Spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium

Molecular knowledge of human gastric corpus epithelium remains incomplete. Here, by integrated analyses using single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) techniques, we uncovered the spatially resolved expression landscape and gene-regulatory network of human gastric corpus epithelium. Specifically, we identified a stem/progenitor cell population in the isthmus of human gastric corpus, where EGF and WNT signaling pathways were activated. Meanwhile, LGR4, but not LGR5, was responsible for the activation of WNT signaling pathway. Importantly, FABP5 and NME1 were identified and validated as crucial for both normal gastric stem/progenitor cells and gastric cancer cells. Finally, we explored the epigenetic regulation of critical genes for gastric corpus epithelium at chromatin state level, and identified several important cell-type-specific transcription factors. In summary, our work provides novel insights to systematically understand the cellular diversity and homeostasis of human gastric corpus epithelium in vivo.

Chromatin Remodeling Factor SMARCA5 is Essential for Hippocampal Memory Maintenance via Metabolic Pathways in Mice / 神经科学通报·英文版

Gene transcription and new protein synthesis regulated by epigenetics play integral roles in the formation of new memories. However, as an important part of epigenetics, the function of chromatin remodeling in learning and memory has been less studied. Here, we showed that SMARCA5 (SWI/SNF related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 5), a critical chromatin remodeler, was responsible for hippocampus-dependent memory maintenance and neurogenesis. Using proteomics analysis, we found protein expression changes in the hippocampal dentate gyrus (DG) after the knockdown of SMARCA5 during contextual fear conditioning (CFC) memory maintenance in mice. Moreover, SMARCA5 was revealed to participate in CFC memory maintenance via modulating the proteins of metabolic pathways such as nucleoside diphosphate kinase-3 (NME3) and aminoacylase 1 (ACY1). This work is the first to describe the role of SMARCA5 in memory maintenance and to demonstrate the involvement of metabolic pathways regulated by SMARCA5 in learning and memory.

Transcriptome Analysis of Schwann Cells at Various Stages of Myelination Implicates Chromatin Regulator Sin3A in Control of Myelination Identity / 神经科学通报·英文版

Enhancing remyelination after injury is of utmost importance for optimizing the recovery of nerve function. While the formation of myelin by Schwann cells (SCs) is critical for the function of the peripheral nervous system, the temporal dynamics and regulatory mechanisms that control the progress of the SC lineage through myelination require further elucidation. Here, using in vitro co-culture models, gene expression profiling of laser capture-microdissected SCs at various stages of myelination, and multilevel bioinformatic analysis, we demonstrated that SCs exhibit three distinct transcriptional characteristics during myelination: the immature, promyelinating, and myelinating states. We showed that suppressor interacting 3a (Sin3A) and 16 other transcription factors and chromatin regulators play important roles in the progress of myelination. Sin3A knockdown in the sciatic nerve or specifically in SCs reduced or delayed the myelination of regenerating axons in a rat crushed sciatic nerve model, while overexpression of Sin3A greatly promoted the remyelination of axons. Further, in vitro experiments revealed that Sin3A silencing inhibited SC migration and differentiation at the promyelination stage and promoted SC proliferation at the immature stage. In addition, SC differentiation and maturation may be regulated by the Sin3A/histone deacetylase2 (HDAC2) complex functionally cooperating with Sox10, as demonstrated by rescue assays. Together, these results complement the recent genome and proteome analyses of SCs during peripheral nerve myelin formation. The results also reveal a key role of Sin3A-dependent chromatin organization in promoting myelinogenic programs and SC differentiation to control peripheral myelination and repair. These findings may inform new treatments for enhancing remyelination and nerve regeneration.

