技术资料

The COVID-19 pandemic has created a global health crisis,with challenges arising from the ongoing evolution of the SARS-CoV-2 virus,the emergence of new strains,and the long-term effects of COVID-19. Aiming to overcome the development of viral resistance,our study here focused on developing broad-spectrum pan-coronavirus antiviral therapies by targeting host protein quality control mechanisms essential for viral replication. Screening an in-house compound library led to the discovery of three candidate compounds targeting cellular proteostasis. The three compounds are (1) the nucleotide analog cordycepin,(2) a benzothiozole analog,and (3) an acyldepsipeptide analog initially developed as part of a campaign to target the mitochondrial ClpP protease. These compounds demonstrated dose-dependent efficacy against multiple coronaviruses,including SARS-CoV-2,effectively inhibiting viral replication in vitro as well as in lung organoids. Notably,the compounds also showed efficacy against SARS-CoV-2 delta and omicron strains. As part of this work,we developed a BSL2-level cell-integrated SARS-CoV-2 replicon,which could serve as a valuable tool for high-throughput screening and studying intracellular viral replication. Our study should aid in the advancement of antiviral drug development efforts. Subject terms: High-throughput screening,Small molecules View Publication

Embryonic stem cells possess the remarkable ability to self-organize into blastocyst-like structures upon induction. These stem cell-based embryo models serve as invaluable platforms for studying embryogenesis and therapeutic developments. Nevertheless,the specific intrinsic regulators that govern this potential for blastoid formation remain unknown. Here we demonstrate an intrinsic program that plays a crucial role in both blastoids and blastocysts across multiple species. We first establish metrics for grading the resemblance of blastoids to mouse blastocysts,and identify the differential activation of gene regulons involved in lineage specification among various blastoid grades. Notably,abrogation of nuclear receptor subfamily 1,group H,member 2 (Nr1h2) drastically reduces blastoid formation. Nr1h2 activation alone is sufficient to rewire conventional ESC into a distinct pluripotency state,enabling them to form blastoids with enhanced implantation capacity in the uterus and contribute to both embryonic and extraembryonic lineages in vivo. Through integrative multi-omics analyses,we uncover the broad regulatory role of Nr1h2 in the transcriptome,chromatin accessibility and epigenome,targeting genes associated with embryonic lineage and the transposable element SINE-B1. The Nr1h2-centred intrinsic program governs and drives the development of both blastoids and early embryos. Subject terms: Embryonic stem cells,Pluripotency,Epigenomics View Publication

Breast cancer is a heterogeneous disease comprising multiple molecularly distinct subtypes with varied prevalence,prognostics,and treatment strategies. Among them,triple-negative breast cancer,though the least prevalent,is the most aggressive subtype,with limited therapeutic options. Recent emergence of competing endogenous RNA (ceRNA) networks has highlighted how long noncoding RNAs (lncRNAs),microRNAs (miRs),and mRNA orchestrate a complex interplay meticulously modulating mRNA functionality. Focusing on TNBC,this study aimed to construct a ceRNA network using differentially expressed lncRNAs,miRs,and mRNAs. We queried the differentially expressed lncRNAs (DElncRNAs) between TNBC and luminal samples and found 389 upregulated and 386 downregulated lncRNAs,including novel transcripts in TNBC. DElncRNAs were further evaluated for their clinical,functional,and mechanistic relevance to TNBCs using the lnc2cancer 3.0 database,which presented LUCAT1 (lung cancer-associated transcript 1) as a putative node. Next,the ceRNA network (lncRNA–miRNA–mRNA) of LUCAT1 was established. Several miRNA–mRNA connections of LUCAT1 implicated in regulating stemness (LUCAT1-miR-375-Yap1,LUCAT1-miR181-5p-Wnt,LUCAT1-miR-199a-5p-ZEB1),apoptosis (LUCAT1-miR-181c-5p-Bcl2),drug efflux (LUCAT1-miR-200c-ABCB1,LRP1,MRP5,MDR1),and sheddase activities (LUCAT1-miR-493-5p-ADAM10) were identified,indicating an intricate regulatory mechanism of LUCAT1 in TNBC. Indeed,LUCAT1 silencing led to mitigated cell growth,migration,and stem-like features in TNBC. This work sheds light on the LUCAT1 ceRNA network in TNBC and implies its involvement in TNBC growth and progression. View Publication

