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Publications and source records attributed to Liu, L..
Withdrawal StatementThe authors have withdrawn this manuscript because of a conflict of interest. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Exploring the fundamental mechanisms of organ regeneration is crucial for advancing regenerative medicine. The axolotl tail represents a unique opportunity to study regeneration of the primary axis including segmented muscle, vertebrae and skin. During tail development, muscle stem cells (MuSCs) displayed expected specificity to the muscle lineage. Tail amputation, however, induced expansion of MuSC potential yielding clonal contribution to muscle, connective tissue including cartilage, pericytes, and fibroblasts. This expanded potential was not observed during limb regeneration, and cross-transplantation showed these differences in potential are intrinsic. ScRNA-Seq profiling revealed that tail MuSCs revert to an embryonic mesoderm-like state. Through genetic manipulation involving the over-expression of constitutively active TGF-{beta} receptors or Smad7 (antagonist of TGF-{beta} signaling) in MuSCs, we demonstrated that the levels of TGF-{beta} signal determine the fate outcome of MuSCs to connective tissue lineage or muscle respectively. Our findings illustrate a fundamental difference between regeneration of primary axis versus limb and offers a novel stem cell source for regeneration of axial skeletal tissues.
Pathogenic microorganisms pose a significant threat to plant health and agricultural productivity worldwide. Herein, this study explores the potential of natural microbial communities as sources of biopesticides. We analyzed 20 soil and water samples from remote areas, isolating 121 colonies using nutrient agar. Antibacterial activity was assessed through agar diffusion, revealing that 12 colonies exhibited significant inhibitory effects against various pathogenic bacteria. Measurement of inhibition zones indicated that these colonies could produce antibiotics. Subsequently, molecular characterization with 16S rRNA and BLAST searches of 12 unidentified sequences highlighted substantial microbial diversity within the samples. This research underscores the promise of these natural microbial communities in developing biocontrol agents for managing plant diseases in greenhouse and field environments. Extraction and purification techniques could further refine these antibiotics, advancing sustainable agricultural practices.
AimThe pathogenesis and therapeutic strategies of Kawasaki disease (KD) are worth further exploring. Using single-cell RNA sequencing (scRNA-seq), our study aimed to explore the landscape of peripheral blood mononuclear cells (PBMCs) in patients with KD. MethodsWe analyzed the scRNA-seq data of three patients with KD and three healthy controls from the GSE168732 dataset. Additionally, we explored the immune profiles and immune cell subtypes of patients with KD. ResultsSignificantly increased B cells and decreased NK cells were observed in the KD group compared with that in the control group. Furthermore, six B cell subsets were identified in the PBMCs of patients with KD. Particularly, plasma cells (CD9+ and S100A9+ B cell clusters) distinctly increased in the KD group. CD9+ B cell cluster was characterized by vascular endothelial growth factor (VEGF) signaling-associated marker genes and DEGs. Meanwhile the S100A9+ B cell cluster was characterized by platelet aggregation marker genes. As for NK cells, CD16+CD56dim NK cells were enriched in the KD group. Cytotoxicity-related activating receptors (KLRD1,KLRC3) and cytotoxicity-associated genes (PRF1, NKG7, GZMA, GZMH, GNLY) were downregulated in the KD group. ConclusionCD9+ and S100A9+ plasma cells may contribute to CALs in KD by upregulating VEGF and activating platelet. In addition, decreased cytotoxicity of NK cells mediated by KLRD1/KLRC3 receptor may play a vital role in the development of KD. Our results suggested that plasma cells and NK cells could be promising targets for the treatment of KD.
Artificial Intelligence virtual cell (AIVC) holds transformative potential for biomedical research. Central to this vision is the systematic modeling of genetic and chemical perturbation phenotypes to accurately predict cellular dynamic states from diverse interventions. However, disparities in screening agents, library scales, experimental technologies, and data production efficiency hinder the integration, modeling, and analysis of the cross-data. Here we present UniPert-G2CP, a two-phase deep learning approach comprising i) UniPert, a multimodal molecular representation model that bridges genetic and chemical domains, and ii) G2CP (Genetic-to-Chemical Perturbation transfer learning), which systematically transforms CRISPR screen-based genetic insights into chemical perturbation modeling for cost-effective in silico drug screening. UniPert not only encodes multimodal perturbagens into a unified functionally interpretable sematic embedding space, but also improves phenotypic effect prediction for previously unseen gene perturbations and drug treatments. Building upon UniPert, G2CP successfully modeled large-scale cellular post-perturbation states spanning 4,994 gene and 7,821 compound perturbagens, while reducing modeling data costs by over 60%. We demonstrate that UniPert-G2CP enables efficient, generalizable simulations of multicellular, multi-domain perturbation cause-effect spaces, revealing differential cellular biological causality and informing mechanism-driven therapy. UniPert-G2CP opens new avenues for biological causal foundation model building, AIVC creation, and AI-powered precision medicine.
