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Biology subjects

Xiao, Y.

Publications and source records attributed to Xiao, Y..

At least 235 records · Page 13Linked to original sources

Bioengineered niches that recreate physiological extracellular matrix organisation to support long-term haematopoietic stem cells

Long-term reconstituting haematopoietic stem cells (LT-HSCs) are used to treat blood disorders via allogeneic stem cell transplantation (alloSCT), to engraft and repopulate the blood system. The very low abundance of LT-HSCs and their rapid differentiation during in vitro culture hinders their clinical utility. Previous developments using stromal feeder layers, defined media cocktails, and bioengineering have enabled HSC expansion in culture, but of mostly short-term HSCs (ST-HSC) and progenitor populations at the expense of naive LT-HSCs. Here, we report the creation of a bioengineered LT-HSC maintenance niche that recreates physiological extracellular matrix organisation, using soft collagen type-I hydrogels to drive nestin expression in perivascular stromal cells (PerSCs or pericytes). We demonstrate that nestin, which is expressed by HSC-supportive bone marrow stromal cells, is cytoprotective and, via regulation of metabolism, is important for HIF-1 expression in PerSCs. When CD34+ve HSCs were added to the bioengineered niches comprising nestin/HIF-1 expressing PerSCs, LT-HSC numbers were maintained with normal clonal and in vivo reconstitution potential, without media supplementation. We provide proof-of-concept that our bioengineered niches can support the survival of CRISPR edited HSCs. Successful editing of LT-HSCs ex vivo can have potential impact on the treatment of blood disorders.

bioengineering↗

Structural basis for differential targeting properties of small RNAs in plants and animals

microRNAs (miRNAs) regulate gene expression in plants and animals. Animals use miRNAs to sculpt the transcriptome, with each miRNA modestly repressing hundreds of otherwise unrelated targets. By contrast, each plant miRNA potently silences a small number of physiologically related targets. Here, we show that this major functional distinction depends on a minor structural difference between plant and animal Argonaute (AGO) proteins. A 7-amino-acid loop in the PIWI domain of Arabidopsis Argonaute10 (AtAGO10) reduces the affinity of the miRNA seed region for target RNAs. Swapping the PIWI-loop from human Argonaute2 (HsAGO2) into AtAGO10 increases seed strength and target-binding promiscuity, resembling animal miRNA targeting. Conversely, swapping the plant PIWI-loop into HsAGO2 increases targeting stringency and elevates target cleavage rates. The loop-swapped HsAGO2-siRNA complex silences targets more potently, with reduced off-targeting, than wild-type HsAGO2 and small interfering RNA (siRNA) duplexes in mammalian cells. Thus, tiny structural differences can tune the targeting properties of AGO proteins for distinct biological roles and HsAGO2 can be engineered for potential applications in siRNA therapeutics.

molecular biology↗

Structural basis for RNA slicing by a plant Argonaute

Argonaute (AGO) proteins use small RNAs to recognize transcripts targeted for silencing in plants and animals. Many AGOs possess an endoribonuclease activity termed RNA slicing, which catalyzes rapid turnover of target RNAs. The nuclease activity of Thermus thermophilus AGO (TtAgo)1,2 is often used as a model for RNA slicing, but how well DNA-guided slicing by this bacterial thermophile resembles RNA-guided slicing by eukaryotic AGOs is not known. We present cryo-EM structures of the Arabidopsis thaliana Argonaute10 (AtAgo10)-guide RNA complex with and without a target RNA representing a slicing substrate. Like TtAgo, AtAgo10 conformation expands in response to target binding. However, the AtAgo10-guide-target complex adopts slicing-competent and -incompetent conformations that are distinct from structures of TtAgo. AtAgo10 slicing activity is licensed by docking target (t) nucleotides t9-t13 into a surface channel containing the AGO endoribonuclease active site. A {beta}-hairpin, conserved in the L1 domain of eukaryotic AGOs, secures the t9-t13 segment and coordinates t9-t13 docking with extended guide-target pairing, preventing the complex from becoming trapped in slicing-incompetent conformations. Results show the mechanism for achieving RNA slicing in eukaryotes is distinct from that of bacteria and provide insights for controlling small interfering RNA (siRNA) potency.

