The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next gene...The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next generation. In addition, recent sperm chromatin genome-wide dissection studies indicate the presence of a differential distribution of the genes and repetitive sequences in the protamine-condensed and histone-condensed sperm chromatin domains, which could be potentially involved in regulatory roles after fertilization. Interestingly, recent proteomic studies have shown that sperm chromatin contains many additional proteins, in addition to the abundant histones and protamines, with specific modifications and chromatin affinity features which are also delivered to the oocyte. Both gene and protein signatures seem to be altered in infertile patients and, as such, are consistent with the potential involvement of the sperm chromatin landscape in early embryo development. This present work reviews the available information on the composition of the human sperm chromatin and its epigenetic potential, with a particular focus on recent results derived from high-throughput genomic and proteomic studies. As a complement, we provide experimental evidence for the detection of phosphorylations and acetylations in human protamine 1 using a mass spectrometry approach. The available data indicate that the sperm chromatin is much more complex than what it was previously thought, raising the possibility that it could also serve to transmit crucial paternal epigenetic information to the embryo.展开更多
The microcolonial black fungus Cryomyces antarcticus is an extremophile organism growing on and in rock in the Antarctic desert. Ecological plasticity and stress tolerance make it a perfect model organism for astrobio...The microcolonial black fungus Cryomyces antarcticus is an extremophile organism growing on and in rock in the Antarctic desert. Ecological plasticity and stress tolerance make it a perfect model organism for astrobiology. 2D-gel electrophoresis and MALDI-TOF/TOF mass spectrometry were performed to explore the protein repertoire, which allows the fungus to survive in the harsh environment. Only a limited number of proteins could be identified by using sequence homologies in public databases. Due to the rather low identification rate by sequence homology, this study reveals that a major part of the proteome of C. antarcticus varies significantly from other fungal species.展开更多
AIM: To study the differential protein profile in serum of hepatitis B patients.METHODS: Serum samples were obtained from patients with chronic hepatitis B who were receiving peginterferon alfa-2b.The serum samples we...AIM: To study the differential protein profile in serum of hepatitis B patients.METHODS: Serum samples were obtained from patients with chronic hepatitis B who were receiving peginterferon alfa-2b.The serum samples were subjected to albumin depletion and analyzed by two-dimensional gel electrophoresis(2-DE).Differentially expressed protein spots were identified by electrospray ionizationquadrupole time-of-flight mass spectrometry.Alpha2-HS-glycoprotein,complement component C3c and CD5 antigen were further analyzed by an enzymelinked immunosorbent assay and immunonephelometry.RESULTS: Nineteen patients with HBeAg-positive chronic hepatitis B(CHB) were studied.These patients were followed for at least 1 year after treatment and were classified according to their treatment response: responders(n = 9) and non-responders(n = 10).2-DE and MS/MS analysis were performed to compare the serum proteins before initiating peginterferon alfa2b.From the quantitative analysis of the 2-D gel,7 proteins were detected between the two groups at different levels before treatment.Among these potential candidates,serum levels of alpha-2-HS-glycoprotein,complement component C3c and CD5 antigen-like precursor were further analyzed.In the validation phase,23 subjects,9 sustained responders and 14 nonresponders,were recruited.Interestingly,the levels of alpha-2-HS-glycoprotein and complement component C3c were elevated in the serum of the non-responders compared to the responders.CONCLUSION: Serum alpha-2-HS-glycoprotein and complement component C3c may be potential serum biomarkers in predicting the treatment response of peginterferon alfa-2b in patients with CHB prior to treatment.展开更多
