. Our method allows for swift parallel sampling of parameters in high dimensions, facilitating efficient and accurate parameter estimation. To validate the effectiveness of the determined parameters, we verify the cells responses under different current stimuli in wild type and mutant cases. Furthermore, we investigate the optimal response frequency of body-wall muscle cells and find that it exhibits a frequency consistent with burst firing mode rather than regular firing mode. Our research introduces the first experimentally validated and biophysically detailed model of muscle cells in C. elegans. Additionally, our modeling and simulation framework for efficient parametric estimation in high-dimensional dynamical systems can be extended to model constructions in other scenarios.

neuroscience↗

bioRxiv2024

Alzheimer Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction

BackgroundAlzheimers disease (AD), a progressive neurodegenerative disorder, continues to increase in prevalence without any effective treatments to date. In this context, knowledge graphs (KGs) have emerged as a pivotal tool in biomedical research, offering new perspectives on drug repurposing and biomarker discovery by analyzing intricate network structures. Our study seeks to build an AD-specific knowledge graph, highlighting interactions among AD, genes, variants, chemicals, drugs, and other diseases. The goal is to shed light on existing treatments, potential targets, and diagnostic methods for AD, thereby aiding in drug repurposing and the identification of biomarkers. ResultsWe annotated 800 PubMed abstracts and leveraged GPT-4 for text augmentation to enrich our training data for named entity recognition (NER) and relation classification. A comprehensive data mining model, integrating NER and relationship classification, was trained on the annotated corpus. This model was subsequently applied to extract relation triplets from unannotated abstracts. To enhance entity linking, we utilized a suite of reference biomedical databases and refine the linking accuracy through abbreviation resolution. As a result, we successfully identified 3,199,276 entity mentions and 633,733 triplets, elucidating connections between 5,000 unique entities. These connections were pivotal in constructing a comprehensive Alzheimers Disease Knowledge Graph (ADKG). We also integrated the ADKG constructed after entity linking with other biomedical databases. The ADKG served as a training ground for Knowledge Graph Embedding models with the high-ranking predicted triplets supported by evidence, underscoring the utility of ADKG in generating testable scientific hypotheses. Further application of ADKG in predictive modeling using the UK Biobank data revealed models based on ADKG outperforming others, as evidenced by higher values in the areas under the receiver operating characteristic (ROC) curves. ConclusionThe ADKG is a valuable resource for generating hypotheses and enhancing predictive models, highlighting its potential to advance ADs disease research and treatment strategies.

bioinformatics↗

bioRxiv2024

Pandemic Vibrio parahaemolyticus wave succession by gene loss

While spontaneous mutation and gene acquisition are well-established drivers of pathogen adaptation, the role of gene loss remains underexplored. Here, we investigated the emergence and diversification of the pandemic clone (PC) of Vibrio parahaemolyticus through large-scale phylogenomic analysis of 8,684 global isolates. The PC rapidly acquired multiple marker genes and genomic islands, subsequently diverging into successive sublineages mediating independent waves of cross-country transmission, as also observed in V. cholerae. Wave succession in the last two decades was driven by loss of putrescine utilization (Puu) genes, conferring phenotypic advantages for environmental adaptation (enhanced biofilm formation) and human transmission (increased cell adhesion/intestinal colonization, reduced virulence), consistent with the virulence trade-off hypothesis. We identified Puu-gene loss in multiple bacterial genera, with effects on biofilm and adhesion replicated in V. cholerae and Escherichia coli, suggesting convergent evolution and universal phenotypic effects. Our results highlight the indispensable role of gene loss in bacterial pathogen adaptation.

microbiology↗

bioRxiv2024

It only takes seconds for a human monoclonal autoantibody to inhibit N-methyl-D-aspartate receptors