molecular biology↗

S373P Mutation of Spike Protein in SARS-CoV-2 Stabilizes Omicron

A cluster of several newly occurring mutations on Omicron are found at the {beta}-core region of spike proteins receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs and applies to the proteins. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ~20% compared with the wild-type. Molecular dynamics simulations revealed that Omicron RBD showed more hydrogen bonds in the {beta}-core region due to the closing of the -helical motif caused primarily by mutation S373P, which was further confirmed experimentally. Moreover, the binding ability of Omicron to ACE2 is promoted with a stabilized RBD. This work reveals the effect of the highly conserved mutation S373P which is present in most Omicron subvariants, including BA.1-5, BQ. 1, XBB, and CH.1.1.

biophysics↗

Orchestration of alternative splicing regulates bone marrow mesenchymal stem cells fate during aging

Senescence and change of differentiation direction in bone marrow stromal cells (BMSCs) are two of the most important causes of age-related bone loss. As an important post-transcriptional regulatory pathway, alternative splicing (AS) regulates diversity of gene expression. However, the role of AS in BMSCs during aging remains poorly defined. Here we identify AS in specific genes disrupt gene expression pattern and result in age-related debility of BMSCs. We demonstrate the deficiency of splicing factor Y-box protein 1 (YBX1) result in mis-splicing in genes such as Fn1, Taz, Sirt2 and Sp7, further contributing to senescence and shift in differentiation direction of BMSCs during aging. Deletion or over-expression of YBX1 in BMSCs accelerate bone loss or stimulate bone formation in mice. Notably, we identify a small compound sciadopitysin which attenuate the degradation of YBX1 and attenuate bone loss in old mice. Our study demonstrates elaborately controlled RNA splicing governs cell fate of BMSCs and provides a potential therapeutic target for age-related osteoporosis. SummaryThis study demonstrates that YBX1 deficiency induces pre-mRNA mis-splicing and causes senescence and shift in differentiation direction of BMSCs and further accelerates aging-related bone loss. This study identifies Sciadopitysin could reverse this process by targeting YBX1.

cell biology↗

Tracking single cell evolution via clock-like chromatin accessibility

Single cell chromatin accessibility sequencing (scATAC) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Here, we show a simple, accurate and phenotypic-neutral measure of cell developmental hierarchy - the fraction of accessible clock-like loci. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. We developed a method, EpiTrace, that counts the fraction of opened clock-like loci from scATAC data to determine cell age and perform lineage tracing. EpiTrace works in various cell lineages and animal species, shows concordance with known developmental hierarchies, correlates well with DNA methylation-based clocks, and is complementary with mutation-based lineage tracing, RNA velocity, and stemness predictions. Applying EpiTrace to scATAC data revealed a multitude of novel biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification. Our work discovered a universal epigenomic hallmark during cellular development, which facilitates the study of cellular hierarchies and organismal aging.

