Epigenomic imbalance drives abnormal transcriptional processes,promoting the onset and progression of cancer.Although defective gene regulation generally affects carcinogenesis and tumor suppression networks,tumor imm...Epigenomic imbalance drives abnormal transcriptional processes,promoting the onset and progression of cancer.Although defective gene regulation generally affects carcinogenesis and tumor suppression networks,tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes,which may have significant implications for the development and application of epigenetic therapy,cancer immunotherapy,and their combinations.Herein,we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes,DNA methylation,histone post-translational modification,and chromatin structure in tumor immunogenicity,and introduce these epigenetic research methods.We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immuno-therapy through the complex interaction between cancer epigenetics and cancer immunology.展开更多
Diagnosis of male infertility has mainly been based on the World Health Organization （WHO） manual-based semen parameter＇s concentration, motility and morphology. It has, however, become apparent that none of these ...Diagnosis of male infertility has mainly been based on the World Health Organization （WHO） manual-based semen parameter＇s concentration, motility and morphology. It has, however, become apparent that none of these parameters are reliable markers for evaluation of the fertility potential of a couple. A search for better markers has led to an increased focus on sperm chromatin integrity testing in fertility work-up and assisted reproductive techniques. During the last couple of decades, numerous sperm DNA integrity tests have been developed. These are claimed to be characterized by a lower intraindividual variation, less intralaboratory and interlaboratory variation and thus less subjective than the conventional sperm analysis. However, not all the sperm chromatin integrity tests have yet been shown to be of clinical value. So far, the test that has been found to have the most stable clinical threshold values in relation to fertility is the sperm chromatin structure assay （SCSA）, a flow cytometric test that measures the susceptibility of sperm DNA to acid-induced DNA denaturation in situ. Sperm DNA fragmentation as measured by SCSA has shown to be an independent predictor of successful pregnancy in first pregnancy planners as well as in couples undergoing intrauterine insemination, and can be used as a tool in investigation, counseling and treatment of involuntary childlessness. More conflicting data exist regarding the role of sperm DNA fragmentation in relation to fertilization, pre-embryo development and pregnancy outcome in in vitro fertilization and intracytoplasmic sperm injection （ICSI）.展开更多
The aim of this study was to investigate whether the sperm chromatin structure assay （SCSA） results after swim-up are related to fertilization rates, embryo quality and pregnancy rates following in vitrofertilizati...The aim of this study was to investigate whether the sperm chromatin structure assay （SCSA） results after swim-up are related to fertilization rates, embryo quality and pregnancy rates following in vitrofertilization （IVF）. A total of 223 couples undergoing IVF in our hospital from October 2008 to September 2009 were included in this study. Data on the IVF process and sperm chromatin structure assay results were collected. Fertilization rate, embryo quality and IVF success rates of different DNA fragmentation index （DFI） subgroups and high DNA stainability （HDS） subgroups were compared. There were no significant differences in fertilization rate, clinical pregnancy or delivery rates between the DFI and HDS subgroups. However, the group with abnormal DFI had a lower good embryo rate. So, we concluded that the SCSA variables, either DFI or HDS after swim-up preparation, were not valuable in predicting fertilization failure or pregnancy rate, but an abnormal DFI meant a lower good embryo rate following IVF.展开更多
Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DN...Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA,such as DNA replication and DNA repair.Many factors,including histone variants,histone modification,DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,is clear,there is still much discussion on the higher-order levels of chromatin structure.Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities.Here,we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription.展开更多
Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain （PHD） finger protein 8 （PHF8） are associated with X-linked m...Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain （PHD） finger protein 8 （PHF8） are associated with X-linked mental retardation and facial anomalies, such as a long face, broad nasal tip, cleft lip/cleft palate and large hands, yet its molecular function and structural basis remain unclear. Here, we report the crystal structures of the catalytic core of PHF8 with or without α-ketoglutarate （α-KG） at high resolution. Biochemical and structural studies reveal that PHF8 is a novel histone demethylase specific for di- and mono-methylated histone H3 lysine 9 （H3K9me2/1）, but not for H3K9me3. Our analyses also reveal how human PHF8 discriminates between methylation states and achieves sequence specificity for methylated H3K9. The in vitro demethylation assay also showed that the F279S mutant observed in clinical patients possesses no demethylation activity, suggesting that loss of enzymatic activity is crucial for pathogenesis of PHF8 patients. Taken together, these results will shed light on the molecular mechanism underlying PHF8-associated developmental and neurological diseases.展开更多
Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more com...Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more complex,high-order structures.The molecular properties of chromatin are dynamically regulated by several factors,such as post-translational modifications and effector proteins,to maintain genome stability.In the past two decades,high-resolution techniques have led to many breakthroughs in understanding the molecular mechanisms that govern chromatin regulation.Nuclear magnetic resonance(NMR)has emerged as one of the major techniques in this field,providing new insights into the nucleosomes and nucleosome-protein complexes in different states ranging from soluble form to condensed states.Solution-state NMR has proven valuable in elucidating the conformational dynamics and molecular interactions for histone N-terminal tails,histone core regions and DNA with the combination of specific isotopic labeling.Solid-state NMR,which is not constrained by the high molecular weights of complexes like nucleosomes,has been applied to capture the structural and dynamical characteristics of both flexible tails and rigid histone core regions in nucleosomes and their complexes with effector proteins.Furthermore,the combination of the two techniques allows tracking molecular properties of nucleosomes during phase separation processes,which potentially play essential roles in chromatin regulation.This review summarizes recent advances in NMR studies of chromatin structure and dynamics.It highlighted that NMR revealed unique molecular characteristics for nucleosomes that are often invisible experimentally by other techniques like cryogenic electron microscopy(cryo-EM)and X-ray diffraction(XRD).I envision that,with future ef-forts such as the development of NMR methods and optimization of sample production protocols,solution-state NMR and solid-state NMR will provide invaluable information to expand our understanding of chromatin activity and its regulatory processes.展开更多
Objective:To assess whether the coronavirus disease 2019(COVID-19)mRNA vaccine affects sperm morphokinetics using a computer-assisted semen analyzer and other semen parameters using a sperm chromatin structure assay.M...Objective:To assess whether the coronavirus disease 2019(COVID-19)mRNA vaccine affects sperm morphokinetics using a computer-assisted semen analyzer and other semen parameters using a sperm chromatin structure assay.Methods:Healthy male volunteers in two Japanese clinics between May 2021 and December 2021 were prospectively analyzed.Participants donated sperm twice,two days apart,in the following phases:before vaccination,2 weeks after the first vaccine dose,and 2,4,and 12 weeks after the second dose.Basic sperm parameters,sperm motility characteristics,and the percentage of DNA-damaged sperm were compared among the different phases.Results:Ninety-six semen samples from ten volunteers,who were vaccinated with the BNT162b2 mRNA vaccine,were evaluated.There were no significant differences between any phases in basic semen findings and parameters of the sperm chromatin structure assays.Regarding sperm motion characteristics,the average linear velocity,beat-cross frequency,and sperm motility index significantly decreased after the second vaccine dose(P=0.018,P=0.003,and P=0.027,respectively),with no significant differences between any two phases by post-hoc pairwise comparisons.Conclusions:After COVID-19 mRNA vaccination,while sperm motion characteristics might fluctuate,no apparent deterioration of basic sperm parameters or sperm DNA integrity was observed.Given the adverse effects of COVID-19 on sperm,our findings suggest that there might be no reason to refrain from vaccination for healthy individuals.展开更多
基金supported by the Startup Foundation for Junior Faculty,Nankai University(Grant No.:63191439)the National Natural Science Foundation of China(Grant Nos.:32100418,3210040345)+1 种基金The Health Commission Foundation of China(Grant No.:2018ZX10712001-017)the Chongqing Medical College Natural Fund(Grant Nos.:ygz2019302 and ygz2019305).
文摘Epigenomic imbalance drives abnormal transcriptional processes,promoting the onset and progression of cancer.Although defective gene regulation generally affects carcinogenesis and tumor suppression networks,tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes,which may have significant implications for the development and application of epigenetic therapy,cancer immunotherapy,and their combinations.Herein,we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes,DNA methylation,histone post-translational modification,and chromatin structure in tumor immunogenicity,and introduce these epigenetic research methods.We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immuno-therapy through the complex interaction between cancer epigenetics and cancer immunology.
