技术资料

The molecular mechanisms regulating CD8 + cytotoxic T lymphocytes (CTL) are not fully understood. Here,we show that the peroxisome proliferator–activated receptor δ (PPARδ) suppresses CTL cytotoxicity by inhibiting RelA DNA binding. Treatment of Apc Min/+ mice with the PPARδ agonist GW501516 reduced the activation of normal and tumor-associated intestinal CD8 + T cells and increased intestinal adenoma burden. PPARδ knockout or knockdown in CTLs increased their cytotoxicity against colorectal cancer cells,whereas overexpression of PPARδ or agonist treatment decreased it. Correspondingly,perforin,granzyme B,and IFNγ protein and mRNA levels were higher in PPARδ knockout or knockdown CTLs and lower in PPARδ overexpressing or agonist-treated CTLs. Mechanistically,we found that PPARδ binds to RelA,interfering with RelA–p50 heterodimer formation in the nucleus,thereby inhibiting its DNA binding in CTLs. Thus,PPARδ is a critical regulator of CTL effector function. Significance: Here,we provide the first direct evidence that PPARδ plays a critical role in suppressing the immune response against tumors by downregulating RelA DNA-binding activity. This results in decreased expression of perforin,granzyme B,and IFNγ. Thus,PPARδ may serve as a valuable target for developing future cancer immunotherapies. View Publication

A hexanucleotide repeat expansion (HRE) in C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Human brain imaging and experimental studies indicate early changes in brain structure and connectivity in C9-ALS/FTD,even before symptom onset. Because these early disease phenotypes remain incompletely understood,we generated iPSC-derived cerebral organoid models from C9-ALS/FTD patients,presymptomatic C9ORF72-HRE (C9-HRE) carriers,and controls. Our work revealed the presence of all three C9-HRE-related molecular pathologies and developmental stage-dependent size phenotypes in cerebral organoids from C9-ALS/FTD patients. In addition,single-cell RNA sequencing identified changes in cell type abundance and distribution in C9-ALS/FTD organoids,including a reduction in the number of deep layer cortical neurons and the distribution of neural progenitors. Further,molecular and cellular analyses and patch-clamp electrophysiology detected various changes in synapse structure and function. Intriguingly,organoids from all presymptomatic C9-HRE carriers displayed C9-HRE molecular pathology,whereas the extent to which more downstream cellular defects,as found in C9-ALS/FTD models,were detected varied for the different presymptomatic C9-HRE cases. Together,these results unveil early changes in 3D human brain tissue organization and synaptic connectivity in C9-ALS/FTD that likely constitute initial pathologies crucial for understanding disease onset and the design of therapeutic strategies. The online version contains supplementary material available at 10.1186/s40478-024-01857-1. View Publication

High-grade serous ovarian cancer remains a poorly understood disease with a high mortality rate. Although most patients respond to cytotoxic therapies,a majority will experience recurrence. This may be due to a minority of drug-resistant cancer stem-like cells (CSC) that survive chemotherapy and are capable of repopulating heterogeneous tumors. It remains unclear how CSCs are supported in the tumor microenvironment (TME) particularly during chemotherapy exposure. Tumor-associated macrophages (TAM) make up half of the immune population of the ovarian TME and are known to support CSCs and contribute to cancer progression. TAMs are plastic cells that alter their phenotype in response to environmental stimuli and thus may influence CSC maintenance during chemotherapy. Given the plasticity of TAMs,we studied the effects of carboplatin on macrophage phenotypes using both THP1- and peripheral blood mononuclear cell (PBMC)–derived macrophages and whether this supports CSCs and ovarian cancer progression following treatment. We found that carboplatin exposure induces an M1-like proinflammatory phenotype that promotes SOX2 expression,spheroid formation,and CD117 + ovarian CSCs,and that macrophage-secreted CCL2/MCP-1 is at least partially responsible for this effect. Depletion of TAMs during carboplatin exposure results in fewer CSCs and prolonged survival in a xenograft model of ovarian cancer. This study supports a role for platinum-based chemotherapies in promoting a transient proinflammatory M1-like TAM that enriches for CSCs during treatment. Improving our understanding of TME responses to cytotoxic drugs and identifying novel mechanisms of CSC maintenance will enable the development of better therapeutic strategies for high-grade serous ovarian cancer. Significance: We show that chemotherapy enhances proinflammatory macrophage phenotypes that correlate with ovarian cancer progression. Given that macrophages are the most prominent immune cell within these tumors,this work provides the foundation for future translational studies targeting specific macrophage populations during chemotherapy,a promising approach to prevent relapse in ovarian cancer. View Publication