AIM: To establish methods for quantitative polymerase chain reaction (PCR) for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of hepatocellular carcinoma (HCC). METHODS: Total R...AIM: To establish methods for quantitative polymerase chain reaction (PCR) for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of hepatocellular carcinoma (HCC). METHODS: Total RNA from paraffin-embedded sections was isolated from 68 paraffin-embedded samples of HCC. Samples came from 54 male and 14 female patients with a mean age of 66.8 ± 7.8 years. Quantitative PCR was performed. Immunohistochemistry and in situ hybridization for hepcidin were also performed. RESULTS: Quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections of HCC was performed successfully. The expression level of hepcidin mRNA in cancer tissues was significantly higher than that in non-cancer tissues. A method of in situ hybridization for hepcidin was established successfully, and this demonstrated that hepcidin mRNA was expressed in non-cancerous tissue but absent in cancerous tissue. CONCLUSION: We have established novel methods for quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of HCC.展开更多
Hepatocellular carcinoma(HCC),which is the most frequent primary liver malignancy,is ranked as the sixth most common cancer and the third leading cause of cancer-related deaths worldwide,with its incidence expected to...Hepatocellular carcinoma(HCC),which is the most frequent primary liver malignancy,is ranked as the sixth most common cancer and the third leading cause of cancer-related deaths worldwide,with its incidence expected to continue rising.One of the reasons is that most patients are diagnosed at an advanced stage when therapeutic options are ineffective.The development of HCC is attributed to a chronic exposition to either one or a combination of low amounts of different hepatotoxins,such as in hepatitis virus infection,alcohol consumption,aflatoxin from contaminated foods,metabolic factors,and exposure to chemical carcinogens from tobacco smoke(Fomer et al.,2018).展开更多
Following an Assessment by the Autonomous University of Hidalgo State and the National Institute of Genomic Medicine,this erratum corrects the authorship of this article by adding Dulce Maria MORENO-GARCiA as the firs...Following an Assessment by the Autonomous University of Hidalgo State and the National Institute of Genomic Medicine,this erratum corrects the authorship of this article by adding Dulce Maria MORENO-GARCiA as the first author.The published article(Zepeda-Bastida et al.,2021)has now been updated with the corrected authorship,author contributions,and acknowledgments,which may be seen in this erratum.展开更多
Objective:a-Synuclein has been studied as a potential biomarker for Parkinson's disease(PD)with no concluding results.Accordingly,there is an urgent need to find out reliable specific biomarkers for PD.GPR37 is an...Objective:a-Synuclein has been studied as a potential biomarker for Parkinson's disease(PD)with no concluding results.Accordingly,there is an urgent need to find out reliable specific biomarkers for PD.GPR37 is an orphan G protein-coupled receptor that toxically accumulates in autosomal recessive juvenile parkinsonism.Here,we investigated whether GPR37 is upregulated in sporadic PD,and thus a suitable potential biomarker for PD.Methods:GPR37 protein density and mRNA expression in postmortem substantia nigra(SN)from PD patients were analysed by immunoblot and RT-qPCR,respectively.The presence of peptides from the N-terminus-cleaved domain of GPR37(i.e.ecto-GPR37)in human cerebrospinal fluid(CSF)was determined by liquid chromatography-mass spectrometric analysis.An engineered in-house nanoluciferase-based immunoassay was used to quantify ecto-GPR37 in CSF samples from neurological control(NC)subjects,PD patients and Alzheimer's disease(AD)patients.Results:GPR37 protein density and mRNA expression were significantly augmented in sporadic PD.Increased amounts of ecto-GPR37 peptides in the CSF samples from PD patients were identified by mass spectrometry and quantified by the in-house ELISA method.However,the CSF total a-synuclein level in PD patients did not differ from that in NC subjects.Similarly,the cortical GPR37 mRNA expression and CSF ecto-GPR37 levels in AD patients were also unaltered.Conclusion:GPR37 expression is increased in SN of sporadic PD patients.The ecto-GPR37 peptides are significantly increased in the CSF of PD patients,but not in AD patients.These results open perspectives and encourage further clinical studies to confirm the validity and utility of ecto-GPR37 as a potential PD biomarker.展开更多
Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has...Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.展开更多