bioinformatics↗

AI inspired discovery of new biomarkers for clinical prognosis of liver cancer

Tissue biomarkers are crucial for cancer diagnosis, prognosis assessment, and treatment planning. However, few of current biomarkers used in clinics are robust enough to show a true analytical and clinical value. Thus the search for additional tissue biomarkers, including the strategies to identify them, is imperative. Recently, the capabilities of deep learning (DL)-based computational pathology in cancer diagnosis and prognosis have been explored, but the limited interpretability and generalizability make the results difficult to be accepted in clinical practice. Here we present an interpretable human-centric DL-guided framework--PathFinder (Pathological-biomarker-finder)-- that can inspire pathologists to discover new tissue biomarkers from well-performing DL models, which bridges the gap between DL and clinical prognosis. By combining sparse multi-class tissue spatial distribution information of whole slide images (WSIs) with attribution methods, PathFinder can achieve localization, characterization, and verification of potential biomarkers, while guaranteeing state-of-the-art prognostic performance. With the inspiration of PathFinder, we discovered that tumor necrosis in liver cancer, a long-neglected factor, has a strong relationship with patient prognosis. Thus we proposed two clinically independent indicators, including necrosis area fraction and tumor necrosis distribution, for practical prognosis, and verified their potentials in clinical prognosis according to Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK)-derived criteria. Our work demonstrates a successful example of introducing artificial intelligence (AI) into clinical practice in a knowledge discovery way, which can be adopted in identifying biomarkers in various cancer types and modalities.

cancer biology↗

CRISPR metabolic screen identifies ATM and KEAP1 as targetable genetic vulnerabilities in solid tumors.

Cancer treatments targeting DNA repair deficiencies often encounter drug resistance, possibly due to alternative metabolic pathways that counteract the most damaging effects. To identify such alternative pathways, we screened for metabolic pathways exhibiting synthetic lethality with inhibition of the DNA damage response kinase ATM using a metabolism-centered CRISPR/Cas9 library. Our data revealed Kelch-like ECH-associated protein 1 (KEAP1) as a key factor involved in desensitizing cancer cells to ATM inhibition both in vitro and in vivo. Cells depleted of KEAP1 exhibited an aberrant overexpression of the cystine transporter SLC7A11, robustly accumulated cystine inducing disulfide stress, and became hypersensitive to ATM inhibition. These hallmarks were reversed in a reducing cellular environment indicating that disulfide stress was a crucial factor. In the TCGA pan-cancer datasets, we found that ATM levels strongly correlated with KEAP1 levels across multiple solid malignancies. Together, our results unveil ATM and KEAP1 as new targetable vulnerabilities in solid tumors.

cancer biology↗

Functional autapses form in striatal parvalbumin interneurons but not medium spiny neurons

Autapses (or self-synapses) selectively form in specific cell types in many brain regions including the neocortex and the hippocampus, where they provide feedback control over self-spiking activities. Previous morphological studies also found putative autapses in medium spiny neurons (MSNs) of the striatum. However, it remains unclear whether striatal neurons indeed form physiologically functional autapses. We performed whole-cell recordings from striatal neurons in acute mouse brain slices, and identify autaptic neurons by the occurrence of prolonged asynchronous release (AR) of neurotransmitter after high-frequency burst of action potentials (APs) in the same cell. To our surprise, we found no autaptic release in all recorded MSNs after the AP burst, even in the presence of Sr2+ that should desynchronize and thus prolong synaptic vesicle release. In sharp contrast, we observed robust autaptic AR events in half of the recorded parvalbumin (PV)-positive neurons. Autaptic responses in PV cells were mediated by GABAA receptors, and the AR strength was dependent on the frequency and the number of APs during the burst. Further simulation results show that autapses regulate burst spiking in PV cells by providing self-inhibition and thus shape network oscillation at certain frequencies. Together, we reveal that, distinct from MSNs, striatal PV neurons form functional autapses, activation of which would regulate self-activities in PV cells, and thereby shape MSN firing and network oscillations. Author summarySynapses, which usually occur between two neurons, are key structures for signal communication in the nervous system. However, some types of neurons form autapses, where a neuron synapses onto itself. Autaptic transmission provides feedback signal regulating self-spiking activities. Neuronal and network activities in the striatum play critical roles in motor control and other brain functions. Previous studies suggest formation of autapses in striatal principal MSNs, but it remains unclear whether striatal neurons form functional autapses. We performed direct recordings from striatal neurons and examined the occurrence of autaptic transmission in acute brain slices. Surprisingly, we did not detect any autaptic responses in MSNs. A large proportion of striatal PV neurons, however, produced robust autaptic GABA release upon high-frequency stimulation, indicating selective formation of autapses in striatal PV cells. Our computation simulations suggest that autapses provide self-inhibition in PV cells and thereby shape activities in MSNs and striatal network, particularly when PV cells discharge at high frequencies corresponding to a high dopamine state. Together, our findings indicate that PV cells, but not MSNs, in the striatum form physiologically functional autapses. Autapses in PV cells could be essential circuit elements in the striatum and contribute to striatal functions, such as motor control.