Erythropoiesis is a crucial process in hematopoiesis,yet it remains highly susceptible to disruption by various diseases,which significantly contribute to the global challenges of anemia and blood shortages. Current treatments like erythropoietin (EPO) or glucocorticoids often fall short,especially for hereditary anemias such as Diamond-Blackfan anemia (DBA). To uncover new erythropoiesis-stimulating agents,we devised a screening system using primary human hematopoietic stem and progenitor cells (HSPCs). We discovered that BRAF inhibitors (BRAFi),commonly used to treat BRAF V600E melanoma,can unexpectedly and effectively promote progenitor cell proliferation by temporarily delaying erythroid differentiation. Notably,these inhibitors exhibited pronounced efficacy even under cytokine-restricted conditions and in patient samples of DBA. Mechanistically,although these BRAFi inhibit the MAPK cascade in BRAF V600E mutant cells,they paradoxically act as amplifiers in wild-type BRAF cells,potently enhancing the cascade. Furthermore,we found that while the oncogenic BRAF V600E mutation disrupts hematopoiesis and erythropoiesis through AP-1 hyperactivation,BRAFi minimally impact HSPC self-renewal and differentiation. In vivo studies have shown that BRAFi can enhance human hematopoiesis and erythropoiesis in severe immunodeficient mouse models and alleviate anemia in the Rpl11 haploinsufficiency DBA model,as well as other relevant anemia models. This discovery underscores the role of the MAPK pathway in hematopoiesis and positions BRAFi as a promising therapeutic option for improving hematopoietic reconstitution and treating anemias,including DBA. Subject terms: Drug screening,Molecular medicine View Publication

Rationale: Immune checkpoint inhibitors (ICIs) have demonstrated significant efficacy against head and neck squamous cell carcinoma (HNSCC),but their overall response rate (ORR) remains limited. Previous studies have highlighted the crucial role of sphingosine kinases (SPHKs) in the tumor microenvironment (TME); however,their function in immunotherapy remains unclear. Methods: We conducted comprehensive bioinformatics analysis,functional studies,and clinical validation,to investigate the role of SPHK1 in the immunology of HNSCC. Results: Functionally,SPHK1 significantly promoted tumor growth by inhibiting anti-tumor immunity in immune-competent HNSCC mouse models and tumor-T cell co-cultures. Mechanistic analysis revealed that SPHK1 regulated matrix metalloproteinase-1 (MMP1) expression via the MAPK1 pathway,which subsequently influenced tumor programmed cell death ligand 1 (PD-L1) expression. Furthermore,SPHK1 and MMP1 could predict the efficacy of programmed cell death 1 monoclonal antibody (PD-1 mAb) immunotherapy in HNSCC and were independent risk factors for survival in patients with HNSCC. Conclusion: Our study reveals a novel role for SPHK1 in mediating immune evasion in HNSCC through the regulation of the MMP1-PD-L1 axis. We identified SPHK1 and MMP1 as predictive biomarkers for the therapeutic response to PD-1 mAb and provided new therapeutic targets for patients with HNSCC. View Publication

Infusion of T cells modified with a chimeric antigen receptor (CAR) targeting CD19 has achieved exceptional responses in patients with non-Hodgkin’s lymphoma (NHL),which led to the approval of CAR targeting CD19 (CART19) (Axi-cel and Liso-cel) as second line of treatment for adult patients with relapsed/refractory NHL. Unfortunately,60% of patients still relapse after CART19 due to either a loss of expression of the target antigen (CD19) in the tumor cell,observed in 27% of relapsed patients,a limited CAR-T persistence,and additional mechanisms,including the suppression of the tumor microenvironment. Clinic strategies to prevent target antigen loss include sequential treatment with CARs directed at CD20 or CD22,which have caused loss of the second antigen,suggesting targeting other antigens less prone to disappear. CD79b,expressed in NHL,is a target in patients treated with antibody-drug conjugates (ADC). However,the limited efficacy of ADC suggests that a CAR therapy targeting CD79b might improve results. We designed three new CARs against CD79b termed CAR for Lymphoma (CARLY)1,2 and 3. We compared their efficacy,phenotype,and inflammatory profiles with CART19 (ARI0001) and CARTBCMA (ARI0002h),which can treat NHL. We also analyzed the target antigen’s expression loss (CD79b,CD19,and B-cell maturation antigen(BCMA)). We found that CARLY2 and CARLY3 had high affinity and specificity towards CD79b on B cells. In vitro,all CAR-T cells had similar anti-NHL efficacy,which was retained in an NHL model of CD19 − relapse. In vivo,CARLY3 showed the highest efficacy. Analysis of the loss of the target antigen demonstrated that CARLY cells induced CD79b and CD19 downregulation on NHL cells with concomitant trogocytosis of these antigens to T cells,being most notorious in CARLY2,which had the highest affinity towards CD79b and CD19,and supporting the selection of CARLY3 to design a new treatment for patients with NHL. Finally,we created a CAR treatment based on dual targeting of CD79b and BCMA to avoid losing the target antigen. This treatment showed the highest efficacy and did not cause loss of the target antigen. Based on specificity,efficacy,and loss of the target antigen,CARLY3 represents a potential novel CAR treatment for NHL. View Publication