Dear Editor,Of all human tumors,pheochromocytomas and paragangliomas(PPGLs)have the highest heritability rate.Over 15%of PPGLs harbor mutations in genes encoding tricarboxylic acid(TCA)cycle-related enzymes that cause...Dear Editor,Of all human tumors,pheochromocytomas and paragangliomas(PPGLs)have the highest heritability rate.Over 15%of PPGLs harbor mutations in genes encoding tricarboxylic acid(TCA)cycle-related enzymes that cause oncometabolite accumulation and drive tumorigenesis via metabolic adaptation to hypoxia and global hypermethylation[1].The dihydrolipoamide S-succinyltransferase(DLST)gene was recently described as a new PPGL susceptibility gene[2].展开更多
文摘The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next generation. In addition, recent sperm chromatin genome-wide dissection studies indicate the presence of a differential distribution of the genes and repetitive sequences in the protamine-condensed and histone-condensed sperm chromatin domains, which could be potentially involved in regulatory roles after fertilization. Interestingly, recent proteomic studies have shown that sperm chromatin contains many additional proteins, in addition to the abundant histones and protamines, with specific modifications and chromatin affinity features which are also delivered to the oocyte. Both gene and protein signatures seem to be altered in infertile patients and, as such, are consistent with the potential involvement of the sperm chromatin landscape in early embryo development. This present work reviews the available information on the composition of the human sperm chromatin and its epigenetic potential, with a particular focus on recent results derived from high-throughput genomic and proteomic studies. As a complement, we provide experimental evidence for the detection of phosphorylations and acetylations in human protamine 1 using a mass spectrometry approach. The available data indicate that the sperm chromatin is much more complex than what it was previously thought, raising the possibility that it could also serve to transmit crucial paternal epigenetic information to the embryo.
文摘The microcolonial black fungus Cryomyces antarcticus is an extremophile organism growing on and in rock in the Antarctic desert. Ecological plasticity and stress tolerance make it a perfect model organism for astrobiology. 2D-gel electrophoresis and MALDI-TOF/TOF mass spectrometry were performed to explore the protein repertoire, which allows the fungus to survive in the harsh environment. Only a limited number of proteins could be identified by using sequence homologies in public databases. Due to the rather low identification rate by sequence homology, this study reveals that a major part of the proteome of C. antarcticus varies significantly from other fungal species.
基金Supported by The 90th Anniversary of Chulalongkorn University Fund(Ratchadaphiseksomphot Endowment Fund)The Thailand Research Fund,No.RMU5180051+2 种基金The Thailand Research Fund Senior Research Scholarship,No.RTA5380005The Higher Education Research Promotion and National Research University Project of Thailand,Office of the Higher Education Commission,No.HR1163AIntegrated Innovation Academic Center,Chulalongkorn University Centenary Academic Development Project,No.CU56-HR05,The Liver Research Unit,Chulalongkorn University
文摘AIM: To study the differential protein profile in serum of hepatitis B patients.METHODS: Serum samples were obtained from patients with chronic hepatitis B who were receiving peginterferon alfa-2b.The serum samples were subjected to albumin depletion and analyzed by two-dimensional gel electrophoresis(2-DE).Differentially expressed protein spots were identified by electrospray ionizationquadrupole time-of-flight mass spectrometry.Alpha2-HS-glycoprotein,complement component C3c and CD5 antigen were further analyzed by an enzymelinked immunosorbent assay and immunonephelometry.RESULTS: Nineteen patients with HBeAg-positive chronic hepatitis B(CHB) were studied.These patients were followed for at least 1 year after treatment and were classified according to their treatment response: responders(n = 9) and non-responders(n = 10).2-DE and MS/MS analysis were performed to compare the serum proteins before initiating peginterferon alfa2b.From the quantitative analysis of the 2-D gel,7 proteins were detected between the two groups at different levels before treatment.Among these potential candidates,serum levels of alpha-2-HS-glycoprotein,complement component C3c and CD5 antigen-like precursor were further analyzed.In the validation phase,23 subjects,9 sustained responders and 14 nonresponders,were recruited.Interestingly,the levels of alpha-2-HS-glycoprotein and complement component C3c were elevated in the serum of the non-responders compared to the responders.CONCLUSION: Serum alpha-2-HS-glycoprotein and complement component C3c may be potential serum biomarkers in predicting the treatment response of peginterferon alfa-2b in patients with CHB prior to treatment.
