Background:Germ cell mitotic arrest is conserved in many vertebrates,including birds,although the time of entry or exit into quiescence phase differs.Mitotic arrest is essential for the normal differentiation of male ...Background:Germ cell mitotic arrest is conserved in many vertebrates,including birds,although the time of entry or exit into quiescence phase differs.Mitotic arrest is essential for the normal differentiation of male germ cells into spermatogonia and accompanies epigenetic reprogramming and meiosis inhibition from embryonic development to post-hatch.However,mitotic arrest was not well studied in chickens because of the difficulty in obtaining pure germ cells from relevant developmental stage.Results:We performed single-cell RNA sequencing to investigate transcriptional dynamics of male germ cells during mitotic arrest in DAZL::GFP chickens.Using differentially expressed gene analysis and K-means clustering to analyze cells at different developmental stages(E12,E16,and hatch),we found that metabolic and signaling pathways were regulated,and that the epigenome was reprogrammed during mitotic arrest.In particular,we found that histone H3K9 and H3K14 acetylation(by HDAC2)and DNA demethylation(by DNMT3B and HELLS)led to a transcriptionally permissive chromatin state.Furthermore,we found that global DNA demethylation occurred gradually after the onset of mitotic arrest,indicating that the epigenetic-reprogramming schedule of the chicken genome differs from that of the mammalian genome.DNA hypomethylation persisted after hatching,and methylation was slowly re-established 3 weeks later.Conclusions:We found a unique epigenetic-reprogramming schedule of mitotic-arrested chicken prospermatogonia and prolonged hypomethylation after hatching.This will provide a foundation for understanding the process of germ-cell epigenetic regulation in several species for which this process is not clearly described.Our findings on the biological processes related to sex-specific differentiation of prospermatogonia could help studying germline development in vitro more elaborately.展开更多
The long-term effectiveness of targeted cancer therapies is limited by the development of resistance.Although epigenetic reprogramming has been implicated in resistance,the mechanisms remain elusive.Herein,we demonstr...The long-term effectiveness of targeted cancer therapies is limited by the development of resistance.Although epigenetic reprogramming has been implicated in resistance,the mechanisms remain elusive.Herein,we demonstrate that increased chromatin accessibility is involved in adaptive BRAF inhibitor(BRAFi)-resistance in melanoma cells.We observed loss of chromatin assembly factor 1(CAF-1)and its related histone H3 lysine 9 trimethylation(H3K9me3)with adaptive BRAFi resistance.We further showed that depletion of CAF-1 provides chromatin plasticity for effective reprogramming by AP1 components to promote BRAFi resistance.Our data sug-gest that therapeutic approaches to restore H3K9me3 levels may compensate for the loss of CAF-1 and,in turn,suppress resistance to BRAF inhibitors.展开更多
Advanced colorectal cancer(CRC)exhibits weak responses to multiple therapies,primarily due to the presence of cancer stem cells(CSCs),which drive high recurrence rates,metastasis,and drug resistance.We have previously...Advanced colorectal cancer(CRC)exhibits weak responses to multiple therapies,primarily due to the presence of cancer stem cells(CSCs),which drive high recurrence rates,metastasis,and drug resistance.We have previously systematically conducted CSC-targeted compound discovery and evaluation studies to inhibit CSC-mediated tumorigenesis and metastasis.Here,we identified ZSH-512,a novel synthetic retinoid that selectively targets retinoic acid receptor(RAR)g,demonstrating its ability to effectively inhibit CRC-CSCs and patient-derived organoids(PDOs)in vitro and significantly reduce CSC-mediated tumor formation and liver metastasis in mouse models without noticeable toxicity.Mechanistically,integrated analysis of Assay for Transposase-Accessible Chromatin sequencing(ATAC-seq)and RNA sequencing(RNA-seq)revealed that ZSH-512 exerted its effect by modulating the RARg-KDM3A axis to mediate epigenetic reprogramming and broadly suppress stemness-related signaling pathways,including Wnt,Hippo,and Hedgehog.ZSH-512 efficiently inhibited tumorigenesis in CRC-patient-derived tumor xenografts(PDXs)with high KDM3A expression,suggesting KDM3A as a potential predictive biomarker.Collectively,ZSH-512 is a promising therapeutic candidate for targeting CRCCSCs with high efficacy.展开更多
Aging is a pivotal risk factor for intervertebral disc degeneration(IVDD)and chronic low back pain(LBP).The restoration of aging nucleus pulposus cells(NPCs)to a youthful epigenetic state is crucial for IVDD treatment...Aging is a pivotal risk factor for intervertebral disc degeneration(IVDD)and chronic low back pain(LBP).The restoration of aging nucleus pulposus cells(NPCs)to a youthful epigenetic state is crucial for IVDD treatment,but remains a formidable challenge.Here,we proposed a strategy to partially reprogram and reinstate youthful epigenetics of senescent NPCs by delivering a plasmid carrier that expressed pluripotency-associated genes(Oct4,Klf4 and Sox2)in Cavin2-modified exosomes(OKS@M-Exo)for treatment of IVDD and alleviating LBP.The functional OKS@M-Exo efficaciously alleviated senescence markers(p16^(INK4a),p21^(CIP1)and p53),reduced DNA damage and H4K20me3 expression,as well as restored proliferation ability and metabolic balance in senescent NPCs,as validated through in vitro experiments.In a rat model of IVDD,OKS@M-Exo maintained intervertebral disc height,nucleus pulposus hydration and tissue structure,effectively ameliorated IVDD via decreasing the senescence markers.Additionally,OKS@MExo reduced nociceptive behavior and downregulated nociception markers,indicating its efficiency in alleviating LBP.The transcriptome sequencing analysis also demonstrated that OKS@M-Exo could decrease the expression of age-related pathways and restore cell proliferation.Collectively,reprogramming by the OKS@M-Exo to restore youthful epigenetics of senescent NPCs may hold promise as a therapeutic platform to treat IVDD.展开更多
