Biology subjects

Liu, X.

Publications and source records attributed to Liu, X..

At least 703 records · Page 39Linked to original sources

bioRxiv2024

Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation

Arginylation installed by arginyltransferase 1 (ATE1) features an addition of arginine (Arg) to the reactive amino acids (e.g., Glu and Asp) at the protein N-terminus or side chain. Systemic removal of arginylation after ATE1 knockout (KO) in mouse models resulted in heart defects leading to embryonic lethality. The biological importance of arginylation has motivated the discovery of arginylation sites on proteins using bottom-up approaches. While bottom-up proteomics is powerful in localizing peptide arginylation, it lacks the ability to quantify proteoforms at the protein level. Here we developed a top-down proteomics workflow for characterizing and quantifying calreticulin (CALR) arginylation. To generate fully arginylated CALR (R-CALR), we have inserted an R residue after the signaling peptide (AA1-17). Upon overexpression in ATE1 KO cells, CALR and R-CALR were purified by affinity purification and analyzed by LCMS in positive mode. Both proteoforms showed charge states ranging from 27-68 with charge 58 as the most intense charge state. Their MS2 spectra from electron-activated dissociation (EAD) showed preferential fragmentation at the protein N-terminals which yielded sufficient c ions facilitating precise localization of the arginylation sites. The calcium-binding domain (CBD) gave minimum characteristic ions possibly due to the abundant presence of >100 D and E residues. Ultraviolet photodissociation (UVPD) compared with EAD and ETD significantly improved the sequence coverage of CBD. This method can identify and quantify CALR arginylation at absence, endogenous (low), and high levels. To our knowledge, our work is the first application of top-down proteomics in characterizing post-translational arginylation in vitro and in vivo.

biochemistry↗

bioRxiv2024

A causative SNP in the promoter of myogenin is essential for myogenic differentiation

Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.

genetics↗

bioRxiv2024

Ganoderma lucidum alleviates kidney aging by modulating gut microbiota

BackgroundGanoderma lucidum, a renowned traditional Chinese medicine known for its multiple health benefits, including anti-aging effect, has the ability to influence gut microbiota. However, its specific role in alleviating aging via gut microbiota has not been thoroughly investigated. Here, we explored the impact of G. lucidum sporoderm-broken spore powder (Gl-SBSP) on kidney aging using naturally aged and radiation-induced premature senescence mouse models. MethodsWe analyzed gut microbiota through high-throughput sequencing in naturally aged and radiation-induced premature senescence mice after oral administration of Gl-SBSP. Additionally, untargeted metabolomics of the gut microbiome in naturally aged mice was performed using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analyses. Transcriptomics was employed to systematically measure gene expression levels throughout kidney tissues. ResultsGl-SBSP effectively mitigated aging-related phenotypic changes and significantly alleviated kidney aging, although outcomes were mixed in the irradiation mouse model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with positive prognostic outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that promoted recovery of senescent kidneys and improved renal function, validated through in vitro and in vivo experiments. Transcriptome analysis revealed that NR regulates kidney steroid metabolism in aging. ConclusionOur findings suggest that Gl-SBSPs anti-aging effect is mediated by NR derived from the Lachnospiraceae family, influencing kidney steroid metabolism via the gut-kidney axis. These results provide new insights into the mechanisms underlying the anti-aging properties of Gl-SBSP. AbstractGanoderma lucidum, also known as "Linzhi," is a well-established traditional Chinese medicine renowned for its multiple health benefits and its influence on gut microbiota. In this study, we investigated the anti-aging effect of G. lucidum sporoderm-broken spore powder (Gl-SBSP) through the gut-kidney axis using naturally aged and radiation-induced premature senescence mouse models. Administration of Gl-SBSP not only effectively mitigated aging-related phenotypic changes but also significantly alleviated kidney aging, although outcomes were mixed in the irradiation model. Importantly, Gl-SBSP modulated gut bacterial composition, particularly enriching Lachnospiraceae in naturally aged mice and in radiation-induced premature senescence mice with favorable and long-lasting outcomes. Nicotinamide riboside (NR), derived from Lachnospiraceae bacteria, was identified as a potential metabolite that facilitated the rejuvenation of senescent kidneys and improved renal function through both in vitro and in vivo experiments. Further investigation revealed that NR regulated steroid metabolic process in kidney. Our findings suggest that the anti-aging effect of Gl-SBSP is mediated by NR derived from the Lachnospiraceae bacteria, thereby influencing kidney steroid metabolism through the gut-kidney axis. This study provides novel insights into the anti-aging mechanisms of Ganoderma.