neuroscience↗

A one-step CRISPR-based strategy for endogenous gene tagging in Drosophila melanogaster

The ability to tag endogenous genes to create fluorescent fusion proteins has revolutionized the studies of protein subcellular localization and dynamics and regulation in live cells. Here, we report a precise, rapid, and one-step endogenous gene tagging system in Drosophila melanogaster, which allows us to screen for engineered lines without the visible eye marker. Specifically, we developed an efficient screening strategy for the identification of the homologous integration events by employing a PCR-based method to characterize individual flies using only a small segment of their middle leg. Here, we detail design and construction of gRNA plasmids and donor plasmid, and methods for screening, and confirmation of engineered lines. Together, these protocols make tagging any endogenous protein in Drosophila more efficient and faster, enabling studies of a wide range of cellular processes in live cells within intact organisms.

molecular biology↗

Identification of large offspring syndrome during pregnancy through ultrasonography and maternal blood transcriptome analyses

The use of assisted reproductive technologies (ART) in cattle can result in large/abnormal offspring syndrome (LOS/AOS) which is characterized by macrosomia. LOS can cause dystocia and lead to the death of dam and calf. Currently, no test exists to identify LOS pregnancies. We hypothesized that fetal ultrasonography and/or maternal blood markers are useful to identify LOS. Bovine fetuses were generated by artificial insemination (control) or ART. Fetal ultrasonographies were taken on gestation day 55 (D55) and fetal collections performed on D56 or D105 (gestation in cattle {approx}280 days). ART fetuses weighing [≥]97 percentile of the control weight were considered LOS. Ultrasonography results show that the product of six D55 measurements can be used to identify extreme cases of LOS. To determine whether maternal blood can be used to identify LOS, leukocyte mRNA from 23 females was sequenced. Unsupervised hierarchical clustering grouped the transcriptomes of the two females carrying the two largest LOS fetuses. Comparison of the leukocyte transcriptomes of these two females to the transcriptome of all other females identified several misregulated transcripts on gestation D55 and D105 with LOC783838 and PCDH1 being misregulated at both time-points. Together our data suggest that LOS is identifiable during pregnancy in cattle.

developmental biology↗

Identification and receptor mechanism of TIR-catalyzed small molecules in plant immunity

Plant nucleotide-binding leucine-rich-repeat receptors (NLRs) with an N-terminal toll/interleukin-1 receptor (TIR) domain sense pathogen effectors to enable TIR-encoded NADase activity for immune signaling. TIR-NLR (TNL) signaling requires conserved helper NLRs NRG1 and ADR1 and the lipase-like protein EDS1 that functions as a heterodimer with each of its paralogs PAD4 and SAG101. We show that TIR-containing proteins catalyze production of 2-(5-phosphoribosyl)-5-adenosine mono-/di-phosphate (pRib-AMP/ADP) in vitro and in planta. Biochemical and structural data demonstrate that EDS1-PAD4 is a receptor complex for pRib-AMP/ADP. pRib-ADP binding triggers a conformational change in the PAD4 C-terminal domain to allosterically promote EDS1-PAD4 interaction with ADR1-L1 but not NRG1A. Our study identifies TIR-catalyzed pRib-AMP/ADP as a missing link in TIR signaling via EDS1-PAD4 and as likely second messengers for plant immunity.

plant biology↗

A-type FHFs mediate resurgent currents through TTX-resistant voltage-gated sodium channels