How metastases develop is not well understood and no genetic mutations have been reported as specific metastatic drivers.Here we have addressed the idea that epigenetic reprogramming by GLI-regulated pluripotent stemn...How metastases develop is not well understood and no genetic mutations have been reported as specific metastatic drivers.Here we have addressed the idea that epigenetic reprogramming by GLI-regulated pluripotent stemness factors promotes metastases.Using primary human colon cancer cells engrafted in mice,we find that transient expression of OCT4,SOX2,KLF41/2 cMYC establishes an enhanced pro-metastatic state in the primary tumor that is stable through sequential engraftments and is transmitted through clonogenic cancer stem cells.Metastatic reprogramming alters NANOG methylation and stably boosts NANOG and NANOGP8 expression.Metastases and reprogrammed EMT-like phenotypes require endogenous NANOG,but enhanced NANOG is not sufficient to induce these phenotypes.Finally,reprogrammed tumors enhance GLI2,and we show that GLI2high and AXIN2low,which are markers of the metastatic transition of colon cancers,are prognostic of poor disease outcome in patients.We propose that metastases arise through epigenetic reprogramming of cancer stem cells within primary tumors.展开更多
Epigenetic reprogramming provides valuable resources for customized pluripotent stem cells generation,which are thought to be important bases of future regenerative medicine.Here we review the commonly used methods fo...Epigenetic reprogramming provides valuable resources for customized pluripotent stem cells generation,which are thought to be important bases of future regenerative medicine.Here we review the commonly used methods for epigenetic reprogramming:somatic cell nuclear transfer,cell fusion,cell extract treatment,inducing pluripotency by defined molecules,and briefly discuss their advantages and limitations.Finally we propose that mechanisms underlying epigenetic reprogramming and safety evaluation platform will be future research directions.展开更多
The development of germ cell tumors(GCTs)is a unique pathogenesis occurring at an early developmental stage during specification,migration or colonization of primordial germ cells(PGCs)in the genital ridge.Since drive...The development of germ cell tumors(GCTs)is a unique pathogenesis occurring at an early developmental stage during specification,migration or colonization of primordial germ cells(PGCs)in the genital ridge.Since driver mutations could not be identified so far,the involvement of the epigenetic machinery during the pathogenesis seems to play a crucial role.Currently,it is investigated whether epigenetic modifications occurring between the omnipotent two-cell stage and the pluripotent implanting PGCs might result in disturbances eventually leading to GCTs.Although progress in understanding epigenetic mechanisms during PGC development is ongoing,little is known about the complete picture of its involvement during GCT development and eventual classification into clinical subtypes.This review will shed light into the current knowledge of the complex epigenetic and molecular contribution during pathogenesis of GCTs by emphasizing on early developmental stages until arrival of late PGCs in the gonads.We questioned how misguided migrating and/or colonizing PGCs develop to either type Ⅰ or type Ⅱ GCTs.Additionally,we asked how pluripotency can be regulated during PGC development and which epigenetic changes contribute to GCT pathogenesis.We propose that SOX2 and SOX17 determine either embryonic stem cell-like(embryonal carcinoma)or PGC-like cell fate(seminoma).Finally,we suggest that factors secreted by the microenvironment,i.e.BMPs and BMP inhibiting molecules,dictate the fate decision of germ cell neoplasia in situ(into seminoma and embryonal carcinoma)and seminomas(into embryonal carcinoma or extraembryonic lineage),indicating an important role of the microenvironment on GCT plasticity.展开更多
High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning. It is known that one of the importa...High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning. It is known that one of the important mechanisms for epigenetic reprogramming is DNA methylation. DNA methylation is established and maintained by DNA methyltransferases （DNMTs）, therefore, it is postulated that the inefficient epigenetic reprogramming of transplanted nuclei may be due to abnormal expression of DNMTs. Since DNA methylation can strongly inhibit gene expression, aberrant DNA methylation of DNMT genes may disturb gene expression. But presently, it is not clear whether the methylation abnormality of DNMT genes is related to developmental failure of somatic cell nuclear transfer embryos. In our study, we analyzed methylation patterns of the 5＇ regions of four DNMT genes including Dnmt3a, Dnmt3b, Dnmtl and Dnmt2 in four aborted bovine clones. Using bisulfite sequencing method, we found that 3 out of 4 aborted bovine clones （AF1, AF2 and AF3） showed either hypermethylation or hypomethylation in the 5＇ regions of Dnmt3a and Dnmt3b, indicating that Dnmt3a and Dnmt3b genes are not properly reprogrammed. However, the individual AF4 exhibited similar methylation level and pattern to age-matched in vitro fertilized （IVF） fetuses. Besides, we found that the 5＇ regions of Dnmtl and Dnmt2 were nearly completely unmethylated in all normal adults, IVF fetuses, sperm and aborted clones. Together, our results suggest that the aberrant methylation of Dnmt3a and Dnmt3b 5＇ regions is probably associated with the high abortion of bovine clones.展开更多
Seed germination is a critical developmental switch from a quiescent state to active growth,which involves extensive changes in metabolism,gene expression,and cellular identity.However,our understanding of epigenetic ...Seed germination is a critical developmental switch from a quiescent state to active growth,which involves extensive changes in metabolism,gene expression,and cellular identity.However,our understanding of epigenetic and transcriptional reprogramming during this process is limited.The histone H3 lysine 27 trimethylation(H3K27me3)plays a key role in regulating gene repression and cell fate specification.Here,we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination in Arabidopsis.Our temporal genome-wide profiling of H3K27me3 and transcription reveals delayed H3K27me3reprogramming compared with transcriptomic changes during germination,with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development.RELATIVE OF EARLY FLOWERING 6(REF6)-mediated H3K27 demethylation is necessary for robust germination but does not significantly contribute to H3K27me3 dynamics during germination,but rather stably establishes an H3K27me3-depleted state that facilitates the activation of hormone-related and expansin-coding genes important for germination.We also show that the REF6 chromatin occupancy is gradually established during germination to counteract increased Polycomb repressive complex 2(PRC2).Our study provides key insights into the H3K27me3 dynamics during germination and suggests the function of H3K27me3 in facilitating cell fate switch.Furthermore,we reveal the importance of H3K27 demethylation-established transcriptional competence in gene activation during germination and likely other developmental processes.展开更多