Transfer of autoantibodies targeting ionotropic N-methyl-D-aspartate receptors in autoimmune encephalitis patients into mice leads to typical disease signs. Long-term effects of the pathogenic antibodies consist of immunoglobulin G-induced crosslinking and receptor internalization. We focused on the direct and immediate impact of a specific pathogenic patient-derived monoclonal autoantibody (immunoglobulin G #003-102) on receptor function. We performed cell-attached recordings in cells transfected with the GluN1 and GluN2A subunit of the N-methyl-D-aspartate receptor. Immunoglobulin G #003-102 binds to the amino-terminal domain of the glycine-binding GluN1 subunit. It reduced simultaneous receptor openings significantly compared to controls at both low and high glutamate and glycine concentrations. Closer examination of our data in 50-second to 2-second intervals revealed, that Immunoglobulin G #003-102 rapidly decreases the number of open receptors. However, antigen-binding fragments of immunoglobulin G #003-102 did not reduce the receptor openings. In conclusion, patient-derived immunoglobulin G #003-102 inhibits N-methyl-D-aspartate receptors rapidly and directly before receptor internalization occurs and the entire immunoglobulin G is necessary for this acute inhibitory effect. This suggests an application of the antigen-binding fragment-like constructs of #003-102 as a potential new treatment strategy for shielding the pathogenic epitopes on the N-methyl-D-aspartate receptors.

neuroscience↗

bioRxiv2024

Single-cell genotype-phenotype mapping identifies therapeutic vulnerabilities in VEXAS syndrome

Somatic evolution leads to the emergence of clonal diversity across tissues with broad implications for human health. A striking example of somatic evolution is the VEXAS (Vacuoles E1 enzyme X-linked Autoinflammatory Somatic) syndrome, caused by somatic UBA1 mutations in hematopoietic stem cells (HSCs), inducing treatment-refractory, systemic inflammation. However, the mechanisms that lead to survival and expansion of mutant HSCs are unknown, limiting the development of effective therapies. The lack of animal or cellular models of UBA1-mutant HSCs has hindered such mechanistic understanding, mandating analysis of primary human VEXAS samples, which harbor admixtures of wild-type and UBA1-mutant HSCs. To address these challenges, we applied single-cell multi-omics to comprehensively define mutant UBA1-induced transcriptome, chromatin accessibility and signaling pathway alterations in VEXAS patients, allowing for the direct comparison of mutant versus wild-type cells within the same environment. We confirmed the expected enrichment of UBA1M41V/T mutations in myeloid cells, and additionally discovered that these mutations were also prevalent in Natural Killer (NK) cells in VEXAS patients, providing new insights into disease phenotypes. Through mapping genotypes to molecular phenotypes, including transcriptome, chromatin accessibility, cell surface protein or intracellular protein profiles, in HSCs, we found that UBA1M41V/T-mutant cells showed an increased inflammation signature (interferon alpha and gamma response pathways), as well as activation of unfolded protein response (UPR) via pro-survival, but not pro-apoptotic, mediators of the PERK pathway, compared to UBA1 wild-type HSCs. Ex vivo validation experiments showed that inhibiting UBA1 in normal CD34+ or using UBA1-mutant HSCs led to PERK pathway up-regulation, increased myeloid differentiation and cell survival, which was reversed by PERK inhibition. Thus, we demonstrated that human VEXAS HSCs show cell-intrinsic inflammatory phenotypes and survive the proteomic stress caused by compromised ubiquitination through PERK-mediated activation of the UPR. Together, these analyses nominate PERK pathway inhibition as a potential new therapeutic strategy for eradicating the VEXAS-inducing clone, demonstrating the power of single-cell multi-omics profiling of primary patient sample to enable genotype-to-phenotype somatic mapping for the discovery of novel candidates for clinical intervention.

genomics↗

bioRxiv2024

Brain-wide functional connectome analysis of 40,000 individuals reveals brain networks that show aging effects in older adults