基金Supported by A research grant from the Biomarker Society
文摘AIM: To establish methods for quantitative polymerase chain reaction (PCR) for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of hepatocellular carcinoma (HCC). METHODS: Total RNA from paraffin-embedded sections was isolated from 68 paraffin-embedded samples of HCC. Samples came from 54 male and 14 female patients with a mean age of 66.8 ± 7.8 years. Quantitative PCR was performed. Immunohistochemistry and in situ hybridization for hepcidin were also performed. RESULTS: Quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections of HCC was performed successfully. The expression level of hepcidin mRNA in cancer tissues was significantly higher than that in non-cancer tissues. A method of in situ hybridization for hepcidin was established successfully, and this demonstrated that hepcidin mRNA was expressed in non-cancerous tissue but absent in cancerous tissue. CONCLUSION: We have established novel methods for quantitative PCR for hepcidin using RNAs isolated from paraffin-embedded sections and in situ hybridization of HCC.
基金funded by the National Council of Science and Technology(CONACYTNo.CF2019-53358)+9 种基金the National Institute of Genomic Medicine(INMEGENNo.06/2017/I)the Unit of Production and Experimentation of Laboratory Animals of Center for Research and Advanced Studies of the National Polytechnic Institute(UPEAL-CINVESTAV-IPNNo.0114-14)the Autonomous University of Hidalgo State(UAEHNo.SEP-PFCE 2018)CONACYT-Mexico for awarding the masters(No.484737)doctoral fellowships(No.752715)CONACYT-Mexico for awarding the doctoral fellowship(No.431419)the Cátedras-CONACYT program。
文摘Hepatocellular carcinoma(HCC),which is the most frequent primary liver malignancy,is ranked as the sixth most common cancer and the third leading cause of cancer-related deaths worldwide,with its incidence expected to continue rising.One of the reasons is that most patients are diagnosed at an advanced stage when therapeutic options are ineffective.The development of HCC is attributed to a chronic exposition to either one or a combination of low amounts of different hepatotoxins,such as in hepatitis virus infection,alcohol consumption,aflatoxin from contaminated foods,metabolic factors,and exposure to chemical carcinogens from tobacco smoke(Fomer et al.,2018).
基金National Council of Science and Technology(CONACYT,No.CF2019-53358)National Institute of Genomic Medicine(INMEGEN,No.06/2017/I)+4 种基金Unit of Production and Experimentation of Laboratory Animals of Center for Research and Advanced Studies of the National Polytechnic Institute(UPEAL-CINVESTAVIPN,No.0114-14)Autonomous University of Hidalgo State(UAEH,No.SEP-PFCE 2018)Brisa Rodope ALARCÓN-SÁNCHEZ gives thanks to CONACYT-Mexico for awarding the masters(No.484737)doctoral fellowships(No.752715)Osiris Germán IDELFONSO-GARCÍA gives thanks to CONACYT-Mexico for awarding the doctoral fellowship(No.431419)。
文摘Following an Assessment by the Autonomous University of Hidalgo State and the National Institute of Genomic Medicine,this erratum corrects the authorship of this article by adding Dulce Maria MORENO-GARCiA as the first author.The published article(Zepeda-Bastida et al.,2021)has now been updated with the corrected authorship,author contributions,and acknowledgments,which may be seen in this erratum.
基金supported by Ministerio de Ciencia,Innovacion y Universidades-Agencia Estatal de Investigacion/FEDER(SAF2017-87349-R and MDM-2017-0729)ISCIII/FEDER(PIE14/00034 and PI19/00144)+5 种基金Generalitat de Catalunya(2017SGR1604,2017SGR595)Fundacio la Marato de TV3(Grant 20152031)FWO(SBO-140028)ERC consolidator grant(Progsy 649116)Stiftelsen for Strategisk Forskning and a Wallenberg Clinical Scholarship to PS.The CRG/UPF Proteomics Unit is part of the Spanish Infrastruaure for Omics Technologies(ICTS OmicsTech)is a member of the ProteoRed PRB3 consortium which is supported by grant PT17/0019 of the PEI+D+i 2013-2016 from the Instituto de Salud Carlos Ⅲ(ISCⅢ)and ERDF.