Chemoresistance remains the major barrier to cancer treatment.Metabolic and epigenetic reprogramming are involved in this process;however,the precise roles and mechanisms are largely unknown.Here,we report that lactat...Chemoresistance remains the major barrier to cancer treatment.Metabolic and epigenetic reprogramming are involved in this process;however,the precise roles and mechanisms are largely unknown.Here,we report that lactate-induced lactylation promotes chemoresistance to anthracyclines by regulating homologous recombination(HR)repair.Using the global lactylome,we revealed the landscape of differentially lactylated sites and proteins in cancer cells isolated from resistant and nonresistant tumors.Specifically,BLM,a crucial helicase in the HR repair process,is highly lactylated at Lys24 by AARS1 in response to chemotherapy.展开更多
Human fetal germ cells(FGCs),referring to the embryonic precursors of oocytes and sperm,are crucial for the transmission of genetic and epigenetic information across generations.The finely orchestrated development of ...Human fetal germ cells(FGCs),referring to the embryonic precursors of oocytes and sperm,are crucial for the transmission of genetic and epigenetic information across generations.The finely orchestrated development of FGCs is of great importance for maintaining reproductive health.In the past several years,various omics techniques have been applied to human FGCs to reveal the global epigenetic reprogramming and transcriptional resetting processes during FGC development.Single-cell RNA sequencing(RNAseq)analysis of human FGCs unraveled the dynamic transcriptome,with simultaneous expression of both pluripotency genes and germline-specific genes(Guo et al.,2015;Li et al.,2017).展开更多
Mammalian fertilization begins with the fusion of two specialized gametes,followed by major epigenetic remodeling leading to the formation of a totipotent embryo.During the development of the pre-implantation embryo,p...Mammalian fertilization begins with the fusion of two specialized gametes,followed by major epigenetic remodeling leading to the formation of a totipotent embryo.During the development of the pre-implantation embryo,precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality,but the underlying molecular mechanisms remain elusive.For the past few years,unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development,taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies.The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals,including DNA methylation,histone modifications,chromatin accessibility and 3D chromatin organization.展开更多
Metabolic and epigenetic reprogramming play important roles in cancer therapeutic resistance.However,their interplays are poorly understood.We report here that elevated TIGAR(TP53-induced glycolysis and apoptosis regu...Metabolic and epigenetic reprogramming play important roles in cancer therapeutic resistance.However,their interplays are poorly understood.We report here that elevated TIGAR(TP53-induced glycolysis and apoptosis regulator),an antioxidant and glucose metabolic regulator and a target of oncogenic histone methyltransferase NSD2(nuclear receptor binding SET domain protein 2),is mainly localized in the nucleus of therapeutic resistant tumor cells where it stimulates NSD2 expression and elevates global H3K36me2 mark.Mechanistically,TIGAR directly interacts with the antioxidant master regulator NRF2 and facilitates chromatin recruitment of NRF2,H3K4me3 methylase MLL1 and elongating Pol-II to stimulate the expression of both new(NSD2)and established(NQO1/2,PRDX1 and GSTM4)targets of NRF2,independent of its enzymatic activity.Nuclear TIGAR confers cancer cell resistance to chemotherapy and hormonal therapy in vitro and in tumors through effective maintenance of redox homeostasis.In addition,nuclear accumulation of TIGAR is positively associated with NSD2 expression in clinical tumors and strongly correlated with poor survival.These findings define a nuclear TIGAR-mediated epigenetic autoregulatory loop in redox rebalance for tumor therapeutic resistance.展开更多
The somatic epigenome can be reprogrammed to a pluri-potent state by a combination of transcription factors.Altering cell fate involves transcription factors coopera-tion,epigenetic reconfi guration,such as DNA methyl...The somatic epigenome can be reprogrammed to a pluri-potent state by a combination of transcription factors.Altering cell fate involves transcription factors coopera-tion,epigenetic reconfi guration,such as DNA methylation and histone modification,posttranscriptional regulation by microRNAs,and so on.Nevertheless,such reprogram-ming is inefficient.Evidence suggests that during the early stage of reprogramming,the process is stochastic,but by the late stage,it is deterministic.In addition to con-ventional reprogramming methods,dozens of small mol-ecules have been identifi ed that can functionally replace reprogramming factors and signifi cantly improve induced pluripotent stem cell(iPSC)reprogramming.Indeed,iPS cells have been created recently using chemical com-pounds only.iPSCs are thought to display subtle genetic and epigenetic variability;this variability is not random,but occurs at hotspots across the genome.Here we dis-cuss the progress and current perspectives in the fi eld.Research into the reprogramming process today will pave the way for great advances in regenerative medicine in the future.展开更多