Antimicrobial activity and acetylcholinesterase inhibition by extracts from chromatin modulated fungi

ABSTRACT Major health challenges as the increasing number of cases of infections by antibiotic multiresistant microorganisms and cases of Alzheimer's disease have led to searching new control drugs. The present study aims to verify a new way of obtaining bioactive extracts from filamentous fungi with potential antimicrobial and acetylcholinesterase inhibitory activities, using epigenetic modulation to promote the expression of genes commonly silenced. For such finality, five filamentous fungal species (Talaromyces funiculosus, Talaromyces islandicus, Talaromyces minioluteus, Talaromyces pinophilus, Penicillium janthinellum) were grown or not with DNA methyltransferases inhibitors (procainamide or hydralazine) and/or a histone deacetylase inhibitor (suberohydroxamic acid). Extracts from T. islandicus cultured or not with hydralazine inhibited Listeria monocytogenes growth in 57.66 ± 5.98% and 15.38 ± 1.99%, respectively. Increment in inhibition of acetylcholinesterase activity was observed for the extract from P. janthinellum grown with procainamide (100%), when compared to the control extract (39.62 ± 3.76%). Similarly, inhibition of acetylcholinesterase activity increased from 20.91 ± 3.90% (control) to 92.20 ± 3.72% when the tested extract was obtained from T. pinophilus under a combination of suberohydroxamic acid and procainamide. Concluding, increases in antimicrobial activity and acetylcholinesterase inhibition were observed when fungal extracts in the presence of DNA methyltransferases and/or histone deacetylase modulators were tested.

Alternativas al modelo de investigación y desarrollo de medicamentos / Alternatives to the drug research and development model

Un tercio de la población mundial carece de acceso a los medicamentos y la situación es peor en los países pobres, en los que hasta un 50% de la población carece de acceso. El fracaso de los sistemas actuales de incentivos, basados en la propiedad intelectual, para ofrecer los productos farmacéuticos necesarios, especialmente en los países del sur, llama a la acción. Los problemas relacionados con el acceso a medicamentos no pueden ser resueltos tan solo a través de mejoras o adaptaciones de los modelos de incentivos existentes. El modelo del sistema de propiedad intelectual no ofrece la innovación necesaria para los países en desarrollo, se necesitan nuevos mecanismos que de forma simultánea y eficaz promuevan la innovación y el acceso a los medicamentos. Un tratado internacional vinculante sobre investigación y desarrollo, que se negocie bajo los auspicios de la Organización Mundial de la Salud, puede proporcionar el marco adecuado para garantizar el establecimiento de prioridades, la coordinación y la financiación sostenible de los medicamentos a precios asequibles para los países en desarrollo.

One-third of the global population lacks access to medications; the situation is worse in poor countries, where up to 50% of the population lacks access. The failure of current incentive systems based in intellectual property to offer the necessary pharmaceutical products, especially in the global south, is a call to action. Problems related to drug access cannot be solved solely through improvements or modifications in the existing incentive models. The intellectual property system model does not offer sufficient innovation for developing countries; new mechanisms that effectively promote innovation and drug access simultaneously are needed. A binding international agreement on research and development, negotiated under the auspices of the World Health Organization, could provide an adequate framework for guaranteeing priority-setting, coordination, and sustainable financing of drugs at reasonable prices for developing countries.

Transactivation of bad by vorinostat-induced acetylated p53 enhances doxorubicin-induced cytotoxicity in cervical cancer cells

Vorinostat (VOR) has been reported to enhance the cytotoxic effects of doxorubicin (DOX) with fewer side effects because of the lower DOX dosage in breast cancer cells. In this study, we investigated the novel mechanism underlying the synergistic cytotoxic effects of VOR and DOX co-treatment in cervical cancer cells HeLa, CaSki and SiHa cells. Co-treatment with VOR and DOX at marginal doses led to the induction of apoptosis through caspase-3 activation, poly (ADP-ribose) polymerase cleavage and DNA micronuclei. Notably, the synergistic growth inhibition induced by the co-treatment was attributed to the upregulation of the pro-apoptotic protein Bad, as the silencing of Bad expression using small interfering RNA (siRNA) abolished the phenomenon. As siRNA against p53 did not result in an increase in acetylated p53 and the consequent upregulation of Bad, the observed Bad upregulation was mediated by acetylated p53. Moreover, a chromatin immunoprecipitation analysis showed that the co-treatment of HeLa cells with VOR and DOX increased the recruitment of acetylated p53 to the bad promoter, with consequent bad transactivation. Conversely, C33A cervical cancer cells containing mutant p53 co-treated with VOR and DOX did not exhibit Bad upregulation, acetylated p53 induction or consequent synergistic growth inhibition. Together, the synergistic growth inhibition of cervical cancer cell lines induced by co-treatment with VOR and DOX can be attributed to the upregulation of Bad, which is induced by acetylated p53. These results show for the first time that the acetylation of p53, rather than histones, is a mechanism for the synergistic growth inhibition induced by VOR and DOX co-treatments.