microbiology↗

bioRxiv2024

Thrombospondin-1 inhibits alternative complement pathway activation in vasculitis synergistically to factor H

Complement activation is a relevant driver in the pathomechanisms of vasculitis. The involved proteins in the interaction between endothelia, complement and platelets in these conditions are only partially understood. Thrombospondin-1 (TSP-1), found in platelet -granules and released from activated endothelial cells, interacts with factor H (FH) and von Willebrand factor (vWF). However, direct regulatory interaction with the complement cascade has not yet been described. We could show that TSP-1 is a potent, FH-independent inhibitor of the alternative complement pathway. TSP-1 binds to complement proteins, inhibits cleavage of C3 and C5 and the formation of the membrane attack complex. Complement-regulatory function is validated in blood samples from patients with primary complement defects. Physiological relevance of TSP-1 is demonstrated in ANCA-vasculitis patients by significantly enhanced TSP-1 staining in glomerular lesions and increased complement activity and NETosis following TSP-1 deficiency in an ANCA-vasculitis model. The newly described complement-inhibiting function of TSP-1 represents an important mechanism in the interaction of endothelia, complement and platelets. In particular, the interplay between released TSP-1, vWF and the complement system locally, especially on surfaces, influences the balance between complement activation and inhibition and may be relevant in various vascular diseases.

molecular biology↗

bioRxiv2024

Deletion of Setd7 protects against cardiac hypertrophy via inhibiting lipid oxidation

Setd7, a catalytic enzyme responsible for histone H3K4 methylation, is implicated in various cardiac diseases. However, the role of Setd7 in pathological cardiac hypertrophy remains unclear. In this study, we observed that Setd7 is significantly elevated in pathological hypertrophy stimuli cardiomyocytes and mouse failing hearts. Subsequently, we found that mice lacking Setd7 remarkably preserved cardiac function after transverse aortic constriction, as demonstrated by improving myocardial hypertrophy and fibrosis, whereas Setd7 overexpression in cardiomyocytes deteriorated hypertrophy phenotype. Further in vitro analyses revealed that Setd7 mediated-E2F1 activation induces E3 ubiquitin protein ligases WWP2 expression to catalyze the lipid-peroxide-reducing enzyme GPx4 ubiquitination degradation, ultimately causing widespread lipid peroxidation and boosting pathological cardiac hypertrophy. Remarkably, loss of activity of GPx4 blunted the Setd7 knockdown exerts antihypertrophic effect in pathological cardiomyocytes hypertrophy, further confirming an important role of lipid peroxidation in Setd7-mediated failing hearts. In summary, the role of Setd7 in pressure overload-induced cardiac hypertrophy is regulated by the Setd7-E2F1-WWP2-GPx4 signaling pathway, suggesting that targeting Setd7 is a promising therapeutic strategy to attenuate pathological cardiac hypertrophy and heart failure.

molecular biology↗

bioRxiv2024

Intraperitoneal programming of tailored CAR macrophages via mRNA-LNP to boost cancer immunotherapy