Immune suppressive microenvironment in tumor emerges as the main obstacle for cancer immunotherapy.In this study,we identified that HIF1α was activated in the tumor associated macrophages and acted as an important fa...Immune suppressive microenvironment in tumor emerges as the main obstacle for cancer immunotherapy.In this study,we identified that HIF1α was activated in the tumor associated macrophages and acted as an important factor for the immune suppressive microenvironment.Epigenetically silencing of Hif1αvia histone H3 methylation in the promoter region was achieved by CRISPR/dCas9-EZH2 system,in which histone H3 methylase EZH2 was recruited to the promoter region specifically.The Hif1αsilenced macrophage,namely HERM(Hif1αEpigenetically Repressed Macrophage)manifested as inheritable tumor suppressing phenotype.In the subcutaneous B16-F10 melanoma syngeneic model,intratumoral injection of HERMs reprogrammed the immune suppressive microenvironment to the active one,reducing tumor burden and prolonging overall survival.Additionally,HERMs therapy remarkably inhibited tumor angiogenesis.Together,our study has not only identified a promising cellular and molecular target for reverting immune suppressive microenvironment,but also provided a potent strategy for reprogramming tumor microenvironment via epigenetically reprogrammed macrophages.展开更多
DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort h...DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development,especially during sexual reproduction.The power of whole-genome sequencing and cell isolation techniques,as well as bioinformatics tools,have enabled recent studies to reveal dynamic changes in DNA methylation during germline development.Furthermore,the combination of these technological advances with genetics,developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines.In this review,we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.展开更多
Mutations in tumors can create a state of increased cellular plasticity that promotes resistance to treatment. Thus, there is an urgent need to develop novel strategies for identifying key factors that regulate cellul...Mutations in tumors can create a state of increased cellular plasticity that promotes resistance to treatment. Thus, there is an urgent need to develop novel strategies for identifying key factors that regulate cellular plasticity in order to combat resistance to chemotherapy and radiation treatment. Here we report that prostate epithelial cell reprogramming could be exploited to identify key factors required for promoting prostate cancer tumorigenesis and cellular plasticity. Deletion of phosphatase and tensin homolog （Pten） and transforming growth factor-beta receptor type 2 （Tgfbr2） may increase prostate epithelial cell reprogramming efficiency in vitro and cause rapid tumor development and early mortality in vivo. Tgfbr2 ablation abolished TGF-β signaling but increased the bone morphogenetic protein （BMP） signaling pathway through the negative regulator Tmeff1. Furthermore, increased BMP signaling promotes expression of the tumor marker genes ID1, Oct4, Nanog, and Sox2; ID1/STAT3/NANOG expression was inversely correlated with patient survival. Thus, our findings provide information about the molecular mechanisms by which BMP signaling pathways render stemness capacity to prostate tumor cells.展开更多
The mucin 1(MUC1)gene emerged in mammals to afford protection of barrier epithelial tissues from the external environment.MUC1 encodes a transmembrane C-terminal(MUC1-C)subunit that is activated by loss of homeostasis...The mucin 1(MUC1)gene emerged in mammals to afford protection of barrier epithelial tissues from the external environment.MUC1 encodes a transmembrane C-terminal(MUC1-C)subunit that is activated by loss of homeostasis and induces inflammatory,proliferative,and remodeling pathways associated with wound repair.As a consequence,chronic activation of MUC1-C promotes lineage plasticity,epigenetic reprogramming,and carcinogenesis.In driving cancer progression,MUC1-C is imported into the nucleus,where it induces NF-κB inflammatory signaling and the epithelial-mesenchymal transition(EMT).MUC1-C represses gene expression by activating(i)DNA methyltransferase 1(DNMT1)and DNMT3b,(ii)Polycomb Repressive Complex 1(PRC1)and PRC2,and(iii)the nucleosome remodeling and deacetylase(NuRD)complex.PRC1/2-mediated gene repression is counteracted by the SWI/SNF chromatin remodeling complexes.MUC1-C activates the SWI/SNF BAF and PBAF complexes in cancer stem cell(CSC)models with the induction of genome-wide differentially accessible regions and expressed genes.MUC1-C regulates chromatin accessibility of enhancer-like signatures in association with the induction of the Yamanaka pluripotency factors and recruitment of JUN and BAF,which promote increases in histone activation marks and opening of chromatin.These and other findings described in this review have uncovered a pivotal role for MUC1-C in integrating lineage plasticity and epigenetic reprogramming,which are transient in wound repair and sustained in promoting CSC progression.展开更多
基金supported by the National Research Foundation of Korea(NRF)grant funded by the Korea government(MSIP)(No.2015R1A3A2033826).
文摘Background:Germ cell mitotic arrest is conserved in many vertebrates,including birds,although the time of entry or exit into quiescence phase differs.Mitotic arrest is essential for the normal differentiation of male germ cells into spermatogonia and accompanies epigenetic reprogramming and meiosis inhibition from embryonic development to post-hatch.However,mitotic arrest was not well studied in chickens because of the difficulty in obtaining pure germ cells from relevant developmental stage.Results:We performed single-cell RNA sequencing to investigate transcriptional dynamics of male germ cells during mitotic arrest in DAZL::GFP chickens.Using differentially expressed gene analysis and K-means clustering to analyze cells at different developmental stages(E12,E16,and hatch),we found that metabolic and signaling pathways were regulated,and that the epigenome was reprogrammed during mitotic arrest.In particular,we found that histone H3K9 and H3K14 acetylation(by HDAC2)and DNA demethylation(by DNMT3B and HELLS)led to a transcriptionally permissive chromatin state.Furthermore,we found that global DNA demethylation occurred gradually after the onset of mitotic arrest,indicating that the epigenetic-reprogramming schedule of the chicken genome differs from that of the mammalian genome.DNA hypomethylation persisted after hatching,and methylation was slowly re-established 3 weeks later.Conclusions:We found a unique epigenetic-reprogramming schedule of mitotic-arrested chicken prospermatogonia and prolonged hypomethylation after hatching.This will provide a foundation for understanding the process of germ-cell epigenetic regulation in several species for which this process is not clearly described.Our findings on the biological processes related to sex-specific differentiation of prospermatogonia could help studying germline development in vitro more elaborately.