Quantitative analysis of nucleolar chromatin distribution in the complex convoluted nucleoli of Didinium nasutum (Ciliophora)

We have earlier shown that the typical Didinium nasutum nucleolus is a complex convoluted branched domain, comprising a dense fibrillar component located at the periphery of the nucleolus and a granular component located in the central part. Here our main interest was to study quantitatively the spatial distribution of nucleolar chromatin structures in these convoluted nucleoli. There are no "classical" fibrillar centers in D.nasutum nucleoli. The spatial distribution of nucleolar chromatin bodies, which play the role of nucleolar organizers in the macronucleus of D.nasutum, was studied using 3D reconstructions based on serial ultrathin sections. The relative number of nucleolar chromatin bodies was determined in macronuclei of recently fed, starved D.nasutum cells and in resting cysts. This parameter is shown to correlate with the activity of the nucleolus. However, the relative number of nucleolar chromatin bodies in different regions of the same convoluted nucleolus is approximately the same. This finding suggests equal activity in different parts of the nucleolar domain and indicates the existence of some molecular mechanism enabling it to synchronize this activity in D. nasutum nucleoli. Our data show that D. nasutum nucleoli display bipartite structure. All nucleolar chromatin bodies are shown to be located outside of nucleoli, at the periphery of the fibrillar component.

Chromatin regulation in schistosomes and histone modifying enzymes as drug targets

Only one drug is currently available for the treatment and control of schistosomiasis and the increasing risk of selecting strains of schistosome that are resistant to praziquantel means that the development of new drugs is urgent. With this objective we have chosen to target the enzymes modifying histones and in particular the histone acetyltransferases and histone deacetylases (HDAC). Inhibitors of HDACs (HDACi) are under intense study as potential anti-cancer drugs and act via the induction of cell cycle arrest and/or apoptosis. Schistosomes like other parasites can be considered as similar to tumours in that they maintain an intense metabolic activity and rate of cell division that is outside the control of the host. We have shown that HDACi can induce apoptosis and death of schistosomes maintained in culture and have set up a consortium (Schistosome Epigenetics: Targets, Regulation, New Drugs) funded by the European Commission with the aim of developing inhibitors specific for schistosome histone modifying enzymes as novel lead compounds for drug development.

Impact of cytomixis on meiosis, pollen viability and pollen size in wild populations of Himalayan poppy (Meconopsis aculeata Royle).

We report the occurrence of cytomixis in wild populations of Himalayan poppy (Meconopsis aculeata Royle),which is considered to be an important and threatened medicinal plant growing in the high hills of the Himalayas. The impact of cytomixis on meiotic behaviour, reduced pollen viability and heterogeneous-sized pollen grains was also studied. Cytological studies in the seven wild populations from the high hills of Himachal Pradesh revealed that all the Himalayan populations exist uniformly at the tetraploid level (2n=56) on x=14. The phenomenon of chromatin transfer among the proximate pollen mother cells (PMCs) in six populations caused various meiotic abnormalities. Chromatin transfer also resulted in the formation of coenocytes, aneuploid, polyploid and anucleated PMCs. Among individuals that showed chromatin transfer, chromosome stickiness and interbivalent connections were frequently observed in some PMCs. The phenomenon of cytomixis in the species seems to be directly under genetic control; it affects the meiotic course considerably and results in reduced pollen viability.

