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Colorectal cancer (CRC) is a prevalent malignant tumor globally,ranking third in incidence and second in mortality. Metastasis is the main cause of death in patients with CRC. Solanum nigrum L. (SNL),a traditional Chinese medicinal herb endowed with detoxification,blood circulation enhancement,and anti-swelling properties,has been widely used in folk prescriptions for cancer treatment in China. Solamargine (SM) is the major steroidal alkaloid glycoside purified from SNL. However,its role and mechanism against metastatic CRC are not yet clear. The purpose of this study was to evaluate the inhibitory effect of SM on human hepatic metastatic CRC and investigate its underlying mechanism. CCK-8 assay,colony-formation assay,transwell assay,flow cytometry,tumoursphere formation assay,reverse-transcription quantitative PCR (RT-qPCR),Western blotting,transcriptomic sequencing and ferroptosis analysis were performed to reveal the efficacy and the underlying mechanism of SM in CRC cell lines. In vivo,allograft model,patient-derived xenograft (PDX) model,and liver metastatic model were performed to verify the effect of SM on the growth and metastasis of CRC. SM was found to suppress hepatic metastasis in CRC by effectively targeting key cellular processes,including proliferation,survival,and stemness. RNA sequencing showed that SM could induce ferroptosis,which was confirmed by elevated lipid reactive oxygen species (ROS) and downregulated glutathione peroxidase 4 (GPX4) and glutathione synthetase (GSS) in CRC cells and xenografts. Induction of ferroptosis by SM was regulated by nuclear factor erythroid 2-related factor 2 (Nrf2). Furthermore,downregulation of β-catenin was found to be fundamental for the SM-enabled cancer stem cells (CSCs) elimination and metastasis blockage in CRC. Our results indicated that SM is a promising therapeutic drug to inhibit hepatic metastasis in CRC by inducing ferroptosis and impeding CSCs. The online version contains supplementary material available at 10.1186/s13020-025-01171-5. View Publication

Cell therapy is promising for heart failure treatment,with growing interest in cardiovascular progenitor cells (CPCs) from pluripotent stem cells. A major challenge is managing the immune response,due to their allogeneic source. Regulatory T cells (Treg) offer an alternative to pharmacological immunosuppression by inducing immune tolerance. This study assesses whether Treg therapy can mitigate the xeno-immune response,improving cardiac outcomes in a mouse model of human CPC intramyocardial transplantation. CPCs stimulated immune responses in allogeneic and xenogeneic settings,causing proliferation in T cell subsets. Tregs showed immunosuppressive effects on T lymphocyte populations when co-cultured with CPCs. Post infarction,CPCs were transplanted intramyocardially into an immune-competent mouse model 3 weeks after myocardial infarction. Human or murine Tregs were intravenously administered on transplantation day and three days later. Control groups received CPCs without Tregs or saline (PBS). CPCs with Tregs improved LV systolic function in three weeks,linked to reduced myocardial fibrosis and enhanced angiogenesis. This was accompanied by decreased splenocyte NK cell populations and pro-inflammatory cytokine levels in cardiac tissue. Treg therapy with CPC transplantation enhances cardiac functional and structural outcomes in mice. Though it does not directly avert graft rejection,it primarily affects NKG2D+ cytotoxic cells,indicating systemic immune modulation and remote heart repair benefits. View Publication

The clinical application of T cells engineered with chimeric antigen receptors (CARs) for solid tumors is challenging. A major reason for this involves tumor immune evasion mechanisms,including the high expression of immune checkpoint molecules,such as the programmed death 1 (PD-1) ligands PD-L1 and PD-L2. The inducible expression of PD-L1 in tumors has been observed after CAR-T-cell infusion,even in tumors natively not expressing PD-L1. Furthermore,numerous types of pediatric cancer do not have suitable targets for CAR-T-cell therapy. Therefore,the present study aimed to develop novel CAR-T cells that target PD-L1 and PD-L2,and to evaluate their efficacy against pediatric solid tumors. A novel CAR harboring the immunoglobulin V-set domain of the human PD-1 receptor as an antigen binding site (PD-1 CAR-T) was developed without using a single-chain variable fragment. PD-1 CAR-T cells were successfully manufactured by adding an anti-PD-1 antibody,nivolumab,to the ex vivo expansion culture to prevent fratricide during the manufacturing process due to the inducible expression of PD-L1 in activated human T cells. The expression of PD-L1 (and PD-L2 to a lesser extent) was revealed to be highly upregulated in various pediatric solid tumor cells,which displayed no or very low expression initially,on in vitro exposure to interferon-γ and/or tumor necrosis factor-α,which are cytokines secreted by tumor-infiltrating T cells. Furthermore,PD-1 CAR-T cells exhibited strong cytotoxic activity against pediatric solid tumor cells expressing PD-L1 and PD-L2. Conversely,the effect of PD-1 CAR-T cells was significantly attenuated against PD-L1-positive cells coexpressing CD80,suggesting that the toxicity of PD-1 CAR-T cells to normal immune cells,including antigen presenting cells,can be minimized. In conclusion,PD-1 ligands are promising therapeutic targets for pediatric solid tumors. PD-1 CAR-T cells,either alone or in combination with CAR-T cells with other targets,represent a potential treatment option for solid tumors. View Publication