基金supported by the National Institutes of Health to R.B.D.(NIH5P30CA015083)the Mayo Clinic Cancer Center Ea-gles Cancer Fund(Z.W.)the Mayo Clinic Center for Biomedical Discovery(S.M.O).
文摘The long-term effectiveness of targeted cancer therapies is limited by the development of resistance.Although epigenetic reprogramming has been implicated in resistance,the mechanisms remain elusive.Herein,we demonstrate that increased chromatin accessibility is involved in adaptive BRAF inhibitor(BRAFi)-resistance in melanoma cells.We observed loss of chromatin assembly factor 1(CAF-1)and its related histone H3 lysine 9 trimethylation(H3K9me3)with adaptive BRAFi resistance.We further showed that depletion of CAF-1 provides chromatin plasticity for effective reprogramming by AP1 components to promote BRAFi resistance.Our data sug-gest that therapeutic approaches to restore H3K9me3 levels may compensate for the loss of CAF-1 and,in turn,suppress resistance to BRAF inhibitors.
基金supported by the National Nature Science Foundation of China(grant nos.82173662,82373719,82373402,and 82172925)the National Key R&D Program of China(2023YFC3605702,2023YFC2308002,and 2024YFC3044700)+3 种基金Clinical Research Foundation of Zhongshan Hospital Affiliated to Fudan University(2020ZSLC02)funding from Science and Technology Commission of Shanghai Municipality(19DZ1910102)Shanghai ShenKang Research Physicians Innovation and Transformation Ability Training Project(SHDC2022CRT001)the Extraordinary 2025 Elite Project of Fudan University.
文摘Advanced colorectal cancer(CRC)exhibits weak responses to multiple therapies,primarily due to the presence of cancer stem cells(CSCs),which drive high recurrence rates,metastasis,and drug resistance.We have previously systematically conducted CSC-targeted compound discovery and evaluation studies to inhibit CSC-mediated tumorigenesis and metastasis.Here,we identified ZSH-512,a novel synthetic retinoid that selectively targets retinoic acid receptor(RAR)g,demonstrating its ability to effectively inhibit CRC-CSCs and patient-derived organoids(PDOs)in vitro and significantly reduce CSC-mediated tumor formation and liver metastasis in mouse models without noticeable toxicity.Mechanistically,integrated analysis of Assay for Transposase-Accessible Chromatin sequencing(ATAC-seq)and RNA sequencing(RNA-seq)revealed that ZSH-512 exerted its effect by modulating the RARg-KDM3A axis to mediate epigenetic reprogramming and broadly suppress stemness-related signaling pathways,including Wnt,Hippo,and Hedgehog.ZSH-512 efficiently inhibited tumorigenesis in CRC-patient-derived tumor xenografts(PDXs)with high KDM3A expression,suggesting KDM3A as a potential predictive biomarker.Collectively,ZSH-512 is a promising therapeutic candidate for targeting CRCCSCs with high efficacy.
基金supported by the Ministry of Science and Technology of China(2020YFA0908900)National Natural Science Foundation of China(21935011 and 82072490)+1 种基金Shenzhen Science and Technology Innovation Commission(KQTD20200820113012029 and KJZD20230923114612025)Guangdong Provincial Key Laboratory of Advanced Biomaterials(2022B1212010003).
文摘Aging is a pivotal risk factor for intervertebral disc degeneration(IVDD)and chronic low back pain(LBP).The restoration of aging nucleus pulposus cells(NPCs)to a youthful epigenetic state is crucial for IVDD treatment,but remains a formidable challenge.Here,we proposed a strategy to partially reprogram and reinstate youthful epigenetics of senescent NPCs by delivering a plasmid carrier that expressed pluripotency-associated genes(Oct4,Klf4 and Sox2)in Cavin2-modified exosomes(OKS@M-Exo)for treatment of IVDD and alleviating LBP.The functional OKS@M-Exo efficaciously alleviated senescence markers(p16^(INK4a),p21^(CIP1)and p53),reduced DNA damage and H4K20me3 expression,as well as restored proliferation ability and metabolic balance in senescent NPCs,as validated through in vitro experiments.In a rat model of IVDD,OKS@M-Exo maintained intervertebral disc height,nucleus pulposus hydration and tissue structure,effectively ameliorated IVDD via decreasing the senescence markers.Additionally,OKS@MExo reduced nociceptive behavior and downregulated nociception markers,indicating its efficiency in alleviating LBP.The transcriptome sequencing analysis also demonstrated that OKS@M-Exo could decrease the expression of age-related pathways and restore cell proliferation.Collectively,reprogramming by the OKS@M-Exo to restore youthful epigenetics of senescent NPCs may hold promise as a therapeutic platform to treat IVDD.