Therapeutic strategies for peritoneal metastasis in solid tumors are urgently needed in the clinic. Programming chimeric antigen receptor macrophages (CAR-Ms) in situ offers opportunities for an unmet demand. However, potential intracellular domains (ICDs) for CAR design and their antitumor mechanisms for macrophage empowerment remain to be explored systematically. By developing a targeted mRNA-LNP delivery system for macrophages, we have investigated 36 CAR combinations to determine the impact of CAR-Ms on immune regulation in vitro and in vivo. In two solid tumor mouse models, intraperitoneal programming of CAR-Ms was shown to elicit robust adaptive immune activation and significantly synergize with PD-1/L1 therapy. Single-cell RNA sequencing (scRNA-seq) analysis revealed that CAR-Ms could reshape the immunosuppressive tumor microenvironment (TME) and boost the TCF1+PD-1+ progenitor- exhausted CD8+ T cells (Tpex) population. Meanwhile, we found that tailored CAR-M with CD3{zeta}/TLR4 ICDs could favorably maintain proinflammatory phenotype and simultaneously upregulate MHC I and PD-L1 expression by perturbing NF-{kappa}B pathways. Moreover, the synergism between macrophage PD-L1 knockdown and CAR-M therapy highlighted the need to block the PD-1/L1 axis in antigen cross-presentation. In short, we developed an mRNA-LNP delivery system for intraperitoneal programming of tailored CAR-Ms in vivo and broadened understanding of both regulatory and feedback mechanisms for CAR-M therapies against solid tumors.

bioengineering↗

bioRxiv2024

Efficient generation of CAR NK cells from human umbilical cord blood CD34+ stem and progenitors for democratizing affordable immunotherapy

Chimeric antigen receptor (CAR) natural killer cells (CAR NK) cells, leveraging safety and not requiring HLA match in adoptive infusion, have emerged as promising alternative cells to CAR-T cells for immunotherapies. High and multiple doses of CAR NK cell infusions are essential to maintain therapeutic efficacy in clinical trials. This requires efficient methods for generating large-scale CAR NK cells and significantly reducing CAR engineering costs. In this study, we develop a three-step strategy to generate highly high yields of induced NK (iNK) and CAR iNK cells from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood CD34+ HSPC, our reliable method efficiently produces 14-83 million mature iNK cells or 7-32 million CAR iNK cells with high expression levels of CD16 and zero T cell contaminations. Introducing CAR expression elements at the HSPC level reduces the quantities of CAR pseudoviruses to 1 / 140.000 - 1 / 600,000 compared to engineering CARs in mature NK cells. The iNK and CAR iNK cells, including fresh cells and thawed cells from cryopreserved conditions, demonstrate remarkable tumoricidal activities against various human cancer cells and significantly prolong the survival of human tumor-bearing animals. The high yields of CAR NK cells and negligible costs of CAR engineering of our method support the broad applications of CAR NK cells for treating cancer patients.

cell biology↗

bioRxiv2024

Longevity or Well-being? A Dual-Dimension Structure of Neuroticism

The development of personality traits is often viewed as evolutionarily adaptive. Current neuroticism research, however, predominantly highlights its negative health impacts, neglecting its potential evolutionary advantages. We propose that neuroticisms inter-individual variability can be structured into two distinct geometric dimensions. One, named the Emotional Reactivity-Instability/Distress Spectrum (ERIS), correlates strongly with longevity and is associated with chronic diseases and risk-averse lifestyle. This dimension is underpinned by evolutionarily conserved subcortical brain regions and genes. The other, resembling the overall neuroticism score, is primarily linked to mental and stress-related disorders, as well as life satisfaction. It involves higher-order emotional brain regions and is genetically enriched in human-accelerated regions. Collectively, these dimensions represent a dual-strategy personality framework that optimizes survival and well-being, with the former being evolutionarily conservative and the latter potentially a unique human adaptation.

neuroscience↗

bioRxiv2024

VEHoP: A Versatile, Easy-to-use, and Homology-based Phylogenomic pipeline accommodating diverse sequences