Human oocyte chromosome analysis: complicated cases and major pitfalls.

Human oocytes that remained unfertilized in programmes of assisted reproduction have been analysed cytogenetically for more than 20 years to assess the incidence of aneuploidy in female gametes. However, the results obtained so far are not indisputable as a consequence of difficulties in evaluating oocyte chromosome preparations. Because of the lack of guidelines, we decided to summarize for the first time, the possible pitfalls in human oocyte chromosome analysis. Therefore, we screened the material from our previous studies and compiled representative, complicated cases with recommendations for their cytogenetic classification. We point out that maturity and size of the oocyte are important parameters and that fixation artefacts, as well as the particular structure of oocyte chromosomes, may predispose one to misinterpretations. Moreover, phenomena related to oocyte activation and fertilization are illustrated and explained. This compilation may help to avoid major problems in future studies and contribute to a more precise, and uniform assessment of human oocyte chromosomes.

Evaluation of nuclear DNA damage in human spermatozoa in men opting for assisted reproduction.

Diagnosis of sperm DNA integrity of semen sample is important for consistently high reproductive efficiency. The conventional parameters of semen analysis take into account morphology, motility, and concentration of spermatozoa in the sample, which are insufficient for evaluation of reproductive potential. Current studies have implicated abnormal organization of genomic material in sperms as a probable cause in 20 per cent cases of male infertility. This is especially important in the era of assisted reproduction technique (ART) when a majority of infertile couples opt for assisted reproduction and in where cases DNA integrity is a better diagnostic and prognostic marker as compared to routine semen analysis. This article reviews and discusses some of the current techniques employed for evaluating chromatin structure or DNA damage in spermatozoa. These different techniques include single cell gel electrophoresis (COMET assay), Terminal tranferase dUTP Nick End Labelling (TUNEL), sperm chromatin structure assay (SCSA), In situ nick translation (ISNT) and acridine orange test. These techniques are independent measure of sperm quality and assist in semen quality assessment by detecting defects in DNA integrity or chromatin structure. The discussed techniques vary in their level of accuracy, cost input, sophistication of analysis and their application depends upon the sensitivity required for analysis. The article also briefly outlines the DNA packaging and the causes of DNA damage in spermatozoa. During chromatin packing 85 per cent of the histones are replaced by protamine while the residual histones act as marker of genes which are expressed in early embryonic development. Among the different aetiological factors observed to be responsible for DNA damage in human spermatozoa increased reactive oxygen species (ROS), oxidative stress is highly correlated with greater DNA fragmentation index (DFI). Oxidative stress leads to single and double strand breaks in sperm DNA. Apoptosis and abnormal chromatin packing also contribute to DNA damage. The significance of chromatin structure studies is more stressed owing to the greater awareness to transmission of genetic diseases because of higher incidence of gene imprinting defects, increased cancer frequency and other congenital and non-congenital defects in children conceived through assisted reproduction techniques.

Postnatal regulation of glucocorticoid receptor in the liver of chicken.

The specific binding of [3H]-dexamethasone to glucocoticoid receptor (GR) and activation of hormone-receptor (H-R) complexes from the liver of chicken at day 0, 5, 10, 30, 60 and 90 were investigated to find out GR regulation during postnatal development. Results showed that GR level (fmol/mg protein) reached a peak by day 5 of postnatal age and was significantly higher (+ 42%) than observed at day-0 (day of hatching), as evidenced also by protein blot experiments and Scatchard analysis of binding data. The GR concentration declined gradually up to day 30, and thereafter, no significant change was observed at day 60 and 90 of postnatal ages. The temperature and salt-dependent activation of GR showed no significant differences in 0 and 30-day old chicken, as determined by DNA-cellulose binding assay. However, nuclear binding of temperature and salt-activated GR complexes was significantly higher in 0-day old chicken. Cross-mixing experiments (wherein nuclei of day-0 were incubated with the H-R complexes of day-30 and vice-versa) revealed the role of nuclear specificity in higher binding of temperature and salt-activated H-R complexes at day-0 of postnatal age. DNase I extraction of nuclei bound to activated H-R complexes showed higher extractability at day-0 (70%), compared to day-30 (44%). Above findings suggested that changes in GR concentration as well as chromatin organization might play an important role in glucocorticoid-mediated responses during postnatal development of chicken.