In search for broad-spectrum antivirals,we discover a small molecule inhibitor,RMC-113,that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrate selective inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Lipidomics analysis reveals alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and links its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We identify PIP4K2C’s roles in SARS-CoV-2 entry,RNA replication,and assembly/egress,validating it as a druggable antiviral target. Integrating proteomics,single-cell transcriptomics,and functional assays,reveals that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced autophagic flux impairment. Promoting viral protein degradation by reversing autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C,an understudied kinase,and propose dual PIP4K2C and PIKfyve inhibition as a candidate strategy to combat emerging viruses. Subject terms: SARS-CoV-2,Target identification,Autophagy View Publication

Huntington’s disease (HD) is a neurodegenerative disorder caused by the expansion of CAG repeats in the HTT gene,which results in a long polyglutamine tract in the huntingtin protein (HTT). One of the earliest key molecular mechanisms underlying HD pathogenesis is transcriptional dysregulation,which is already present in the developing brain. In this study,we searched for networks of deregulated RNAs crucial for initial transcriptional changes in HD- and HTT-deficient neuronal cells. RNA-seq (including small RNAs) was used to analyze a set of isogenic human neural stem cells. The results were validated using additional methods,rescue experiments,and in the medium spiny neuron-like cells. We observed numerous changes in gene expression and substantial dysregulation of miRNA expression in HD and HTT -knockout ( HTT -KO) cell lines. The overlapping set of genes upregulated in both HD and HTT -KO cells was enriched in genes associated with DNA binding and the regulation of transcription. We observed substantial upregulation of the following transcription factors: TWIST1,SIX1,TBX1,TBX15,MSX2,MEOX2 and FOXD1 . Moreover,we identified miRNAs that were consistently deregulated in HD and HTT -KO cells,including miR-214,miR-199,and miR-9. These miRNAs may function in the network that regulates TWIST1 and HTT expression via a regulatory feed-forward loop in HD. On the basis of overlapping changes in the mRNA and miRNA profiles of HD and HTT -KO cell lines,we propose that transcriptional deregulation in HD at early neuronal stages is largely caused by a deficiency of properly functioning HTT rather than a typical gain-of-function mechanism. The online version contains supplementary material available at 10.1186/s13578-025-01443-5. View Publication

Genome‐wide association studies have implicated complement in Alzheimer's disease (AD). The CR1*2 variant of complement receptor 1 (CR1; CD35),confers increased AD risk. We confirmed CR1 expression on glial cells; however,how CR1 variants influence AD risk remains unclear. Induced pluripotent stem cell‐derived microglia and astrocytes were generated from donors homozygous for the common CR1 variants (CR1*1/CR1*1;CR1*2/CR1*2). CR1 expression was quantified and phagocytic activity assessed using diverse targets ( Escherichia coli bioparticles,amyloid β aggregates,and synaptoneurosomes),with or without serum opsonization. Expression of CR1*1 was significantly higher than CR1*2 on glial lines. Phagocytosis for all targets was markedly enhanced following serum opsonization,attenuated by Factor I‐depletion,demonstrating CR1 requirement for C3b processing. CR1*2‐expressing glia showed significantly enhanced phagocytosis of all opsonized targets compared to CR1*1‐expressing cells. CR1 is critical for glial phagocytosis of opsonized targets. CR1*2,despite lower expression,enhances glial phagocytosis,providing mechanistic explanation of increased AD risk. Induced pluripotent stem cell (iPSC)‐derived glia from individuals expressing the Alzheimer's disease (AD) risk variant complement receptor (CR) 1*2 exhibit lower CR1 expression compared to those from donors expressing the non‐risk form CR1*1. The iPSC‐derived glia from individuals expressing the AD risk variant CR1*2 exhibit enhanced phagocytic activity for opsonized bacterial particles,amyloid‐β aggregates and human synaptoneurosomes compared to those from donors expressing the non‐risk form CR1*1. We suggest that expression of the CR1*2 variant confers risk of AD by enhancing the phagocytic capacity of glia for opsonized targets. View Publication