Phylogenomics has emerged as a transformative approach in systematics, conservation biology, and biomedicine, enabling the inference of evolutionary relationships by leveraging hundreds to thousands of genes from genomic or transcriptomic data. However, acquiring high-quality genomes and transcriptomes necessitates samples with intact DNA and RNA, substantial sequencing investments, and extensive bioinformatic processing, such as genome/transcriptome assembly and annotation. This challenge is particularly pronounced for rare or difficult-to-collect species, such as those inhabiting the deep sea, where only fragmented DNA reads are often available due to environmental degradation or suboptimal preservation conditions. To address these limitations, we introduce VEHoP (Versatile, Easy-to-use Homology-based Phylogenomic pipeline), a tool designed to infer protein-coding regions from diverse inputs, including raw reads (short and long), draft genomes, transcriptomes, and annotated genomes. VEHoP automates the generation of orthologous sequence alignments, concatenated matrices, and phylogenetic trees, streamlining phylogenomic analyses for researchers across disciplines. The tool aims to (1) expand taxonomic sampling by accommodating a wide range of input data types and (2) simplify phylogenomic workflows, making them accessible to researchers with varying levels of bioinformatic expertise. We evaluated VEHoPs performance using datasets from oysters, catfish, and insects, demonstrating its ability to produce robust phylogenetic trees with strong bootstrap support, outperforming assembly-free methods. Additionally, we applied VEHoP to reconstruct the phylogeny of the enigmatic deep-sea gastropod order Neomphalida, successfully resolving a well-supported phylogenetic backbone for this poorly understood group. VEHoP is freely available on GitHub (https://github.com/ylify/VEHoP), with dependencies easily installable via Bioconda.

bioinformatics↗

bioRxiv2024

The Impact of Preprints on the Citations of Journal Articles Related to COVID-19

To investigate the impact of preprints on the citation counts of COVID-19-related papers, this study compares the number of citations received by drafts initially distributed as preprints and later published in journals with those received by papers directly submitted to journals. The difference in the median number of citations between COVID-19 preprint-distributed papers and COVID-19 directly submitted papers published in 184 journals was tested using the Mann-Whitney U test. The results showed that 129 journals had a statistically significant higher median citation count for COVID-19 preprint-distributed papers compared to directly submitted papers, with a p-value of less than 0.05. In contrast, no journals had a statistically significant higher median citation count for COVID-19 directly submitted papers. This indicates that 70.11% of the journals that published preprint-distributed papers experienced a significant increase in citations. We also identified that among the 184 journals, 13 journals garnered a substantial number of citations. Among the 74,037 COVID-19 papers, preprint-distributed papers (9,028) accounted for only 12.19%. However, among the 2,015,997 citations received by COVID-19 papers, preprint-distributed papers garnered 542,715 citations, representing a substantial 26.92%. These results suggest that distributing preprints prior to formal publication may help COVID-19 research reach a wider audience, potentially leading to increased readership and citations.

scientific communication and education↗

bioRxiv2024

Bioadhesive Hydrogel-Coupled and Miniaturized Ultrasound Transducer System for Long-Term, Wearable Neuromodulation

Transcranial focused ultrasound has become a promising non-invasive approach for neuromodulation applications, particularly for neurodegenerative diseases and psychiatric illnesses. However, its implementation in wearable neuromodulation has thus far been limited due to the devices large size, which needs external supporting systems for the neuromodulation process. Furthermore, the need for ultrasound gel for acoustic coupling between the device and skin limits the viability for long-term use, due to its inherent susceptibility to dehydration and lack of adhesiveness to form a stable interface. Here, we report a wearable miniaturized ultrasound device with size comparable to standard EEG/ECG electrodes integrated with bioadhesive hydrogel to achieve efficient acoustic intensity upon ultrasound stimulation for long-term, wearable primary somatosensory cortical stimulation. Specifically, air-cavity Fresnel lens (ACFAL) based self-focusing acoustic transducer (SFAT) was fabricated using a lithography-free microfabrication process. Our transducer was able to achieve an acoustic intensity of up to 30.7 W/cm2 (1.92 MPa) in free-field with a focal depth of 10 mm. Bioadhesive hydrogel was developed to address the need for long-term stability of acoustic couplant for ultrasound application. The hydrogel demonstrated less than 13% attenuation in acoustic intensity and stable adhesion force of 0.961 N/cm over 35 days. Leveraging our bioadhesive hydrogel-integrated wearable ultrasound transducer, we were able to suppress somatosensory evoked potentials elicited by median nerve stimulation via functional electrical stimulation over 28 days, demonstrating the efficacy of our transducer for long-term, wearable neuromodulation in the brain.