文摘Diagnosis of male infertility has mainly been based on the World Health Organization （WHO） manual-based semen parameter＇s concentration, motility and morphology. It has, however, become apparent that none of these parameters are reliable markers for evaluation of the fertility potential of a couple. A search for better markers has led to an increased focus on sperm chromatin integrity testing in fertility work-up and assisted reproductive techniques. During the last couple of decades, numerous sperm DNA integrity tests have been developed. These are claimed to be characterized by a lower intraindividual variation, less intralaboratory and interlaboratory variation and thus less subjective than the conventional sperm analysis. However, not all the sperm chromatin integrity tests have yet been shown to be of clinical value. So far, the test that has been found to have the most stable clinical threshold values in relation to fertility is the sperm chromatin structure assay （SCSA）, a flow cytometric test that measures the susceptibility of sperm DNA to acid-induced DNA denaturation in situ. Sperm DNA fragmentation as measured by SCSA has shown to be an independent predictor of successful pregnancy in first pregnancy planners as well as in couples undergoing intrauterine insemination, and can be used as a tool in investigation, counseling and treatment of involuntary childlessness. More conflicting data exist regarding the role of sperm DNA fragmentation in relation to fertilization, pre-embryo development and pregnancy outcome in in vitro fertilization and intracytoplasmic sperm injection （ICSI）.
基金ACKNOWLEDGMENTS This study was supported by grants from the Natural Science Foundation of Shanghai （No. 10JC1410800）. The support of Jian-Bin Liu in collecting the patient data is gratefully acknowledged.
文摘The aim of this study was to investigate whether the sperm chromatin structure assay （SCSA） results after swim-up are related to fertilization rates, embryo quality and pregnancy rates following in vitrofertilization （IVF）. A total of 223 couples undergoing IVF in our hospital from October 2008 to September 2009 were included in this study. Data on the IVF process and sperm chromatin structure assay results were collected. Fertilization rate, embryo quality and IVF success rates of different DNA fragmentation index （DFI） subgroups and high DNA stainability （HDS） subgroups were compared. There were no significant differences in fertilization rate, clinical pregnancy or delivery rates between the DFI and HDS subgroups. However, the group with abnormal DFI had a lower good embryo rate. So, we concluded that the SCSA variables, either DFI or HDS after swim-up preparation, were not valuable in predicting fertilization failure or pregnancy rate, but an abnormal DFI meant a lower good embryo rate following IVF.
基金supported by the National Natural Science Foundation of China(Grant Nos.31000566 and 31071147)the National Basic Research Program(973 Program)of China(Grant No.2009CB825501).
文摘Eukaryotic DNA is hierarchically packaged into chromatin to fit inside the nucleus.Dynamics of the chromatin structure plays a critical role in transcriptional regulation and other biological processes that involve DNA,such as DNA replication and DNA repair.Many factors,including histone variants,histone modification,DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin.Although the structure of nucleosomes,the fundamental repeating unit of chromatin,is clear,there is still much discussion on the higher-order levels of chromatin structure.Identifying the structural details and dynamics of higher-order chromatin fibers is therefore very important for understanding the organization and regulation of gene activities.Here,we review studies on the dynamics of chromatin higherorder structure and its relationship with gene transcription.
基金Supplementary information is linked to the online version of the paper on the Cell Research website.Acknowledgments We thank Dr Dawei Li （China Agricultural University） for generously providing us with the experimental conditions during the early stages of this project. We thank Dr Ruiming Xu （Institute of Biophysics, Chinese Academy of Sciences） for critical reading of this manuscript and advice. We thank Dr Pinchao Mei （Chinese Academy of Medical Sciences and Peking Union Medical College）, Xinqi Liu （Nankai University） and Jiemin Wong （East China Normal University） for discussions and advice. The synchrotronradiation experiments were performed at Shanghai Synchrotron Radiation Facility （SSRF） and NE3A in the Photon Factory. Z.C. is supported by the National Basic Research Program of China （973 Program, 2009CB825501）, the National Natural Science Foundation of China （30870494 and 90919043）, the New Century Excellent Talents in University （NCET-07-0808） and the Innovative Project of SKLAB. S. H. is supported by the National Key Laboratory Special Fund 2060204. Z. D. is supported by the National Natural Science Foundation of China （J0730639）.