文摘Objective:a-Synuclein has been studied as a potential biomarker for Parkinson's disease(PD)with no concluding results.Accordingly,there is an urgent need to find out reliable specific biomarkers for PD.GPR37 is an orphan G protein-coupled receptor that toxically accumulates in autosomal recessive juvenile parkinsonism.Here,we investigated whether GPR37 is upregulated in sporadic PD,and thus a suitable potential biomarker for PD.Methods:GPR37 protein density and mRNA expression in postmortem substantia nigra(SN)from PD patients were analysed by immunoblot and RT-qPCR,respectively.The presence of peptides from the N-terminus-cleaved domain of GPR37(i.e.ecto-GPR37)in human cerebrospinal fluid(CSF)was determined by liquid chromatography-mass spectrometric analysis.An engineered in-house nanoluciferase-based immunoassay was used to quantify ecto-GPR37 in CSF samples from neurological control(NC)subjects,PD patients and Alzheimer's disease(AD)patients.Results:GPR37 protein density and mRNA expression were significantly augmented in sporadic PD.Increased amounts of ecto-GPR37 peptides in the CSF samples from PD patients were identified by mass spectrometry and quantified by the in-house ELISA method.However,the CSF total a-synuclein level in PD patients did not differ from that in NC subjects.Similarly,the cortical GPR37 mRNA expression and CSF ecto-GPR37 levels in AD patients were also unaltered.Conclusion:GPR37 expression is increased in SN of sporadic PD patients.The ecto-GPR37 peptides are significantly increased in the CSF of PD patients,but not in AD patients.These results open perspectives and encourage further clinical studies to confirm the validity and utility of ecto-GPR37 as a potential PD biomarker.
文摘Deposition of the H2A.Z histone variant by the SWR1 complex （SWRI-C） in regulatory regions of specific loci modulates transcription. Characterization of mutations in Arabidopsis thaliana homologs of yeast SWRI-C has revealed a role for H2A.Z exchange in a variety of developmental processes. Nevertheless, the exact composition of plant SWRI-C and how it is recruited to target genes remains to be established. Here we show that SWC4, the Arabidopsis homolog of yeast SANT domain protein Swc4/Eaf2, is a DNA-binding protein that interacts with SWR1-C subunits. We demonstrate that the swc4-1 knockout mutant is embryo- lethal, while SWC4 RNAi knockdown lines display pleiotropic phenotypic alterations in vegetative and repro- ductive traits, including acceleration of flowering time, indicating that SWC4 controls post-embryonic processes. Transcriptomic analyses and genome-wide profiling of H2A.Z indicate that SWC4 represses tran- scription of a number of genes, including the floral integrator FT and key transcription factors, mainly by modulating H2A.Z deposition. Interestingly, SWC4 silencing does not affect H2A.Z deposition at the FLC locus nor expression of this gene, a master regulator of flowering previously shown to be controlled by SWR1-C. Importantly, we find that SWC4 recognizes specific AT-rich DNA elements in the chromatin regions of target genes and that SWC4 silencing impairs SWRI-C binding at FT. Collectively, our data suggest that SWC4 regulates plant growth and development by aiding SWR1-C recruitment and modulating H2A.Z deposition.
基金supported by the Instituto de Salud CarlosⅢ(ISCⅢ)through the“Acción Estratégica en Salud”(AES)(projects PI18/00454 and PI22/01490 to A.C.and PI20/01169 to M.R.)cofounded by the European Regional Development Fund(ERDF)+1 种基金supported by the Spanish Ministry of Science,Innovation and Universities“Formación del Profesorado Universitario-FPU”fellowship with ID number FPU19/04940supported by‘la Caixa’Foundation(ID 100010434)under agreement LCF/BQ/PI20/11760011.
文摘Dear Editor,Of all human tumors,pheochromocytomas and paragangliomas(PPGLs)have the highest heritability rate.Over 15%of PPGLs harbor mutations in genes encoding tricarboxylic acid(TCA)cycle-related enzymes that cause oncometabolite accumulation and drive tumorigenesis via metabolic adaptation to hypoxia and global hypermethylation[1].The dihydrolipoamide S-succinyltransferase(DLST)gene was recently described as a new PPGL susceptibility gene[2].