bioengineering↗

bioRxiv2024

A neurofunctional signature of affective arousal generalizes across valence domains and distinguishes subjective experience from autonomic reactivity

Arousal is fundamental for affective experience and, together with valence, defines the core affective space. Precise brain models of affective arousal are lacking, leading to continuing debates of whether the neural systems generalize across valence domains and are separable from those underlying autonomic arousal or wakefulness. Here, we combined naturalistic fMRI with predictive modeling to develop a brain affective arousal signature (BAAS, discovery-validation design, n=60, 36). We demonstrate its (1) sensitivity and generalizability across mental processes and valence, and (2) neural distinction from autonomic arousal, wakefulness, and stimulation modality (24 studies, n=868). Affective arousal was encoded in distributed cortical-subcortical (e.g., prefrontal, PAG) systems with local similarities in thalamo-amygdala-insula systems between affective and autonomous arousal. We demonstrate application of the BAAS to improve specificity of established valence-specific neuromarkers. Our study provides a biologically plausible model for affective arousal that aligns with the affective space and has a high application potential.

neuroscience↗

bioRxiv2024

Molecular basis of enhanced GLP-1 signaling mediated by GLP-1(9-36) in conjunction with LSN3318839

Glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) is essential for glucose metabolism and energy balance. It is primarily activated by the endogenous hormone GLP-1(7-36) and its weaker metabolite GLP-1(9-36). Although GLP-1(9-36) was previously considered biologically inactive, emerging evidence indicate that it exerts cardioprotective and insulinotropic actions. Here, we present cryo-electron microscopy structures showing that GLP-1(9-36) binds to an atypical site composed of the upper halves of transmembrane helices 1 (TM1) and 2 (TM2), extracellular loop 1, and the extracellular domain, distinct from the binding site of GLP-1(7-36). Meanwhile, LSN3318839, an orally effective positive allosteric modulator selective for GLP-1(9-36), anchors in the TM1-TM2 cleft and repositions GLP-1(9-36) to adopt a binding pose like GLP-1(7-36), thereby enhancing GLP-1R-mediated signal transduction. Mutagenesis and molecular dynamics simulations confirmed the crucial interactions and structural adjustments involved in this modulation. Our study uncovers a novel binding mode of GLP-1 metabolite and allosteric modulation that augments GLP-1R signaling, both are potentially insightful to unveil the physiological role of GLP-1(9-36) and design better small molecule therapeutics targeting GLP-1R.

molecular biology↗

bioRxiv2024

Genomics-FM: Universal Foundation Model for Versatile andData-Efficient Functional Genomic Analysis