Immunosenescence describes the gradual remodeling of immune responses,leading to disturbed immune homeostasis and increased susceptibility of older adults for infections,neoplasia and autoimmunity. Decline in cellular immunity is associated with intrinsic changes in the T cell compartment,but can be further pushed by age-related changes in cells regulating T cell immunity. Myeloid-derived suppressor cells (MDSCs) are potent inhibitors of T cell activation and function,whose induction requires chronic inflammation. Since aging is associated with low grade inflammation (inflammaging) and increased myelopoiesis,age-induced changes in MDSC induction and function in relation to T cell immunity were analyzed. MDSC numbers and functions were compared between “healthy” young and old adults,who were negatively diagnosed for severe acute and chronic diseases known to induce MDSC accumulation. MDSCs were either isolated from peripheral blood or generated in vitro from blood-derived CD14 cells. Aging was associated with significantly increased MDSC numbers in the monocytic- (M-) and polymorphonuclear (PMN-) MDSC subpopulations. MDSCs could be induced more efficiently from CD14 cells of old donors and these MDSCs inhibited CD3/28-induced T cell proliferation significantly better than MDSCs induced from young donors. Serum factors of old donors supported MDSC induction comparable to serum factors from young donors,but increased immunosuppressive activity of MDSCs was only achieved by serum from old donors. Elevated immunosuppressive activity of MDSCs from old donors was associated with major metabolic changes and increased intracellular levels of neutral and oxidized lipids known to promote immunosuppressive functions. Independent of age,MDSC-mediated suppression of T cell proliferation required direct MDSC– T cell contact. Besides their increased ability to inhibit activation-induced T cell proliferation,MDSCs from old donors strongly shift the immune response towards Th2 immunity and might thereby further contribute to impaired cell-mediated immunity during aging. These results indicate that immunosenescence of innate immunity comprises accumulation and functional changes in the MDSC compartment,which directly impacts T cell functions and contribute to age-associated impaired T cell immunity. Targeting MDSCs during aging might help to maintain functional T cell responses and increase the chance of healthy aging. The online version contains supplementary material available at 10.1186/s12979-025-00524-w. View Publication

Duplication 15q (dup15q) syndrome is a leading genetic cause of autism spectrum disorder,offering a key model for studying autism-related mechanisms. Using single-cell and single-nucleus RNA sequencing of cortical organoids from dup15q patient-derived iPSCs and post-mortem brain samples,we identify increased glycolysis,disrupted layer-specific marker expression,and aberrant morphology in deep-layer neurons during fetal-stage organoid development. In adolescent-adult postmortem brains,upper-layer neurons exhibit heightened transcriptional burden related to synaptic signaling,a pattern shared with idiopathic autism. Using spatial transcriptomics,we confirm these cell-type-specific disruptions in brain tissue. By gene co-expression network analysis,we reveal disease-associated modules that are well preserved between postmortem and organoid samples,suggesting metabolic dysregulation that may lead to altered neuron projection,synaptic dysfunction,and neuron hyperexcitability in dup15q syndrome. Subject terms: Autism spectrum disorders,Autism spectrum disorders,Disease model View Publication

R2 elements,a class of non-long terminal repeat (non-LTR) retrotransposons,have the potential to be harnessed for transgene insertion. However,efforts to achieve this are limited by our understanding of the retrotransposon mechanisms. Here,we structurally and biochemically characterize R2 from Taeniopygia guttata (R2Tg). We show that R2Tg cleaves both strands of its ribosomal DNA target and binds a pseudoknotted RNA element within the R2 3′ UTR to initiate target-primed reverse transcription. Guided by these insights,we engineer and characterize an all-RNA system for transgene insertion. We substantially reduce the system’s size and insertion scars by eliminating unnecessary R2 sequences on the donor. We further improve the integration efficiency by chemically modifying the 5′ end of the donor RNA and optimizing delivery,creating a compact system that achieves over 80% integration efficiency in several human cell lines. This work expands the genome engineering toolbox and provides mechanistic insights that will facilitate future development of R2-mediated gene insertion tools. Subject terms: Transferases,Protein design,Genetic engineering View Publication