Hematopoietic stem cells (HSCs) react to various stress conditions. However,it is unclear whether and how HSCs respond to severe anemia. Here,we demonstrate that upon induction of acute anemia,HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia,lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs,transcription levels of lipid metabolism-related genes,such as very low-density lipoprotein receptor ( Vldlr ),are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential,whereas HSCs in Apoe knockout mice do not respond to anemia induction. Vldlr high HSCs show higher erythroid potential,which is enhanced after acute anemia induction. Vldlr high HSCs are epigenetically distinct because of their low chromatin accessibility,and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays an important role in HSC regulation under severe anemic conditions. Subject terms: Haematopoietic stem cells,Fat metabolism,Chromatin,Anaemia View Publication

A hexanucleotide GGGGCC repeat expansion in the C9orf72 gene is the most frequent genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). C9orf72 repeat expansions are currently identified with long-range PCR or Southern blot for clinical and research purposes,but these methods lack accuracy and sensitivity. The GC-rich and repetitive content of the region cannot be amplified by PCR,which leads traditional sequencing approaches to fail. We turned instead to PacBio single-molecule sequencing to detect and size the C9orf72 repeat expansion without amplification. We isolated high molecular weight genomic DNA from patient-derived iPSCs of varying repeat lengths and then excised the region containing the C9orf72 repeat expansion from naked DNA with a CRISPR/Cas9 system. We added adapters to the cut ends,capturing the target region for sequencing on PacBio’s Sequel,Sequel II,or Sequel IIe. This approach enriches the C9orf72 repeat region without amplification and allows the repeat expansion to be consistently and accurately sized,even for repeats in the thousands. Key features • This protocol is adapted from PacBio’s previous “no-amp targeted sequencing utilizing the CRISPR-Cas9 system.” • Optimized for sizing C9orf72 repeat expansions in patient-derived iPSCs and applicable to DNA from any cell type,blood,or tissue. • Requires high molecular weight naked DNA. • Compatible with Sequel I and II but not Revio. View Publication

Although bone marrow-derived cells with high aldehyde dehydrogenase activity (ALDH br ) have shown therapeutic potential against various diseases in animal studies,clinical trials have failed to show concurrent findings. We aimed to clarify the optimal conditions for the efficacy of ALDH br cells by using a murine bleomycin-induced pulmonary fibrosis model. We intravenously transferred male or female donor C57BL/6 mice-derived ALDH br cells into recipient C57BL/6 mice under various conditions,and used mCherry-expressing mice as a donor to trace the transferred ALDH br cells. Pulmonary fibrosis improved significantly when (1) female-derived,not male-derived,and (2) lineage (Lin)-negative,not lineage-positive,ALDH br cells were transferred during the (3) fibrotic,not inflammatory,phase. Consistent with the RNA-sequencing results,female-derived Lin − /ALDH br cells were more resistant to oxidative stress than male-derived cells in vitro,and transferred female-derived Lin − /ALDH br cells were more viable than male-derived cells in the fibrotic lung. The mechanism underlying the antifibrotic effects of Lin − /ALDH br cells was strongly associated with reduction of oxidative stress. Our results indicated that Lin − /ALDH br cell therapy could ameliorate pulmonary fibrosis by reducing oxidative stress and suggested that their efficacy was mediated by sex-related differences. Thus,sex-awareness strategies may be important for clinical application of bone marrow ALDH br cells as a therapeutic tool. The online version contains supplementary material available at 10.1186/s13287-024-03933-8. View Publication