Artificial intelligence (AI) plays a crucial role in functional genomic analysis, offering great potential for comprehending biological phenomena such as heredity, development, diseases, and evolution. However, the development of AI models needs substantial labeled data, and these models are typically task-specific with limited generalizability to various applications. Here, we develop Genomics-FM, a genomic vocabulary driven foundation model that enables versatile and label-efficient functional genomic analysis. Specifically, Genomics-FM is first pretrained with ensemble genomic vocabulary on vast unlabelled data to learn comprehensive and generalizable representations and then finetuned with specific genomic vocabulary on limited labeled data to selectively activate and adapt the pretraining knowledge for specific tasks. We show that Genomics-FM significantly reduces the dependence on labeled data, and demonstrates the capability to outperform existing models across a comprehensive suite of tasks including genome annotation, epigenomic and expression profile prediction, and variant effect assessment. Remarkably, Genomics-FM even shows impressive zero-shot predictive capabilities across diverse species and tissues and exhibits noticeable adaptability to RNA-related tasks. With feasibility in data scarcity and even cross-domain biological scenarios, Genomics-FM will promote the broad application of AI and empower researchers to tackle previously insurmountable challenges, paving the way for groundbreaking research and discoveries.

bioinformatics↗

bioRxiv2024

Prkra is the double-stranded RNA sensor to mediate an embryonic integrated stress response

Double-stranded RNAs (dsRNAs), known as conserved pathogen-associated molecular patterns, are recognized by interferon-induced protein kinase R (PKR) to trigger an integrated stress response, characterized by the inhibition of global translation. However, the interferon system is inactive in pluripotent cells, thus the mechanism underlying dsRNA sensing and translational control is unclear. In this study, we utilized early zebrafish embryos as a model of pluripotent cells and discovered a PKR-independent blockage of translation initiation induced by dsRNA stimulation. Prkra dimer was identified as the genuine dsRNA sensor. Upon binding to dsRNAs, the dimerized dsRNA binding domain 3 becomes activated to sequester the eIF2 complexes from the translation machinery, leading to a hindrance in global protein synthesis. This distinctive embryonic stress response restricts RNA virus SVCV replication in zebrafish embryos but is also conserved in early mouse embryos and embryonic stem cells. Therefore, the Prkra-mediated dsRNA sensing and translation blocking mechanism potentially represents a common strategy for reestablishing physiological homeostasis in response to environmental stresses.

immunology↗

bioRxiv2024

Equip Fusobacterium nucleatum genetic tool kits with compatible shuttle vectors and engineered intermediatory E. coli strains for enhanced transformation efficiency

Fusobacterium nucleatum, an oral microbe, is implicated in various human diseases, including oral-related diseases and tumors. However, efficient transformation was only achieved in limited strains of this bacterium. The challenges in conducting molecular level investigations of most strains due to their genetic intractability have hindered the biological studies of F. nucleatum. The restriction-modification (RM) systems is one of the known obstacles for efficient DNA transformation. Here, we used single molecule real time sequencing to elucidate the RM recognition sites and the corresponding methyltransferases (MTases) in two F. nucleatum strains. Based on the identified MTases, we engineered intermediatory E. coli host strains to bypass the RM systems, and showed that the plasmids harbored by these intermediatory strains can be efficiently electro-transformed, reaching 5000 transformants per microgram plasmids, paving the way for the development of efficient genetic modification tools. Furthermore, we successfully demonstrated that the conjugation-based DNA delivery to F. nucleatum can bypass the requirement of MTase methylations. By exploring the native plasmids from F. nucleatum, we identified new backbones for construction of shuttle vectors and established a dual-plasmid system for the first time, offering new avenues for genetic manipulation in this bacterium. Additionally, we evaluate promoters with variable strengths with a luciferase-based reporter system in F. nucleatum, providing valuable insights for future gene editing studies in bacterium and contributing to our understanding of its pathogenesis. All the tools developed in this study was shared via the WeKwikgene (https://wekwikgene.wllsb.edu.cn/). Impact StatementFusobacterium nucleatum, a key opportunistic pathogen implicated in periodontal diseases, rheumatoid arthritis, and tumors, presents significant challenges due to its limited transformation efficiency and lack of gene-editing tools. In this study, we present an advancement -a streamlined and robust pipeline that enhances transformation efficiency by approximately 103-fold in F. nucleatum, reaching 5000 CFU per microgram plasmids. This represents a significant breakthrough, marking the first report to achieve such a remarkable improvement in transformation efficiency in this pathogen. This improvement paves the way for the genome-wide level mutagenesis study in this bacterium.