Besides the loss of blood and oxygen reaching the ischemic tissue, many secondary effects of ischemic stroke can cause additional tissue death, including inflammation, oxidative stress, and proteomic disturbances. Receptor-interacting serine/threonine kinase 2 (RIPK2) is an important mediator in the post-stroke inflammatory cascade that responds to signals and molecular patterns released by dead or dying cells in the ischemic area. We hypothesize that RIPK2 signaling worsens injury and neurological recovery post-stroke and that global deletion of Ripk2 will be protective following ischemic stroke in aged mice. Aged (18-24 months) male mice were subjected to permanent middle cerebral artery occlusion (pMCAO). Vertical grid, weight grip, and open field were conducted at baseline and on days 1, 2, 3, 8, 15, and 22 post-stroke. Cognitive tests (novel object recognition and Y-maze) were performed at baseline and day 28 post-stroke. Infarct size was measured using cresyl violet staining, and reactive gliosis was measured using Iba1 and GFAP staining at day 28 post-stroke. Global deletion of Ripk2 (Ripk2-/-) in aged mice resulted in smaller infarct volume and improved performance on vertical grid and weight grip tests compared to aged wildtype (WT) mice. Additionally, aged Ripk2-/- mice had less Iba1 staining in the ipsilateral cortex than the aged WT control mice. This study further elucidates the role of RIPK2 signaling in the ischemic cascade and expands our knowledge of RIPK2 in stroke to aged mice. These results support the hypothesis that RIPK2 signaling worsens injury post-stroke and may be an attractive candidate for therapeutic intervention.
Colonisation of the mosquito by the malarial parasite is critically reliant on the invasive ookinete stage. Ookinete invasion of mosquito is coordinated by the apical complex, a specialised parasite structure containing components for secretion, attachment and penetration. While studies have investigated cytoskeletal and secretory elements, it is currently unknown if signalling modules are present or functional at the apical complex. Here we elucidate the role of a cryptic cyclic nucleotide binding protein which we name CBP-O. PbCBP-O showed a marked localisation to the ookinete apex and disruption of the protein severely compromised ookinete invasion of mosquitos. Domain dissection analysis revealed that the N- and C-termini have distinct functions. Intriguingly, PbCBP-O exhibits dual binding specificity to both cGMP and cAMP. Our findings suggest the apical tip of the ookinete is a platform to transduce cyclic nucleotide signals essential for malaria parasite transmission. Author summaryMalaria parasites complete their life-cycle within mammalian and mosquito hosts requiring specialised forms to invade and establish infection in host tissue. In order to transmit to the mosquito, the parasite forms a motile ookinete that uses the apical end to attach and penetrate the mosquito midgut membrane. Previous studies have identified several proteins localised to the apex of the ookinete. However, functions of many of these proteins are unknown. Here, we dissect the role of a putative cyclic nucleotide binding protein, CBP-O, in establishing ookinete infection within the mosquito. We discovered that in the absence of the protein, efficiency of transmission is significantly compromised. Interestingly the ability of ookinetes to move was not affected, but the parasites were unable to pass through the midgut membrane. We also reveal that both N- and C-terminal domains of the protein perform distinct functions and are both required for parasite transmission. Sequence and spatial conservation of the protein across the phylum Apicomplexa suggests an equivalent and crucial function of CBP-O in these parasites.