The chromatin structure of the lysozyme GAS41 origin of DNA replication changes during the cell cycle

We used a rapid and simple protocol using lysolecithin for mapping HS sites in vivo. The protocol is based on partial digestion with DNase I of exponentially growing cells following permeabilization by short treatment with lysolecithin. Using this protocol, we analyzed the chromatin structure of the region surrounding two overlapping elements, an origin of bidirectional DNA replication and the GAS41 promoter, in chicken myelomonocytic HD11 cells arrested in G0, G0 and S phases as well as at the G0/S border. The results show that the chromatin of this region became more nuclease sensitive when cells were arrested in G0 phase and that this change in chromatin structure was reversible after the cells began to enter S phase.

The use of the acridine orange test and the TUNEL assay to assess the integrity of freeze-dried bovine spermatozoa DNA

The ability to detect nuclear damage is an important tool for the development of sperm preservation methods. We used the acridine orange test (AOT) and the terminal deoxynucleotidyl transferase-mediated dUDP nick-end labeling (TUNEL) assay to assess the DNA status of sperm cells preserved with different lyophilization media. The AOT did not detect any differences between different lyophilization media. However, differences in DNA integrity were observed among treatments with the TUNEL assay, suggesting that TUNEL is a more sensitive method to evaluate sperm DNA. The use of TCM 199 and 10% FCS as a lyophilization medium resulted in 14% of the cells with DNA fragmentation in TUNEL test. The AOT indicated only 4% of the cells with chromatin damage, with this same treatment, with no significant differences when compared to the other treatments. The degree of DNA fragmentation was negatively related to fertilizing potential, as sperm DNA damage was inversely correlated with pro-nucleus formation. The TUNEL assay was found to be an efficient method to detect DNA damage in sperm, and it could be used as a tool to predict male fertility

Cytomixis impairs meiosis and influences reproductive success in Chlorophytum comosum (Thunb) Jacq. - an additional strategy and possible implications.

Spontaneous intercellular chromatin migration/cytomixis was observed to occur in the pollen mother cells (PMCs) of the Chlorophytum comosum for the first time. The migration through cytomictic channels was more pronounced in meiosis-I and very rare in meiosis-II. The process was associated with erratic meiosis, which was characterized by defects in chromosome organization and segregation. Cytomixis was more intense in the month of April than in July and consequently the frequency of meiotic irregularities was much more pronounced during the month of April. As a consequence of abnormal meiosis, fertility was drastically reduced resulting in meager seed efficiency of 17% only. Recombination system also does not guarantee the release of sufficient variability. We view the phenomenon of cytomixis as genetically controlled mechanism involving meiotic genes and operating through signal transduction pathway triggered by the environmental stimuli. The evolutionary significance and tenable hypothesis in the backdrop of existing literature is also proposed.

Does human sperm nuclear DNA integrity affect embryo quality?