microbiology↗

bioRxiv2024

Single-Cell and Spatial Transcriptomic Analyses Deciphering the Three-Layer Architecture of Human Tuberculosis Granulomas

BackgroundGranulomas (defining tuberculosis histopathological feature) are central to the hosts defense against Mycobacterium tuberculosis, critically influencing patient outcomes. However, knowledge of human granulomas structure and function are incomplete. This study employs single-cell and spatial transcriptomics to dissect human granulomas cellular composition, structure, communication and function from 19 pulmonary, lymphatic and skeletal samples. ResultsOur study identified nine key immune-activated/signaling-active cell clusters. Notably, we delineated a three-layered granuloma structure: a core with macrophages (Macro-c09, Macro-c10) and occasional fibroblasts (Fib-c03); a fibroblast-rich (Fib-c01) periphery; and an immune-infiltrated intermediate layer comprising diverse immune-cells recruited by strong signaling-molecules (SPP1/MIF) from core/periphery cells. This study also shows granuloma heterogeneity across individuals and tissues. ConclusionsBy merging scRNA-seq with ST-seq, we offer an intricate single-cell perspective of granulomas spatial-structure and formation mechanisms, identify signaling-molecules and significantly changed genes as potential targets for host-directed tuberculosis immunotherapy, highlight fibroblasts crucial role in granuloma formation, and provide an important reference/improved understanding of TB.

microbiology↗

bioRxiv2024

Optimization of gene knockout approaches and practical solutions to sgRNA selection challenges in hPSCs with inducible Cas9 system

RationaleCRISPR/Cas9 has been extensively used to knock out genes, allowing the study of genetic loss-of-function in human pluripotent stem cells (hPSCs). However, the current use of the Cas9-sgRNA plasmid or iCas9 system for gene editing in hPSCs has resulted in limited and inconsistent editing efficiency, as well as labor-intensive work. Additionally, identifying single-guide RNAs (sgRNAs) with high cleavage efficiency and distinguishing them from ineffective ones, which efficiently induce frameshift INDELs (Indels and Deletions) but fail to eliminate target proteins expression, are major challenges in gene knockout experiments. MethodsThis study addresses above issues using an optimized doxycycline-induced spCas9-expressing hPSCs (hPSCs-iCas9) system. We initially developed this system by optimizing a number of parameters to maximize INDELs introducing efficiency in hPSCs-iCas9 cells. The INDELs determined by this system were then compared to predicted scores from three cleavage efficiency scoring algorithms to validate the algorithms accuracy and consistency. Furthermore, we conducted gene knockout using a set of sgRNAs targeting different exons of the ACE2 gene to achieve approximately 80% INDELs for each targeting locus. Western blotting was then performed to detect ACE2 protein expression levels, enabling the identification of potentially ineffective sgRNAs. ResultsSeveral critical factors, including cell tolerance to nucleofection stress, sgRNA stability, nucleofection frequency, and the cell-to-sgRNA ratio, were found to have significant impact on editing efficiency in hPSCs-iCas9. Fine-tuning these parameters markedly improved this efficiency, resulting in up to 93% INDELs for single gene knockout. The three scoring algorithms exhibited significant differences or even conflicts in scoring cleavage efficiency. Through comparing experimental observations to predicted scores, we discovered that the Benchling algorithm outperformed the other two in terms of accuracy and consistency. Furthermore, a sgRNA targeting exon 2 of ACE2 gene was quickly identified as ineffective, as evidenced by the edited cells pool containing 80% INDELs while ACE2 protein expression retained unchanged detected by Western blot. ConclusionThe findings of this study offer valuable insights into the optimal design of gene knockout experiments in hPSCs and provide practical solutions to sgRNA selection challenges for gene editing.

cell biology↗