Hypertrophic scar (HS) is a prevalent yet unresolved wound healing complication characterized by persistent hyperactive and proliferative fibroblasts, leading to excessive extracellular matrix (ECM) synthesis and collagen contraction. Our previous studies have identified epidermal stem cells (ESCs) as critical for wound healing and HS remodeling, with its extracellular vesicles (EVs) playing a vital role. However, the specific mechanisms remain unclear. In this study, we first discovered that ESC-EVs could effectively induce the mesenchymal-epidermal transition (MET) of HS fibroblasts (HSFs) and inhibit their biological activity. Furthermore, by next-generation sequencing and multiplexed CRISPR/Cas9 system, we elucidated that this therapeutic effect is mediated by the miR-200 family (miR-200s) encapsulated in ESC-EVs, which targeted and inhibited ZEB1 and ZEB2 in HSFs. This vital role and mechanism have been thoroughly validated in both in vitro cell experiments and in vivo rat tail HS (RHS) models. These findings not only shed light on a previously unidentified mechanism of ESC-EVs for HS, but also provide potential novel targets and strategies for its precise treatment.
The wide use of Streptococcus pneumoniae capsular polysaccharide (CPS) conjugate vaccines is causing serotype replacement and the emergence of serotype 35B is concerning because of its multidrug resistance. CPS of 35B is composed of pentasaccharide repeating units that are linked through phosphodiester linkages. One of the galactofuranose residues of the pentasaccharide is acetylated, which distinguishes it from the invasive serotype 35D lacking the acetyl ester. Here, we describe a synthetic approach that can provide oligosaccharides derived of CPS 35B and 35D composed of up to 15 monosaccharides using a pentasaccharide building block equipped with four orthogonal protecting groups. The synthetic compounds were used to examine binding properties of ficolin-2, which is a protein that can activate the lectin pathway of the complement system. It was found that O-acetylation is essential for recognition by ficolin-2 requiring at least two repeating units. The data provides a rationale why 35D may escape immune detection and be more invasive. The synthetic oligosaccharides were also investigated for binding to pneumococcal serum factor 35a and 29b, which are employed for serotype identification. It indicates that immunization with 35B CPS will not provide protection against 35D and thus inclusion of 35B in vaccines may result in serotype replacement by 35D. On the other hand, antibodies that can bind 35D can recognize 35B and thus 35D CPS may provide cross protection. Our findings have direct implementation for the development of the next generation pneumococcal vaccine and provide an understanding of disease severity by the emerging serotype 35B and 35D.
The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.
Conventional management of diabetes via injection or external insulin pumps suffers from inconvenience and inability to accurately maintain blood glucose levels. A potential solution to these problems consists of implanting synthetic artificial {beta}-cells that can sense glucose and transcribe insulin protein. We focus on one such artificial {beta}-cell recently described in the work of Xie et al. Experimental results show these cells are able to release insulin and somewhat improve postprandial glucose levels in diabetic mice. However, they fail to achieve the degree of glucose regulation as in healthy mice. In our analysis, we explain that this artificial {beta}-cell system has a major disadvantage: it is a high-dimensional dynamic system but with little tuning space. Here, we propose a PID-controller-based enhanced artificial {beta}-cell design to solve this issue. Our results based on an analytical model and numerical simulations show that the computational method of PID-control can enhance engineered artificial {beta}-cells, such that they could perform better in regulating glucose levels in Type 1 diabetic mice compared with artificial {beta}-cells without PID-control: they could shut down the production of insulin in time and maintain a proper glycemia level, and there is more tuning space for artificial {beta}-cells with PID control.
Acute myeloid leukemia (AML) patients are often older, which brings challenges of endurance and persistent efficacy of autologous CAR-T cell therapies. Allogenic CAR-NK cell therapies may offer reduced toxicities and enhanced anti-leukemic potential against AML. In this study, we designed a novel CD33-mesothelin loop CAR (Loop CAR) and evaluated its anti-tumor efficacy in human umbilical cord blood-derived NK (UCB-NK) cells and human pluripotent stem cell-derived NK (hPSC-iNK) cells. The Loop CAR exhibited superior cytotoxicity against dual-antigen-positive tumor cell lines and primary AML cells. To further avoid fratricide caused by endogenous CD33 expression in NK cells, we established a hPSC-derived cell line via knockout of CD33 gene (CD33KO) and engineered Loop CAR. Rather than enforced expression of exogenous CD16, we generated abundant mature CD33KO-Loop CAR-iNK cells highly expressing endogenous CD16 via an organoid induction approach. This innovative strategy effectively mitigated NK cell fratricide and significantly enhanced CD33 and mesothelin-mediated specific cytotoxicity. Moreover, the CD33KO-Loop CAR-iNK cells demonstrated superior tumor-killing activity in AML xenograft mice and significantly prolonged survival. hPSC-derived CD33KO-Loop CAR-iNK cells possess unique advantages and translational potential for treating AML.