Abnormalities in the male genome are a clear potential reason for post fertilization failure. Male infertility may arise due to high levels of loosely packaged chromatin and damaged DNA. The achievement of a correct chromatin packaging level is essential for successful fertilization. The chromatin contained in the nuclei of mammalian spermatozoa is an extremely compact and stable structure. The reports on mammalian spermatozoa indicate that available volume is insufficient to contain sperm chromatin packed in nucleosome like structure and thus is organized in a special way. Different unique properties of sperm DNA like high degree of inertness and stability, absence of transcription, replacement of somatic histone by protamine etc have made the study of sperm chromatin more interesting. Increased levels of sperm nuclear DNA damage exist in infertile men with abnormal sperm parameters (i.e. concentration, motility and morphology), and various assay techniques have been developed to evaluate sperm chromatin maturity/DNA integrity. These assays are based on the facts that defects in chromatin structure have been shown to lead to increased DNA instability and sensitivity to denaturing stress. DNA integrity in the sperm is essential for the accurate and successful transmission of genetic information. Importance of sperm DNA has also become more obvious in the context of assisted reproductive techniques. While recent advances in assisted reproductive technologies have made possible and practical for many infertile men to become father, the risk of transmission of genetic mutation to the offspring, however, still remains. Further research is necessary to devise techniques for identification and selection of sperm with undamaged DNA for ICSI or to remove sperm with damaged DNA from the semen sample to improve the pregnancy outcome in ICSI.

Mammalian histone acetyltransferase complexes

Over the last decade, great progress has been made in elucidating how the human genome operates in the chromatin context. This paper describes our work on two human acetyltransferases, PCAF and TIP60, and their interaction partners. This study provides new clues on the function of these enzymes. In a striking parallel with the general transcription factor TFIID, PCAF complex contains proteins that have histone-like domains. We speculate that these subunits can presumably form a nucleosome-like structure on DNA, which would allow PCAF to contribute to the maintenance of an active state of chromatin. On the other hand, TIP60 complex contains two eukaryotic homologs of bacterial RuvB helicase/ATPse, involved in recombination and repair. Accordingly, expression of a dominant negative mutant of TIP60 in living cells interferes with their ability to repair DNA damage, which points out, for the first time, a role for a histone acetyltransferase in a process other than transcription. We also have evidence implicating TIP60 in the apoptotic response to DNA damage.

Characterization of primed lymphocytes on the basic of sensitivity of chromatin to DNase I.

Certain qualitative criteria for primed lymphocytes in the expression of cytotoxic function have been studied. Unlike normal lymphocytes, primed lymphocytes expressed cytotoxicity even when DNA synthesis and new gene expression were inhibited by hydroxyurea (HU) and bromodeoxyuridine (BU) respectively. Such differential cytotoxic expression in presence of HU and BU by primed lymphocytes might have their basis in conformational change within the chromatin. Chromatin from primed lymphocytes was more susceptible to DNase I digestion than virgin lymphocytes indicating exposition of more DNase I sensitive sites in primed state. The result suggest the presence of more ready to act sites for the polymerases in the genomic material of primed lymphocytes even at quiescent state.

Testis-specific histone (H1t) is not phosphorylated and has a weak interaction with chromatin.

Soluble chromatin was prepared from rat testes after a brief micrococcal nuclease digestion. After adsorption onto hydroxylapatite at low ionic strength, the histone H1 subtypes were eluted with a shallow salt gradient of 0.3 M NaCl to 0.7 M NaCl. Histone H1t was eluted at 0.4 M NaCl, while histones H1a and H1c were eluted at 0.43 M NaCl and 0.45 M respectively. The extreme divergence of the amino acid sequence of the C-terminal half of histone H1t, the major DNA binding domain of histone H1, from that of the somatic consensus sequence may contribute to the weaker interaction of histone H1t with the rat testis chromatin. Further, histone H1t was not phosphorylated in vivo in contrast to histone H1a and H1c, as is evident from the observation that histone H1t lacks the SPKK motif recognized by the CDC-2kinase or the RR/KXS motif recognized by protein kinase A.

Isolation and characterization of nonhistone proteins associated with DNase-II hypersensitive sites of Sarcoma-180 chromatin.

Limited digestion (2 min) of Sarcoma-180 nuclei by DNase-II released two nonhistone proteins from the hypersensitive sites of chromatin. The apparent molecular weights of these two proteins were 34 and 21 kDa. These proteins showed a moderate but specific inhibition in in vitro cell free transcription assay with native chromatin as template as opposed to no effect on native DNA transcription.