Hematopoietic stem progenitor cells (HSPCs) undergo phenotypical and functional changes during their emergence and development. Although the molecular programs governing the development of human hematopoietic stem cells (HSCs) have been investigated broadly,the relationships between dynamic metabolic alterations and their functions remain poorly characterized. In this study,we comprehensively described the proteomics of HSPCs in the human fetal liver (FL),umbilical cord blood (UCB),and adult bone marrow (aBM). The metabolic state of human HSPCs was assessed via a Seahorse assay,RT‒PCR,and flow cytometry-based metabolic-related analysis. To investigate whether perturbing glutathione metabolism affects reactive oxygen species (ROS) production,the metabolic state,and the expansion of human HSPCs,HSPCs were treated with buthionine sulfoximine (BSO),an inhibitor of glutathione synthetase,and N-acetyl-L-cysteine (NAC). We investigated the metabolomic landscape of human HSPCs from the fetal,perinatal,and adult developmental stages by in-depth quantitative proteomics and predicted a metabolic switch from the oxidative state to the glycolytic state during human HSPC development. Seahorse assays,mitochondrial activity,ROS level,glucose uptake,and protein synthesis rate analysis supported our findings. In addition,immune-related pathways and antigen presentation were upregulated in UCB or aBM HSPCs,indicating their functional maturation upon development. Glutathione-related metabolic perturbations resulted in distinct responses in human HSPCs and progenitors. Furthermore,the molecular and immunophenotypic differences between human HSPCs at different developmental stages were revealed at the protein level for the first time. The metabolic landscape of human HSPCs at three developmental stages (FL,UCB,and aBM),combined with proteomics and functional validations,substantially extends our understanding of HSC metabolic regulation. These findings provide valuable resources for understanding human HSC function and development during fetal and adult life. The online version contains supplementary material available at 10.1186/s13287-024-03930-x. View Publication

In recent years,Raman spectroscopy has garnered growing interest in the field of biomedical research. It offers a non-invasive and label-free approach to defining the molecular fingerprint of immune cells. We utilized Raman spectroscopy on optically trapped immune cells to investigate their molecular compositions. While numerous immune cell types have been studied in the past,the characterization of living human CD3/CD28-stimulated T cell subsets remains incomplete. In this study,we demonstrate the capability of Raman spectroscopy to readily distinguish between naïve and stimulated CD4 and CD8 cells. Additionally,we compared these cells with monocytes and discovered remarkable similarities between stimulated T cells and monocytes. This paper contributes to expanding our knowledge of Raman spectroscopy of immune cells and serves as a launching point for future clinical applications. View Publication

Intervertebral disc disease (IDD) is a debilitating spine condition that can be caused by intervertebral disc (IVD) damage which progresses towards IVD degeneration and dysfunction. Recently,human pluripotent stem cells (hPSCs) were recognized as a valuable resource for cell-based regenerative medicine in skeletal diseases. Therefore,adult somatic cells reprogrammed into human induced pluripotent stem cells (hiPSCs) represent an attractive cell source for the derivation of notochordal-like cells (NCs) as a first step towards the development of a regenerative therapy for IDD. Utilizing a differentiation method involving treatment with a four-factor cocktail targeting the BMP,FGF,retinoic acid,and Wnt signaling pathways,we differentiate CRISPR/Cas9-generated mCherry-reporter knock-in hiPSCs into notochordal-like cells. Comprehensive analysis of transcriptomic changes throughout the differentiation process identified regulation of histone methylation as a pivotal driver facilitating the differentiation of hiPSCs into notochordal-like cells. We further provide evidence that specific inhibition of histone demethylases KDM2A and KDM7A/B enhanced the lineage commitment of hiPSCs towards notochordal-like cells. Our results suggest that inhibition of KDMs could be leveraged to alter the epigenetic landscape of hiPSCs to control notochord-specific gene expression. Thus,our study highlights the importance of epigenetic regulators in stem cell-based regenerative approaches for the treatment of disc degeneration. View Publication