The functional connectome changes with aging. We systematically evaluated aging related alterations in the functional connectome using a whole-brain connectome network analysis in 39,675 participants in UK Biobank project. We used adaptive dense network discovery tools to identify networks directly associated with aging from resting-state fMRI data. We replicated our findings in 499 participants from the Lifespan Human Connectome Project in Aging study. The results consistently revealed two motor-related subnetworks (both permutation test p-values <0.001) that showed a decline in resting-state functional connectivity (rsFC) with increasing age. The first network primarily comprises sensorimotor and dorsal/ventral attention regions from precentral gyrus, postcentral gyrus, superior temporal gyrus, and insular gyrus, while the second network is exclusively composed of basal ganglia regions, namely the caudate, putamen, and globus pallidus. Path analysis indicates that white matter fractional anisotropy mediates 19.6% (p<0.001, 95% CI [7.6% 36.0%]) and 11.5% (p<0.001, 95% CI [6.3% 17.0%]) of the age-related decrease in both networks, respectively. The total volume of white matter hyperintensity mediates 32.1% (p<0.001, 95% CI [16.8% 53.0%]) of the aging-related effect on rsFC in the first subnetwork.

neuroscience↗

bioRxiv2024

Opto-chemogenetic inhibition of L-type CaV1 channels in neurons through a membrane-assisted molecular linkage

Acute, specific, and robust inhibition of L-type Ca2+ (CaV1) channels has been sought after for both research and therapeutic applications. Compared to other available CaV1 antagonists, genetically-encoded modulators, such as CMI (C-terminus mediated inhibition) peptides encoded by CaV1 DCT (distal C-terminus), hold great potentials due to its affirmative mechanisms of action on both gating and signaling. Here, we find that membrane-anchoring with a Ras tag could essentially help form a type of intramolecular-equivalent linkage, by which the tag anchored-peptide appears to dimerize with another protein or peptide on the membrane, supported by the evidence from patch-clamp electrophysiology and FRET imaging. We then design and implement the constitutive and inducible CMI modules, with appropriate dynamic ranges targeting the short and long variants of CaV1.3, both naturally occurring in neurons. Upon optical (infrared-responsive nanoparticles) and/or chemical (rapamycin) induction of FRB/FKBP binding, DCT peptides with no CMI in the cytosol acutely translocate onto the membrane via FRB-Ras, where the physical linkage requirement could be fulfilled. The peptides robustly produce acute and potent inhibitions on both recombinant CaV1.3 channels and neuronal CaV1 activities, and thus the Ca2+ influx-neuritogenesis coupling. Validated through opto-chemogenetic induction, this prototype demonstrates channel modulation via membrane-assisted molecular linkage, promising broad applicability to diverse membrane proteins.

bioengineering↗

bioRxiv2024

Cross-domain information fusion for enhanced cell population delineation in single-cell spatial-omics data

Cell population delineation and identification is an essential step in single-cell and spatial-omics studies. Spatial-omics technologies can simultaneously measure information from three complementary domains related to this task: expression levels of a panel of molecular biomarkers at single-cell resolution, relative positions of cells, and images of tissue sections, but existing computational methods for performing this task on single-cell spatial-omics datasets often relinquish information from one or more domains. The additional reliance on the availability of "atlas" training or reference datasets limits cell type discovery to well-defined but limited cell population labels, thus posing major challenges for using these methods in practice. Successful integration of all three domains presents an opportunity for uncovering cell populations that are functionally stratified by their spatial contexts at cellular and tissue levels: the key motivation for employing spatial-omics technologies in the first place. In this work, we introduce Cell Spatio- and Neighborhood-informed Annotation and Patterning (CellSNAP), a self-supervised computational method that learns a representation vector for each cell in tissue samples measured by spatial-omics technologies at the single-cell or finer resolution. The learned representation vector fuses information about the corresponding cell across all three aforementioned domains. By applying CellSNAP to datasets spanning both spatial proteomic and spatial transcriptomic modalities, and across different tissue types and disease settings, we show that CellSNAP markedly enhances de novo discovery of biologically relevant cell populations at fine granularity, beyond current approaches, by fully integrating cells molecular profiles with cellular neighborhood and tissue image information.