基金funded by grants from the Swiss National Science Foundation,the Swiss Cancer League,the European Union grant HEALING,a James McDonnell 21st Century Brain Cancer Award,and funds from the Departement d’Instruction Publique de la Republique et Canton de Geneve,Switzerland。
文摘How metastases develop is not well understood and no genetic mutations have been reported as specific metastatic drivers.Here we have addressed the idea that epigenetic reprogramming by GLI-regulated pluripotent stemness factors promotes metastases.Using primary human colon cancer cells engrafted in mice,we find that transient expression of OCT4,SOX2,KLF41/2 cMYC establishes an enhanced pro-metastatic state in the primary tumor that is stable through sequential engraftments and is transmitted through clonogenic cancer stem cells.Metastatic reprogramming alters NANOG methylation and stably boosts NANOG and NANOGP8 expression.Metastases and reprogrammed EMT-like phenotypes require endogenous NANOG,but enhanced NANOG is not sufficient to induce these phenotypes.Finally,reprogrammed tumors enhance GLI2,and we show that GLI2high and AXIN2low,which are markers of the metastatic transition of colon cancers,are prognostic of poor disease outcome in patients.We propose that metastases arise through epigenetic reprogramming of cancer stem cells within primary tumors.
基金This study was supported by grants from the National Natural Science Foundation of China(Grant Nos.30525040 and 30670229).
文摘Epigenetic reprogramming provides valuable resources for customized pluripotent stem cells generation,which are thought to be important bases of future regenerative medicine.Here we review the commonly used methods for epigenetic reprogramming:somatic cell nuclear transfer,cell fusion,cell extract treatment,inducing pluripotency by defined molecules,and briefly discuss their advantages and limitations.Finally we propose that mechanisms underlying epigenetic reprogramming and safety evaluation platform will be future research directions.
文摘The development of germ cell tumors(GCTs)is a unique pathogenesis occurring at an early developmental stage during specification,migration or colonization of primordial germ cells(PGCs)in the genital ridge.Since driver mutations could not be identified so far,the involvement of the epigenetic machinery during the pathogenesis seems to play a crucial role.Currently,it is investigated whether epigenetic modifications occurring between the omnipotent two-cell stage and the pluripotent implanting PGCs might result in disturbances eventually leading to GCTs.Although progress in understanding epigenetic mechanisms during PGC development is ongoing,little is known about the complete picture of its involvement during GCT development and eventual classification into clinical subtypes.This review will shed light into the current knowledge of the complex epigenetic and molecular contribution during pathogenesis of GCTs by emphasizing on early developmental stages until arrival of late PGCs in the gonads.We questioned how misguided migrating and/or colonizing PGCs develop to either type Ⅰ or type Ⅱ GCTs.Additionally,we asked how pluripotency can be regulated during PGC development and which epigenetic changes contribute to GCT pathogenesis.We propose that SOX2 and SOX17 determine either embryonic stem cell-like(embryonal carcinoma)or PGC-like cell fate(seminoma).Finally,we suggest that factors secreted by the microenvironment,i.e.BMPs and BMP inhibiting molecules,dictate the fate decision of germ cell neoplasia in situ(into seminoma and embryonal carcinoma)and seminomas(into embryonal carcinoma or extraembryonic lineage),indicating an important role of the microenvironment on GCT plasticity.
基金the National Basic Re-search Program of China (973 Program) (No. 2006CB504004 and 2006CB944004)the National Natural Science Foundation of China (No. 30430530)the Knowledge Innovation Program of the Chinese Academy of Sciences (No. KSCX2-YW-N-017).
文摘High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning. It is known that one of the important mechanisms for epigenetic reprogramming is DNA methylation. DNA methylation is established and maintained by DNA methyltransferases （DNMTs）, therefore, it is postulated that the inefficient epigenetic reprogramming of transplanted nuclei may be due to abnormal expression of DNMTs. Since DNA methylation can strongly inhibit gene expression, aberrant DNA methylation of DNMT genes may disturb gene expression. But presently, it is not clear whether the methylation abnormality of DNMT genes is related to developmental failure of somatic cell nuclear transfer embryos. In our study, we analyzed methylation patterns of the 5＇ regions of four DNMT genes including Dnmt3a, Dnmt3b, Dnmtl and Dnmt2 in four aborted bovine clones. Using bisulfite sequencing method, we found that 3 out of 4 aborted bovine clones （AF1, AF2 and AF3） showed either hypermethylation or hypomethylation in the 5＇ regions of Dnmt3a and Dnmt3b, indicating that Dnmt3a and Dnmt3b genes are not properly reprogrammed. However, the individual AF4 exhibited similar methylation level and pattern to age-matched in vitro fertilized （IVF） fetuses. Besides, we found that the 5＇ regions of Dnmtl and Dnmt2 were nearly completely unmethylated in all normal adults, IVF fetuses, sperm and aborted clones. Together, our results suggest that the aberrant methylation of Dnmt3a and Dnmt3b 5＇ regions is probably associated with the high abortion of bovine clones.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(Precision Seed Design and Breeding,XDA24020303)the National Key R&D Program of China(2019YFA0903903)the National Natural Science Foundation of China(31970527,32170545,and 32150610472)。
文摘Seed germination is a critical developmental switch from a quiescent state to active growth,which involves extensive changes in metabolism,gene expression,and cellular identity.However,our understanding of epigenetic and transcriptional reprogramming during this process is limited.The histone H3 lysine 27 trimethylation(H3K27me3)plays a key role in regulating gene repression and cell fate specification.Here,we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination in Arabidopsis.Our temporal genome-wide profiling of H3K27me3 and transcription reveals delayed H3K27me3reprogramming compared with transcriptomic changes during germination,with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development.RELATIVE OF EARLY FLOWERING 6(REF6)-mediated H3K27 demethylation is necessary for robust germination but does not significantly contribute to H3K27me3 dynamics during germination,but rather stably establishes an H3K27me3-depleted state that facilitates the activation of hormone-related and expansin-coding genes important for germination.We also show that the REF6 chromatin occupancy is gradually established during germination to counteract increased Polycomb repressive complex 2(PRC2).Our study provides key insights into the H3K27me3 dynamics during germination and suggests the function of H3K27me3 in facilitating cell fate switch.Furthermore,we reveal the importance of H3K27 demethylation-established transcriptional competence in gene activation during germination and likely other developmental processes.