Monocytes,the circulating macrophage precursors,contribute to diseases like atherosclerosis and asthma. Long non-coding RNAs (lncRNAs) have been shown to modulate the phenotype and inflammatory capacity of monocytes. We previously discovered the lncRNA SMANTIS,which contributes to cellular phenotype expression by controlling BRG1 in mesenchymal cells. Here,we report that SMANTIS is particularly highly expressed in monocytes and lost during differentiation into macrophages. Moreover,different types of myeloid leukemia presented specific SMANTIS expression patterns. Interaction studies revealed that SMANTIS binds RUNX1,a transcription factor frequently mutated in AML,primarily through its Alu-element on the RUNT domain. RNA-seq after CRISPR/Cas9-mediated deletion of SMANTIS or RUNX1 revealed an association with cell adhesion and both limited the monocyte adhesion to endothelial cells. Mechanistically,SMANTIS KO reduced RUNX1 genomic binding and altered the interaction of RUNX1 with EP300 and CBFB. Collectively,SMANTIS interacts with RUNX1 and attenuates monocyte adhesion,which might limit monocyte vascular egress. Subject terms: Long non-coding RNAs,Transcription View Publication

Despite their role as innate sentinels,macrophages can serve as cellular reservoirs of chikungunya virus (CHIKV),a highly-pathogenic arthropod-borne alphavirus that has caused large outbreaks among human populations. Here,with the use of viral chimeras and evolutionary selection analysis,we define CHIKV glycoproteins E1 and E2 as critical for virion production in THP-1 derived human macrophages. Through proteomic analysis and functional validation,we further identify signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 subunit K (eIF3k) as E1-binding host proteins with anti-CHIKV activities. We find that E1 residue V220,which has undergone positive selection,is indispensable for CHIKV production in macrophages,as its mutation attenuates E1 interaction with the host restriction factors SPCS3 and eIF3k. Finally,we show that the antiviral activity of eIF3k is translation-independent,and that CHIKV infection promotes eIF3k translocation from the nucleus to the cytoplasm,where it associates with SPCS3. These functions of CHIKV glycoproteins late in the viral life cycle provide a new example of an intracellular evolutionary arms race with host restriction factors,as well as potential targets for therapeutic intervention. View Publication

The roles of the transcriptional factor SIX2 have been identified in several tumors. However,its roles in gastric cancer (GC) progression have not yet been revealed. Our objective is to explore the impact and underlying mechanisms of SIX2 on the stemness of GC cells. Lentivirus infection was employed to establish stable expression SIX2 or PFN2 in GC cells. Gain- and loss-of-function experiments were conducted to detect changes of stemness markers,flow cytometry profiles,tumor spheroid formation,and tumor-initiating ability. ChIP,RNA-sequencing,tissue microarray,and bioinformatics analysis were performed to reveal the correlation between SIX2 and PFN2. The mechanisms underlying the SIX2/PFN2 loop-mediated effects were elucidated through tissue microarray analysis,RNA stability assay,IP-MS,Co-Immunoprecipitation,and inhibition of the JNK signaling pathway. The stemness of GC cells was enhanced by SIX2. Mechanistically,SIX2 directly bound to PFN2’s promoter and promoted PFN2 activity. PFN2,in turn,promoted the mRNA stability of SIX2 by recruiting RNA binding protein YBX-1,subsequently activating the downstream MAPK/JNK pathway. This study unveils the roles of SIX2 in governing GC cell stemness,defining a novel SIX2/PFN2 regulatory loop responsible for this regulation. This suggests the potential of targeting the SIX2/PFN2 loop for GC treatment (Graphical Abstracts). The online version contains supplementary material available at 10.1186/s12967-024-05618-5. View Publication