bioinformatics↗

bioRxiv2024

pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells

Serotonylation has been identified as a novel protein post-translational modification for decades, where an isopeptide bond is formed between the glutamine residue and serotonin through transamination. Transglutaminase 2 (also known as TGM2 or TGase2) was proven to act as the main "writer" enzyme for this PTM and a number of key regulatory proteins (including small GTPases, fibronectin, fibrinogen, serotonin transporter, and histone H3) have been characterized as the substrates of serotonylation. However, due to the lack of pan-specific antibodies for serotonylated glutamine, the precise enrichment and proteomic profiling of serotonylation still remain challenging. In our previous research, we developed an aryldiazonium probe to specifically label protein serotonylation in a bioorthogonal manner, which depended on a pH-controlled chemoselective rapid azo-coupling reaction (CRACR). Here, we report the application of a photoactive aryldiazonium-biotin probe for the global profiling of serotonylation proteome in cancer cells. Thus, over 1,000 serotonylated proteins were identified from HCT 116 cells, many of which are highly related to carcinogenesis. Moreover, a number of modification sites of these serotonylated proteins were determined, attributed to the successful application of our chemical proteomic approach. Overall, these findings provided new insights into the significant association between cellular protein serotonylation and cancer development, further suggesting that to target TGM2-mediated monoaminylation may serve as a promising strategy for cancer therapeutics. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/593574v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@67e538org.highwire.dtl.DTLVardef@f9f722org.highwire.dtl.DTLVardef@cfe5fdorg.highwire.dtl.DTLVardef@104674f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells

Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid residue of H3 (i.e., glutamine) and dopamine. In our previous studies, we discovered that the dynamics of this post-translational modification (including installation, removal, and replacement) were regulated by a single enzyme, transglutaminase 2 (TGM2), through reversible transamination. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of TGM2 in colon cancer cells. Due to the enzyme promiscuity of TGM2, non-histone proteins have also been identified as targets of dopaminylation on glutamine residues, however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of modification sites of these dopaminylated proteins were identified, attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that to block the installation of protein dopaminylation may become a promising anti-cancer strategy. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/591460v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a3e9dorg.highwire.dtl.DTLVardef@104ecddorg.highwire.dtl.DTLVardef@5ab948org.highwire.dtl.DTLVardef@3a5d8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

The enhancement of electricity generation using cellulose based on ternary microbial consortium

Cooperation between microorganisms is crucial to design an efficient inoculum for enhancing the electricity-producing ability of carboxymethyl cellulose (CMC) fed bioreactors. In the present study, the influence of microbial mutualistic interactions and electricity generation capability were investigated by designing several co-culture and ternary culture systems. It was found that a ternary culture system of Cellulomonas Lsc-8, Bacillus subtilis C9 and Geobacter sulfurreducens PCA was used to efficiently convert cellulose into electricity. The maximum current density of 796 {+/-} 30 {micro}A{middle dot}cm-2 were achieved by the ternary culture, which were much higher than that Geobacter sulfurreducens PCA using acetate and co-culture systems to utilize CMC in bioreactors, respectively. In this consortium, Cellulomonas Lsc-8, and Bacillus subtilis C9 simultaneously digested CMC to produce acetate and secreted riboflavin as an electron shuttle; Geobacter sulfurreducens PCA utilized acetate to generate electricity. The introduction of Bacillus subtilis C9 further promoted the degradation of CMC and secreted more riboflavin to enhance electricity generation of the ternary culture. This work suggested that the synergistic interaction between interspecies in microbial consortia is emergent in designing specific community for achieving maximum power generation using CMC as substrate. This research shows new insight into the design of more efficient, stable, and robust microbial consortia applicable in waste treatment and power generation. IMPORTANCEMicrobial fuel cells (MFCs) may benefit from microbial consortia that efficiently convert carbon sources to electricity. A key challenge with this system is how to manage microbial community assembly to maximize electricity generation. Herein, we constructed and tested a three-species microbial consortium to enhance conversion of cellulose to electricity. Cellulomonas Lsc-8 and Bacillus subtilis C9 efficiently converted cellulose to acetate (electron donor) and riboflavin (electron shuttle), which enabled Geobacter sulfurreducens to generate electricity. This study laid the foundation for design of more efficient, stable, and robust microbial consortia for waste treatment and energy applications.

microbiology↗