BackgroundT cell malignancies are highly aggressive hematological tumors with limited effective treatment options. CAR-NK cell therapy targeting CD7 has emerged as a promising approach for treating T-cell malignancies. However, conventional CAR-NK cell therapy faces the challenges of cell fratricide due to CD7 expression on both malignant cells and normal NK cells. Additionally, engineering CARs into human tissue-derived NK cells demonstrates heterogeneity, low transduction efficiency, and high manufacturing costs. MethodsThe human pluripotent stem cells (hPSCs) were genetically modified by knocking out the CD7 gene and introducing the CD7 CAR expression cassette to generate CD7 KO-CD7 CAR-hPSCs. These modified hPSCs were subsequently differentiated into CD7 KO-CD7 CAR-iNK cells using an efficient organoid induction method. The cytotoxicity of CD7 KO-CD7 CAR-iNK cells against CD7+ tumor cells was evaluated. Furthermore, we overexpressed the CXCR4 gene in CD7 KO-CD7 CAR-hPSCs and derived CXCR4-expressing CD7 KO-CD7 CAR-iNK (CRO-CD7 CAR-iNK) cells. The dynamics of CRO-CD7 CAR-iNK cells in vivo were tracked, and their therapeutic efficacy was assessed using human T-cell acute lymphoblastic leukemia (T-ALL) xenograft models. ResultsThe CD7 KO-CD7 CAR-iNK cells derived from CD7 KO-CD7 CAR-hPSCs effectively avoided fratricide, demonstrated normal expansion, and exhibited potent and specific anti-tumor activity against CD7+ T-cell tumor cell lines and primary T-ALL cells. CXCR4 overexpression in CRO-CD7 CAR-iNK cells improved their homing capacity and extended their persistence in vivo. The CRO-CD7 CAR iNK cells significantly suppressed tumor growth and prolonged the survival of T-ALL tumor-bearing mice. ConclusionsOur study provides a reliable strategy for the large-scale generation of fratricide-resistant CD7 CAR-iNK cells with robust anti-tumor effects from hPSCs, offering a promising cell product to treat T-cell malignancy.
Plant volatiles shape plant-plant interactions by acting as defense regulators and response factors. While plant volatile biosynthesis is well understood, how their emission is regulated remains largely elusive. Here, we show that small peptide signaling regulates induced volatile release in maize. Following herbivore attack, green leaf volatiles such as (Z)-3-hexenyl acetate (HAC) are released and induce terpene and indole emissions from neighboring plants. This process is accompanied by reduced expression of the ZmCLE1E9 gene and the ZmBAM1A, ZmBAM1B and ZmBAM3C receptor genes in HAC-exposed plants. Exogenous ZmCLE1E9 peptide inhibits HAC-triggered volatile release by limiting stomatal aperture. This inhibition disappears in the Zmbam1a/Zmbam1b/Zmbam3c triple mutant. Molecular docking supports ZmCLE1E9 and ZmBAMs as ligand-receptor pairs. Furthermore, Zmcle1e9 and Zmbams triple mutants show increased volatile emissions upon HAC exposure. In summary, we show that upon HAC perception, maize plants enhance their capacity to release terpenes and indole via the suppression of CLE1E9 signaling. This behavior allows maize plants to rapidly deploy volatile cues in response to stress volatiles and thus shape the infochemical dynamics of multitrophic environments.
MicroRNAs (miRNAs) are generally evolutionarily conserved, but a small number of them are found exclusively in primates. MiR-1202 is a primate-specific miRNA that was previously revealed as being involved in major depression disorder (MDD). Moreover, the genomic locus where miR-1202 locates (6q25.3) is strongly associated with recurrent early-onset MDD and neurodevelopmental disorder. We hypothesize that miR-1202 plays a unique role in the brain in fine-tuning the transcriptional network that governs neurogenesis. Here, we reported that microdeletion of miR-1202 resulted in retarded organoid growth but enhanced dopaminergic (DA) neuron differentiation in midbrain organoids. Integrated analysis of miRNA-interacting targets and transcriptional changes in miR-1202 knockout cells revealed that APC2, a negative regulator of canonical WNT/{beta}-catenin pathway, was a downstream target of miR-1202. Knockdown of APC2 resulted in attenuated DA neurogenesis, in contrast to the enhanced DA neurogenesis in miR-1202 knockout cells. Treatments of the brain organoids with antidepressants increased miR-1202 expression and simultaneously inhibited APC2 expression. Consistently, APC2 expression was found to increase in MDD patients. Our results suggest that miR-1202 regulates dopamine neurogenesis by inhibiting the APC2/WNT signaling pathway, which plays a distinct role in the midbrain-hindbrain regional patterning during the early development of the central nervous system.