基金supported by the Noncommunicable Chronic Diseases-National Science and Technology Major Project(2024ZD0525700 to T.L.)the National Natural Science Foundation of China(82403698 to X.L.)+5 种基金the Postdoctoral Fellowship Program of CPSF grant(GZC20233348 to X.L.)the National Natural Science Foundation of China grant(82472779 to X.G.)the National Natural Science Foundation of China grant(82372881 to W.H.)the Chongqing Natural Science Foundation(CSTB2024NSCQ-MSX1030 to X.L.)the Chongqing Medical Youth Top Talent Project(YXQN202431 to X.L.)the Qiande Excellent Young Talent Project(2025QDYQ-06 to X.L.).
文摘Chemoresistance remains the major barrier to cancer treatment.Metabolic and epigenetic reprogramming are involved in this process;however,the precise roles and mechanisms are largely unknown.Here,we report that lactate-induced lactylation promotes chemoresistance to anthracyclines by regulating homologous recombination(HR)repair.Using the global lactylome,we revealed the landscape of differentially lactylated sites and proteins in cancer cells isolated from resistant and nonresistant tumors.Specifically,BLM,a crucial helicase in the HR repair process,is highly lactylated at Lys24 by AARS1 in response to chemotherapy.
基金supported by the National Natural Science Foundation of China(32288101,32200485,32270658)National Key R&D Program of China(2022YFC2703800)Shanghai Hospital Development Center Foundation(SHDC12023121).
文摘Human fetal germ cells(FGCs),referring to the embryonic precursors of oocytes and sperm,are crucial for the transmission of genetic and epigenetic information across generations.The finely orchestrated development of FGCs is of great importance for maintaining reproductive health.In the past several years,various omics techniques have been applied to human FGCs to reveal the global epigenetic reprogramming and transcriptional resetting processes during FGC development.Single-cell RNA sequencing(RNAseq)analysis of human FGCs unraveled the dynamic transcriptome,with simultaneous expression of both pluripotency genes and germline-specific genes(Guo et al.,2015;Li et al.,2017).
基金This work was supported by the National Key R&D Program of China(2016YFA0100400 and 2018YFC1004000)and the National Natural Science Foundation of China(31721003,31820103009,31701262,81630035).
文摘Mammalian fertilization begins with the fusion of two specialized gametes,followed by major epigenetic remodeling leading to the formation of a totipotent embryo.During the development of the pre-implantation embryo,precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality,but the underlying molecular mechanisms remain elusive.For the past few years,unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development,taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies.The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals,including DNA methylation,histone modifications,chromatin accessibility and 3D chromatin organization.
基金This work was supported by the National Natural Science Foundation of China(81872891)the Guangdong Natural Science Funds for Distinguished Young Scholar(No.2019B151502016,China)+4 种基金Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program(2017BT01Y093,China)National Engineering and Technology Research Center for New drug Druggability Evaluation(Seed Program of Guangdong Province,2017B090903004,China)the Fundamental Research Funds for the Central Universities(No.19ykzd23,China)The Manitoba Breast Tumor Bank,a member of the Canadian Tissue Repository Network,was funded in part by the Cancer Care Manitoba Foundation(CCMF,Canada)previously the Canadian Institutes of Health Research(CIHR,PRG80155,Canada).
文摘Metabolic and epigenetic reprogramming play important roles in cancer therapeutic resistance.However,their interplays are poorly understood.We report here that elevated TIGAR(TP53-induced glycolysis and apoptosis regulator),an antioxidant and glucose metabolic regulator and a target of oncogenic histone methyltransferase NSD2(nuclear receptor binding SET domain protein 2),is mainly localized in the nucleus of therapeutic resistant tumor cells where it stimulates NSD2 expression and elevates global H3K36me2 mark.Mechanistically,TIGAR directly interacts with the antioxidant master regulator NRF2 and facilitates chromatin recruitment of NRF2,H3K4me3 methylase MLL1 and elongating Pol-II to stimulate the expression of both new(NSD2)and established(NQO1/2,PRDX1 and GSTM4)targets of NRF2,independent of its enzymatic activity.Nuclear TIGAR confers cancer cell resistance to chemotherapy and hormonal therapy in vitro and in tumors through effective maintenance of redox homeostasis.In addition,nuclear accumulation of TIGAR is positively associated with NSD2 expression in clinical tumors and strongly correlated with poor survival.These findings define a nuclear TIGAR-mediated epigenetic autoregulatory loop in redox rebalance for tumor therapeutic resistance.
基金the National Institutes of Health(NS079625 and HD073162 to P.J.).