文摘Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain （PHD） finger protein 8 （PHF8） are associated with X-linked mental retardation and facial anomalies, such as a long face, broad nasal tip, cleft lip/cleft palate and large hands, yet its molecular function and structural basis remain unclear. Here, we report the crystal structures of the catalytic core of PHF8 with or without α-ketoglutarate （α-KG） at high resolution. Biochemical and structural studies reveal that PHF8 is a novel histone demethylase specific for di- and mono-methylated histone H3 lysine 9 （H3K9me2/1）, but not for H3K9me3. Our analyses also reveal how human PHF8 discriminates between methylation states and achieves sequence specificity for methylated H3K9. The in vitro demethylation assay also showed that the F279S mutant observed in clinical patients possesses no demethylation activity, suggesting that loss of enzymatic activity is crucial for pathogenesis of PHF8 patients. Taken together, these results will shed light on the molecular mechanism underlying PHF8-associated developmental and neurological diseases.
基金supported by funds from the National Natural Science Foundation of China(grant number:32201006)Guangdong Province(grant number:2021QN02Y103,2022ZDZX2061,2022KCXTD034)2023 Stable Support Plan Program of Shenzhen Colleges and Universities Fund.
文摘Eukaryotic deoxyribonucleic acid(DNA)is wrapped around histone octamers(HOs)to form nucleosome core particles(NCPs),which in turn interact with linker DNA and linker histones to assemble chromatin fibers with more complex,high-order structures.The molecular properties of chromatin are dynamically regulated by several factors,such as post-translational modifications and effector proteins,to maintain genome stability.In the past two decades,high-resolution techniques have led to many breakthroughs in understanding the molecular mechanisms that govern chromatin regulation.Nuclear magnetic resonance(NMR)has emerged as one of the major techniques in this field,providing new insights into the nucleosomes and nucleosome-protein complexes in different states ranging from soluble form to condensed states.Solution-state NMR has proven valuable in elucidating the conformational dynamics and molecular interactions for histone N-terminal tails,histone core regions and DNA with the combination of specific isotopic labeling.Solid-state NMR,which is not constrained by the high molecular weights of complexes like nucleosomes,has been applied to capture the structural and dynamical characteristics of both flexible tails and rigid histone core regions in nucleosomes and their complexes with effector proteins.Furthermore,the combination of the two techniques allows tracking molecular properties of nucleosomes during phase separation processes,which potentially play essential roles in chromatin regulation.This review summarizes recent advances in NMR studies of chromatin structure and dynamics.It highlighted that NMR revealed unique molecular characteristics for nucleosomes that are often invisible experimentally by other techniques like cryogenic electron microscopy(cryo-EM)and X-ray diffraction(XRD).I envision that,with future ef-forts such as the development of NMR methods and optimization of sample production protocols,solution-state NMR and solid-state NMR will provide invaluable information to expand our understanding of chromatin activity and its regulatory processes.
文摘Objective:To assess whether the coronavirus disease 2019(COVID-19)mRNA vaccine affects sperm morphokinetics using a computer-assisted semen analyzer and other semen parameters using a sperm chromatin structure assay.Methods:Healthy male volunteers in two Japanese clinics between May 2021 and December 2021 were prospectively analyzed.Participants donated sperm twice,two days apart,in the following phases:before vaccination,2 weeks after the first vaccine dose,and 2,4,and 12 weeks after the second dose.Basic sperm parameters,sperm motility characteristics,and the percentage of DNA-damaged sperm were compared among the different phases.Results:Ninety-six semen samples from ten volunteers,who were vaccinated with the BNT162b2 mRNA vaccine,were evaluated.There were no significant differences between any phases in basic semen findings and parameters of the sperm chromatin structure assays.Regarding sperm motion characteristics,the average linear velocity,beat-cross frequency,and sperm motility index significantly decreased after the second vaccine dose(P=0.018,P=0.003,and P=0.027,respectively),with no significant differences between any two phases by post-hoc pairwise comparisons.Conclusions:After COVID-19 mRNA vaccination,while sperm motion characteristics might fluctuate,no apparent deterioration of basic sperm parameters or sperm DNA integrity was observed.Given the adverse effects of COVID-19 on sperm,our findings suggest that there might be no reason to refrain from vaccination for healthy individuals.