More than half of epileptic patients ultimately turned to intractable epilepsy. Mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), the most common type of intractable epilepsies, whose pathological mechanism remains elusive. Here, using 42 human hippocampal samples from surgical donors of MTLE (32 with and 10 without HS) through single-cell resolution Stereo-seq and histologcial experiments, we revealed spatially pathological changes of gene expression and cell type composition with HS systematically. After precise parcellation of hippocampal subregions and differentially expressed gene (DEG) analysis between each region with and without sclerosis, we found Cornu Ammonis (CA) subregions with higher number of DEGs were vulnerable to sclerosis, especially CA1 and CA3. Within CA1, we found that CA1-superficial and proximal areas were more vulnerable than CA1-deep and distal areas in sclerosis. Meanwhile, after analyzing 350,795 segmented cells from Stereo-seq, we found dramatically increasing density of astrocyte accompanied with significantly decreasing density of excitatory neurons in CA1, especially superficial and proximal CA1, and CA3 in sclerosis. In these two vulnerable subregions, proliferative astrocyte (P_astrocyte) and reactive astrocyte (R_astrocyte) were found to be enriched whereas apoptotic subtype of astrocyte (A_astrocyte), related with apoptotic pathway, was mainly located in alveus, which strengthened cell communication with reactive microglia (R_microglia) in HS, revealing the novel pathological feature in our work. The pseudotime analysis indicated that CA excitatory neurons underwent synaptic impairment, energy dysfunction, aging, and finally losing cell identity until death through autophagy or apoptosis. Besides, we also found a resilient subtype, EX_CA2-4.3, highly expressed extracellular matrix related genes including PDYN, and was increasing the interaction of BDNF-NTRK, NFASC-CNTN1 to withstand the damage from sclerosis. Together, our study provided a reference of human hippocampus with and without HS caused by MTLE, and highlighted the potential pathological mechanism on molecular and cellular level of MTLE-HS.
Adaptive immunity, mediated by T and B cell responses, is essential for defending against infections and cancers while also being implicated in autoimmune diseases. Tracking T and B cell repertoires in situ at single-cell resolution is essential for understanding adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we developed Stereo-XCR-seq, an efficient strategy for retrieving and sequencing TCR and BCR from Stereo-seq cDNA libraries at subcellular resolution. Stereo-XCR-seq provides unbiased full-length XCR reads alongside spatial transcriptomics, enabling the identification of heterogeneous lymphoid aggregates with distinct clonal activities in cancers and inflammatory bowel disease (IBD). We identified plasma cell aggregates that differ from tertiary lymphoid structures (TLSs) in both transcriptomic profiles and clonal activities, with spatial positioning potentially mediating unique immune responses. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities within tissue microenvironments, providing insights into lymphocyte adaption to environmental stimuli. This technology provides potential for advancing our understanding of tissue immunity and the development of therapeutic strategies for immune disorders.
The link between cancer maintenance and an ability to sustain continued growth through stresses conferred by the cancer state itself is growing. However, there are significant gaps in our understanding of how this stress is managed, particularly at the level of cancer initiating cells. Here, we identify proteins comprising the dynamic, stress-adaptive ribonucleoprotein complexes known as stress granules (SG) to be enriched among the factors essential for leukemic stem cell (LSC)-driven leukemic propagation. Focusing on core SG nucleator G3BP1, we dissect the role of SGs in human acute myeloid leukemia (AML), their targetability, and the mechanisms they govern to uncover a novel propensity for AML, and in particular LSC-enriched fractions, to prime the expression of SG components, form SGs with greater fidelity and to be reliant on their establishment and continued integrity for LSC maintenance. We further unveil the transcript and protein interactome of G3BP1 in the AML context and show that consolidated control of innate immune signaling, and apoptosis repression is executed through regional binding specificity of G3BP1 to highly structured 3UTRs and cooperation with the RNA helicase UPF1 to mediate transcript decay in SGs. Altogether our findings advance novel fundamental principles of stress adaptation exploited in AML and LSCs that may extend to other cancers and uncover SGs as a novel axis for therapy development.