文摘The somatic epigenome can be reprogrammed to a pluri-potent state by a combination of transcription factors.Altering cell fate involves transcription factors coopera-tion,epigenetic reconfi guration,such as DNA methylation and histone modification,posttranscriptional regulation by microRNAs,and so on.Nevertheless,such reprogram-ming is inefficient.Evidence suggests that during the early stage of reprogramming,the process is stochastic,but by the late stage,it is deterministic.In addition to con-ventional reprogramming methods,dozens of small mol-ecules have been identifi ed that can functionally replace reprogramming factors and signifi cantly improve induced pluripotent stem cell(iPSC)reprogramming.Indeed,iPS cells have been created recently using chemical com-pounds only.iPSCs are thought to display subtle genetic and epigenetic variability;this variability is not random,but occurs at hotspots across the genome.Here we dis-cuss the progress and current perspectives in the fi eld.Research into the reprogramming process today will pave the way for great advances in regenerative medicine in the future.
基金This work was funded by the National Natural Science Foundation of China(NSFC31573244 to L Liu,NSFC31771507 and NSFC81970737 to G Yang)Key Projects of Shaanxi Province(2018ZDXM-SF-063 to L Liu).
文摘Immune suppressive microenvironment in tumor emerges as the main obstacle for cancer immunotherapy.In this study,we identified that HIF1α was activated in the tumor associated macrophages and acted as an important factor for the immune suppressive microenvironment.Epigenetically silencing of Hif1αvia histone H3 methylation in the promoter region was achieved by CRISPR/dCas9-EZH2 system,in which histone H3 methylase EZH2 was recruited to the promoter region specifically.The Hif1αsilenced macrophage,namely HERM(Hif1αEpigenetically Repressed Macrophage)manifested as inheritable tumor suppressing phenotype.In the subcutaneous B16-F10 melanoma syngeneic model,intratumoral injection of HERMs reprogrammed the immune suppressive microenvironment to the active one,reducing tumor burden and prolonging overall survival.Additionally,HERMs therapy remarkably inhibited tumor angiogenesis.Together,our study has not only identified a promising cellular and molecular target for reverting immune suppressive microenvironment,but also provided a potent strategy for reprogramming tumor microenvironment via epigenetically reprogrammed macrophages.
文摘DNA methylation plays essential homeostatic functions in eukaryotic genomes.In animals,DNA methylation is also developmentally regulated and,in turn,regulates development.In the past two decades,huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development,especially during sexual reproduction.The power of whole-genome sequencing and cell isolation techniques,as well as bioinformatics tools,have enabled recent studies to reveal dynamic changes in DNA methylation during germline development.Furthermore,the combination of these technological advances with genetics,developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines.In this review,we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
基金This work was supported by grants from the National Key Research and Development Program of China （2017YFA0103800）, the National Natural Science Foundation of China （81572766 and 31771630）, Guangdong Innovative and Entrepreneurial Research Team Program （2016ZT06S029）, 6uangdong Natural Science Foundation （2016A030313215 and 2016A030313238）, SYSU Young Teachers Training Program （16YKZD14）, the National Cancer Institute （NCl）, the National Institutes of Health （NIH） （ROICA090327 and RO1CA101795）, and the Cancer Prevention and Research Institute of Texas （CPRIT） （RP170537）.
文摘Mutations in tumors can create a state of increased cellular plasticity that promotes resistance to treatment. Thus, there is an urgent need to develop novel strategies for identifying key factors that regulate cellular plasticity in order to combat resistance to chemotherapy and radiation treatment. Here we report that prostate epithelial cell reprogramming could be exploited to identify key factors required for promoting prostate cancer tumorigenesis and cellular plasticity. Deletion of phosphatase and tensin homolog （Pten） and transforming growth factor-beta receptor type 2 （Tgfbr2） may increase prostate epithelial cell reprogramming efficiency in vitro and cause rapid tumor development and early mortality in vivo. Tgfbr2 ablation abolished TGF-β signaling but increased the bone morphogenetic protein （BMP） signaling pathway through the negative regulator Tmeff1. Furthermore, increased BMP signaling promotes expression of the tumor marker genes ID1, Oct4, Nanog, and Sox2; ID1/STAT3/NANOG expression was inversely correlated with patient survival. Thus, our findings provide information about the molecular mechanisms by which BMP signaling pathways render stemness capacity to prostate tumor cells.
基金Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under grant numbers CA97098,CA166480 and CA233084 awarded to D.Kufe。
文摘The mucin 1(MUC1)gene emerged in mammals to afford protection of barrier epithelial tissues from the external environment.MUC1 encodes a transmembrane C-terminal(MUC1-C)subunit that is activated by loss of homeostasis and induces inflammatory,proliferative,and remodeling pathways associated with wound repair.As a consequence,chronic activation of MUC1-C promotes lineage plasticity,epigenetic reprogramming,and carcinogenesis.In driving cancer progression,MUC1-C is imported into the nucleus,where it induces NF-κB inflammatory signaling and the epithelial-mesenchymal transition(EMT).MUC1-C represses gene expression by activating(i)DNA methyltransferase 1(DNMT1)and DNMT3b,(ii)Polycomb Repressive Complex 1(PRC1)and PRC2,and(iii)the nucleosome remodeling and deacetylase(NuRD)complex.PRC1/2-mediated gene repression is counteracted by the SWI/SNF chromatin remodeling complexes.MUC1-C activates the SWI/SNF BAF and PBAF complexes in cancer stem cell(CSC)models with the induction of genome-wide differentially accessible regions and expressed genes.MUC1-C regulates chromatin accessibility of enhancer-like signatures in association with the induction of the Yamanaka pluripotency factors and recruitment of JUN and BAF,which promote increases in histone activation marks and opening of chromatin.These and other findings described in this review have uncovered a pivotal role for MUC1-C in integrating lineage plasticity and epigenetic reprogramming,which are transient in wound repair and sustained in promoting CSC progression.