Resurgent currents (INaR) produced by voltage-gated sodium channels are required for many neurons to maintain high-frequency firing, and contribute to neuronal hyperexcitability and disease pathophysiology. Here we show, for the first time, that INaR can be reconstituted in a heterologous system by co-expression of sodium channel -subunits and A-type fibroblast growth factor homologous factors (FHFs). Specifically, A-type FHFs induces INaR from Nav1.8, Nav1.9 tetrodotoxin-resistant neuronal channels and, to a lesser extent, neuronal Nav1.7 and cardiac Nav1.5 channels. Moreover, we identified the N-terminus of FHF as the critical molecule responsible for A-type FHFs-mediated INaR. Among the FHFs, FHF4A is the most important isoform for mediating Nav1.8 and Nav1.9 INaR. In nociceptive sensory neurons, FHF4A knockdown significantly reduces INaR amplitude and the percentage of neurons that generate INaR, substantially suppressing excitability. Thus, our work reveals a novel molecular mechanism underlying TTX-resistant INaR generation and provides important potential targets for pain treatment.

neuroscience↗

Increased core body temperature exacerbates defective protein prenylation in mouse avatars of mevalonate kinase deficiency

Mevalonate kinase deficiency (MKD) is caused by biallelic loss-of-function mutations in MVK, leading to recurrent fevers and systemic inflammation. We describe new mouse avatars of MKD bearing p.Val377Ile (the commonest variant) or deletions in Mvk. Compound heterozygous mice recapitulated the biochemical phenotype of MKD, with build-up of unprenylated GTPases and increased plasma mevalonic acid. Mice with different deficiencies in mevalonate kinase revealed new insights into the genotype-phenotype relationship and mirrored the variability in the prenylation defect in human MKD, with p.V377I homozygous mice having a milder phenotype than compound heterozygous animals. The inflammatory response to LPS was enhanced in compound heterozygous mice in vivo and elevated serum interleukin-1{beta} was abrogated by NLRP3 inflammasome inhibition. Increased temperature dramatically but reversibly exacerbated the deficit in the mevalonate pathway and defective prenylation in vitro and in vivo, highlighting increased body temperature as a likely trigger of inflammatory flares and an additional potential target for future therapeutic approaches.

physiology↗

Identification of a small molecule, Mebendazole, as a novel ethylene signaling activator reveals a role of ethylene signaling on the regulation of lateral root angles

The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Despite its importance, only few regulatory pathways and mechanisms that determine GSA are known, and these mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule, Mebendazole (MBZ) that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. We uncover that MBZ directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only reveals that the ethylene signaling pathway is essential for GSA regulation, but it also identifies a small molecular modulator of RSA and the first small molecule that acts downstream of ethylene receptors and that directly activates ethylene signaling. In briefHe et al. identify a small molecule that regulates lateral root angle. They show that the compound increases lateral root angle by inhibiting CTR1 kinase activity, which in turn activates ethylene signaling. Therefore, they uncover that the ethylene pathway is involved in lateral root angle regulation. HighlightsO_LIMBZ increases lateral root angle C_LIO_LIMBZ regulates lateral root angle by activating ethylene signaling C_LIO_LIMBZ inhibits CTR1 kinase activity C_LIO_LIThe ethylene pathway is involved in lateral root angle regulation C_LI

plant biology↗

A unique mineralizing pool of Gli1+ stem cells builds the tendon enthesis and demonstrates therapeutic potential