Our study highlights the role of epigenetic machinery in transformation of normal pluripotent stem cells to variant pluripotent state. We demonstrate the importance of non-histone protein methylation,which underlie the EMT and abnormal differentiation behaviour of variant hESCs. View Publication

PRDX2 is significantly expressed in various cancers and is associated with the proliferation of tumor cells. Nonetheless,the precise mechanism of PRDX2 in tumor immunity remains incompletely understood. This study aims to investigate the impact of PRDX2,which is highly expressed in lung adenocarcinoma,on T cells in the tumor immune microenvironment,and its immune action target to promote the immune escape of lung cancer cells,to provide a theoretical basis for lung adenocarcinoma treatment with PRDX2 as the target. Mouse animal models to verify the effect of Conoidin A treatment on tumor growth and T cell infiltration. Flow cytometry and Western blot verified tumor cell apoptosis in the in vitro co-culture system as well as granzyme B and perforin expression in T cells. RNA-Seq was used to obtain the downstream immune molecule. si-RNA knockdown of Galectin-9 was co-cultured with T cells in vitro. Immunofluorescence and Western blot verified that PRDX2 regulates Galectin-9 expression through HDAC3. PRDX2 expression was negatively correlated with CD8 + T cell expression in LUAD patients. Inhibition of PRDX2 significantly enhanced T-cell killing of LUAD cells and reduced tumor load in both in vitro and in vivo models. Mechanistically,Conoidin A or shRNA_PRDX2 decreased Galectin-9 expression by down-regulating the phosphorylation of HDAC3,consequently enhancing the infiltration and function of CD8 + T cells. This study reveals the role of the PRDX2/HDAC3/Galectin-9 axis in LUAD immune escape and indicates Galectin-9 as a promising target for immunotherapy. The online version contains supplementary material available at 10.1186/s12967-024-05888-z. View Publication

Chordoma is a slow-growing,primary malignant bone tumor that arises from notochordal tissue in the midline of the axial skeleton. Surgical excision with negative margins is the mainstay of treatment,but high local recurrence rates are reported even with negative margins. High-dose radiation therapy (RT),such as with proton or carbon ions,has been used as an alternative to surgery,but late local failure remains a problem. B7-H3 is an immune checkpoint,transmembrane protein that is dysregulated in many cancers,including chordoma. This study explores the efficacy of B7-H3 chimeric antigen receptor T (CAR-T) therapy in vitro and in vivo. Chordoma cancer stem cells (CCSCs) were identified using flow cytometry,sphere formation,and western blot analysis. The expression of B7-H3 in paraffin-embedded chordoma tissue was determined by immunohistochemical staining,and the expression of B7-H3 in chordoma cells was measured by flow cytometry. Retroviral particles containing either B7-H3 or CD19 CAR-expressing virus were transduced into T cells derived from peripheral blood mononuclear cells isolated from healthy human donor blood to prepare CAR-T cells. Animal bioluminescent imaging was used to evaluate the killing effect of CAR-T cells on chordoma cells in vivo. An irradiator was used for all irradiation (IR) experiments. The combination of B7-H3 CAR-T cell therapy and IR has a greater killing effect on killing radiation-resistant CCSCs and bulk chordoma cells compared with CAR-T cell or IR monotherapy. Additionally,increased expression of B7-H3 antigens on CCSCs and bulk tumor cells is associated with enhanced CAR-T cell killing in vitro and in vivo xenograft mouse models. Upregulation of B7-H3 expression by IR increases CCSCs sensitivity to B7-H3 CAR-T cell-mediated killing. Our preliminary data show that IR and B7-H3 CAR-T cell therapy is synergistically more effective than either IR or CAR-T cell monotherapy in killing chordoma cells in vitro and in a xenograft mouse model. These results provide preclinical evidence for further developing this combinatorial RT and B7-H3 CAR-T cell therapy model in chordoma View Publication