p18 INK4 C (CDKN2C,encoded by p18 INK4c or Cdkn2c ) is an early G1-phase cyclin-dependent kinase inhibitor protein. Previous studies demonstrated enhanced self-renewal capacity of hematopoietic stem cells (HSCs) in p18 −/− mice compared to wild-type (WT) mice. Given the critical role of bone marrow niche cells-particularly mesenchymal stromal cells (MSCs)-in hematopoiesis,this study investigated the functional alterations of p18 −/− MSCs and their impact on hematopoietic support. Bone marrow derived MSCs were isolated from p18 −/− and WT mice. Their proliferation and differentiation capacities were assessed,followed by evaluation of hematopoietic support using cobblestone area-forming cell assay and long-term culture-initiating cell assay. RNA sequencing was performed to analyze the transcriptional profile of p18 −/− MSCs,with a focus on differentially expressed genes (DEGs). Key pathways associated with hematopoietic support were identified using Ingenuity Pathway Analysis. A candidate protein was quantified by ELISA,and its functional role in hematopoietic support was validated via a modified coculture system. p18 −/− MSCs displayed an increased proliferation rate,preferential differentiation toward osteogenesis over adipogenesis,and enhanced hematopoietic support. RNA sequencing analysis identified 137 DEGs,with secreted phosphoprotein 1 ( Spp1,encoding osteopontin,Opn) being significantly upregulated in p18 −/− MSCs. Elevated Opn levels were confirmed in both bone marrow and MSC-conditioned media from p18 −/− mice. Functional validation further demonstrated that Opn enhanced the hematopoietic supportive capacity of MSCs in vitro. p18 deficiency promotes osteogenic differentiation and enhances the hematopoietic supportive function of MSCs,likely mediated by Opn upregulation. These findings suggest a potential therapeutic strategy for improving bone regeneration and HSC expansion. The online version contains supplementary material available at 10.1186/s13287-025-04402-6. View Publication

The impact of exogenous stressors,such as cancer chemotherapies,on the genomic integrity and clonal dynamics of normal hematopoiesis is not well defined. We conducted whole-genome sequencing on 1,276 single-cell-derived hematopoietic stem and progenitor cell (HSPC) colonies from ten patients with multiple myeloma treated with chemotherapies and six normal donors. Melphalan treatment significantly increased the mutational burden,producing a distinctive mutation signature,whereas other chemotherapeutic agents had minimal effects. Consequently,the clonal diversity and architecture of post-treatment HSPCs resemble those observed in normal elderly individuals,particularly through the progression of oligoclonal hematopoiesis,thereby suggesting that chemotherapy accelerates clonal aging. Integrated phylogenetic analysis of matched therapy-related myeloid neoplasm samples traced their clonal origin to a single-HSPC clone among multiple competing clones,supporting a model of oligoclonal to monoclonal transformation. These findings underscore the need for further systematic research on the long-term hematological consequences of cancer chemotherapy. Subject terms: Genetics research,Acute myeloid leukaemia View Publication

Kidney organoids derived from human induced pluripotent stem cells lack a proper vasculature,hampering their applicability. Transplantation prevents the loss of organoid endothelial cells (ECs) observed in vitro,and promotes vascularization. In this study,we transplanted kidney organoids in chicken embryos and deployed single-cell RNA sequencing of ~12,000 organoid ECs to delineate their molecular landscape and identify key changes associated with transplantation. Transplantation significantly altered EC phenotypic composition. Consistent with angiogenesis,proliferating EC populations expanded 8 days after transplantation. Importantly,ECs underwent a major vein-to-arterial phenotypic shift. One of the transplantation-specific arterial EC populations,characterized by laminar shear stress response and Notch signalling,showed a similar transcriptome as human fetal kidney arterial/afferent arteriolar ECs. Consistently,transplantation-induced transcriptional changes involved proangiogenic and arteriogenic SOX7 transcription factor upregulation and regulon enrichment. These findings point to blood flow and candidate transcription factors such as SOX7 as possible targets to enhance kidney organoid vascularization. Subject terms: Nephrons,Transcriptomics,Angiogenesis,Angiogenesis,Stem cells,Stem-cell differentiation View Publication