The enthesis, a fibrocartilaginous transition between tendon and bone, is necessary for the transfer of force from muscle to bone to produce joint motion. The enthesis is prone to injury due to mechanical demands, and it cannot regenerate. A better understanding of how the enthesis develops will lead to more effective therapies to prevent pathology and promote regeneration. Here, we used single-cell RNA sequencing to define the development transcriptome of the entheses over postnatal stages. Six resident cell types, including enthesis progenitors and mineralizing chondrocytes, were identified along with their transcription factor regulons and temporal regulation. Following our prior discovery of the necessity of Gli1-lineage cells for enthesis development and healing, we then examined their transcriptomes at single cell resolution and demonstrated their clonogenicity and multipotency. Transplantation of these Gli1- lineage cells to enthesis injuries improved healing, demonstrating their therapeutic potential for enthesis regeneration. HighlightsO_LIThe transcriptome and differentiation trajectory of enthesis stem cells during postnatal development are defined at single cell resolution. C_LIO_LITranscription factor regulons drive enthesis stem cell differentiation. C_LIO_LIGli1-lineage enthesis stem cells demonstrate in vivo and in vitro clonogenicity and multipotency. C_LIO_LITransplantation of Gli1-lineage enthesis stem cells to enthesis injuries improves healing. C_LI

developmental biology↗

Anti-seed PNAs targeting multiple oncomiRs for brain tumor therapy

Glioblastoma (GBM) is one of the most lethal malignancies in the United States with poor survival and high recurrence rates, suggesting the need for approaches targeting the most important molecular drivers of tumor growth. Here, we aimed to simultaneously target oncomiRs 10b and 21, which have been reported to drive the aggressive growth and invasiveness of GBM. We designed short (8-mer bases) gamma-({gamma})-modified peptide nucleic acids (s{gamma}PNAs), which target the seed region of oncomiRs 10b and 21 with high affinity. We entrapped these anti-miR s{gamma}PNAs in nanoparticles (NPs) formed from a block copolymer of poly(lactic acid) and hyperbranched polyglycerol (PLA-HPG); the NPs were also functionalized with aldehydes to produce bioadhesive NPs. We have previously shown that these bioadhesive NPs (BNPs) produce superior transfection efficiency, with a tropism for tumor cells. The s{gamma}PNA BNPs showed superior anti-miR efficacy in comparison to the regular full length PNA BNPs in vitro. When combined with temozolomide, s{gamma}PNA BNPs administered via convention-enhanced delivery (CED) inhibited the growth of intracranial tumors and significantly improved the survival of animals (>120 days). RNA sequencing analysis revealed the role of vascular endothelial growth factor A (VEGFA) and integrin beta 8 (ITGB8), direct targets of both miR-10b and miR-21, in mediating the tumor growth. Hence, we established that BNPs loaded with anti-seed s{gamma}PNAs targeting multiple oncomiRs is a promising approach to improve the treatment of GBM, with a potential to personalize treatment based on tumor specific oncomiRs. SummaryO_ST_ABSTargeting oncomiRs 21 and 10b to improve GBM survivalC_ST_ABSGlioblastoma (GBM) is an aggressive malignant disorder with high recurrence rates and poor survival. Here, we aimed to simultaneously inhibit two aberrant oncomiRs--miR 21 and miR 10b--which have been previously associated with GBM invasiveness and progression. We synthesized short, gamma-modified peptide nucleic acids (s{gamma}PNA) targeted to the miR seed regions and loaded the s{gamma}PNAs into bioadhesive nanoparticles (BNPs). When the s{gamma}PNA-BNPs were added to cultured tumor cells, we observed significant reduction of target oncomiRs and increase of apoptosis in vitro. When delivered in vivo by convection-enhanced delivery, s{gamma}PNA BNPs dramatically increased the survival in two orthotopic (intracranial) mouse models of GBM. Moreover, the combination of s{gamma}PNA BNPs with temozolomide (TMZ) increased the survival of mice with GBM beyond the planned endpoint (120 days) with significant improvements in histopathology. The proposed strategy of s{gamma}PNA BNP with TMZ provides an alternative, promising approach for treatment of GBM.

cancer biology↗

Identification of Piperlongumine (PL) as an new E3 ligase ligand to induce targeted protein degradation

PROteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS-032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-Ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.

cancer biology↗