GABA B receptor (GABA B R) activation is known to alleviate pain by reducing neuronal excitability,primarily through inhibition of high voltage‐activated (HVA) calcium (Ca V 2.2) channels and potentiating G protein–coupled inwardly rectifying potassium (GIRK) channels. Although the analgesic properties of small molecules and peptides have been primarily tested on isolated murine dorsal root ganglion (DRG) neurons,emerging strategies to develop,study,and characterise human pluripotent stem cell (hPSC)‐derived sensory neurons present a promising alternative. In this study,hPSCs were efficiently differentiated into peripheral DRG‐induced sensory neurons (iSNs) using a combined chemical and transcription factor‐driven approach via a neural crest cell intermediate. Molecular characterisation and transcriptomic analysis confirmed the expression of key DRG markers such as BRN3A,ISLET1,and PRPH,in addition to GABA B R and ion channels including Ca V 2.2 and GIRK1 in iSNs. Functional characterisation of GABA B R was conducted using whole‐cell patch clamp electrophysiology,assessing neuronal excitability under current‐clamp conditions in the absence and presence of GABA B R agonists baclofen and α‐conotoxin Vc1.1. Both baclofen (100 μM) and Vc1.1 (1 μM) significantly reduced membrane excitability by hyperpolarising the resting membrane potential and increasing the rheobase for action potential firing. In voltage‐clamp mode,baclofen and Vc1.1 inhibited HVA Ca 2+ channel currents,which were attenuated by the selective GABA B R antagonist CGP 55845. However,modulation of GIRK channels by GABA B Rs was not observed in the presence of baclofen or Vc1.1,suggesting that functional GIRK1/2 channels were not coupled to GABA B Rs in hPSC‐derived iSNs. This study is the first to report GABA B R modulation of membrane excitability in iSNs by baclofen and Vc1.1,highlighting their potential as a future model for studying analgesic compounds. View Publication

Hematopoietic stem and progenitor cells (HSPCs) are critical for the treatment of blood diseases in clinic. However,the limited source of HSPCs severely hinders their clinical application. In the embryo,hematopoietic stem cells (HSCs) arise from hemogenic endothelial (HE) cells lining the major arteries in vivo. In this work,by engineering vascular niche endothelial cells (VN-ECs),we generated functional HSPCs in vitro from ECs at various sites,including the aorta-gonad-mesonephros (AGM) region and the placenta. Firstly,we converted mouse embryonic HE cells from the AGM region (aHE) into induced HSPCs (iHSPCs),which have the abilities for multilineage differentiation and self-renewal. Mechanistically,we found that VN-ECs can promote the generation of iHSPCs via secretion of CX3CL1 and IL1A. Next,through VN-EC co-culture,we showed that placental HE (pHE) cells,a type of extra-embryonic HE cells,were successfully converted into iHSPCs (pHE-iHSPCs),which have multilineage differentiation capacity,but exhibit limited self-renewal ability. Furthermore,comparative transcriptome analysis of aHE-iHSPCs and pHE-iHSPCs showed that aHE-iHSPCs highly expressed HSC-specific and self-renewal-related genes. Moreover,experimental validation showed that retinoic acid (RA) treatment promoted the transformation of pHE cells into iHSPCs that have self-renewal ability. Collectively,our results suggested that pHE cells possess the potential to transform into self-renewing iHSPCs through RA treatment,which will facilitate the clinical application of placental endothelial cells in hematopoietic cell generation. Subject terms: Haematopoietic stem cells,Haematopoietic stem cells View Publication

In contrast to mammals,adult zebrafish achieve complete heart regeneration via proliferation of cardiomyocytes. Surprisingly,we found that regenerating cardiomyocytes experience DNA replication stress,which represents one reason for declining tissue regeneration during aging in mammals. Pharmacological inhibition of ATM and ATR kinases revealed that DNA damage response signaling is essential for zebrafish heart regeneration. Manipulation of Bone Morphogenetic Protein (BMP)-Smad signaling using transgenics and mutants showed that BMP signaling alleviates cardiomyocyte replication stress. BMP signaling also rescues neonatal mouse cardiomyocytes,human fibroblasts and human hematopoietic stem and progenitor cells (HSPCs) from replication stress. DNA fiber spreading assays indicate that BMP signaling facilitates re-start of replication forks after replication stress-induced stalling. Our results identify the ability to overcome replication stress as key factor for the elevated zebrafish heart regeneration capacity and reveal a conserved role for BMP signaling in promotion of stress-free DNA replication. Subject terms: Cardiac regeneration,DNA damage and repair,Ageing View Publication