Coronavirus disease 2019(COVID-19),caused by the novel human coronavirus SARS-CoV-2,is currently a major threat to public health worldwide.The viral spike protein binds the host receptor angiotensin-converting enzyme ...Coronavirus disease 2019(COVID-19),caused by the novel human coronavirus SARS-CoV-2,is currently a major threat to public health worldwide.The viral spike protein binds the host receptor angiotensin-converting enzyme 2(ACE2)via the receptor-binding domain(RBD),and thus is believed to be a major target to block viral entry.Both SARS-CoV-2 and SARS-CoV share this mechanism.Here we functionally analyzed the key amino acid residues located within receptor binding motif of RBD that may interact with human ACE2 and available neutralizing antibodies.The in vivo experiments showed that immunization with either the SARS-CoV RBD or SARS-CoV-2 RBD was able to induce strong clade-specific neutralizing antibodies in mice;however,the cross-neutralizing activity was much weaker,indicating that there are distinct antigenic features in the RBDs of the two viruses.This finding was confirmed with the available neutralizing monoclonal antibodies against SARS-CoV or SARS-CoV-2.It is worth noting that a newly developed SARS-CoV-2 human antibody,HA001,was able to neutralize SARS-CoV-2,but failed to recognize SARS-CoV.Moreover,the potential epitope residues of HA001 were identified as A475 and F486 in the SARS-CoV-2 RBD,representing new binding sites for neutralizing antibodies.Overall,our study has revealed the presence of different key epitopes between SARS-CoV and SARSCoV-2,which indicates the necessity to develop new prophylactic vaccine and antibody drugs for specific control of the COVID-19 pandemic although the available agents obtained from the SARS-CoV study are unneglectable.展开更多
Ferroptosis is a novel form of iron-dependent cell death characterized by lipid per-oxidation.While the importance and disease relevance of ferroptosis is gaining recognition,much remains unknown about various genetic...Ferroptosis is a novel form of iron-dependent cell death characterized by lipid per-oxidation.While the importance and disease relevance of ferroptosis is gaining recognition,much remains unknown about various genetic and non-genetic determinants of ferroptosis.Hippo signaling pathway is an evolutionarily conserved pathway that responds to various envi-ronmental cues and controls organ size,cell proliferation,death,and self-renewal capacity.In cancer biology,Hippo pathway is a potent tumor suppressing mechanism and its dysregulation contributes to apoptosis evasion,cancer development,metastasis,and treatment resistance.Hippo dysregulation leads to aberrant activation of YAP and TAZ,the two major transcription co-activators of TEADs,that induce the expression of genes triggering tumor-promoting pheno-types,including enhanced cell proliferation,self-renewal and apoptosis inhibition.The Hippo pathway is regulated by the cell-cell contact and cellular density/confluence.Recently,fer-roptosis has also been found being regulated by the cellular contact and density.The YAP/TAZ activation under low density,while confers apoptosis resistance,renders cancer cells sensitivity to ferroptosis.These findings establish YAP/TAZ and Hippo pathways as novel deter-minants of ferroptosis.Therefore,inducing ferroptosis may have therapeutic potential for YAP/TAZ-activated chemo-resistant and metastatic tumor cells.Reciprocally,various YAP/TAZ-targeting treatments under clinical development may confer ferroptosis resistance,limiting the therapeutic efficacy.展开更多
Objective:Uterine corpus endometrial carcinoma(UCEC),a kind of gynecologic malignancy,poses a significant risk to women’s health.The precise mechanism underlying the development of UCEC remains elusive.Zinc finger pr...Objective:Uterine corpus endometrial carcinoma(UCEC),a kind of gynecologic malignancy,poses a significant risk to women’s health.The precise mechanism underlying the development of UCEC remains elusive.Zinc finger protein 554(ZNF554),a member of the Krüppel-associated box domain zinc finger protein superfamily,was reported to be dysregulated in various illnesses,including malignant tumors.This study aimed to examine the involvement of ZNF554 in the development of UCEC.Methods:The expression of ZNF554 in UCEC tissues and cell lines were examined by qRT-PCR and Western blot assay.Cells with stably overexpressed or knocked-down ZNF554 were established through lentivirus infection.CCK-8,wound healing,and Transwell invasion assays were employed to assess cell proliferation,migration,and invasion.Propidium iodide(PI)staining combined with fluorescence-activated cell sorting(FACS)flow cytometer was utilized to detect cell cycle distribution.qRT-PCR and Western blotting were conducted to examine relative mRNA and protein levels.Chromatin immunoprecipitation assay and luciferase reporter assay were used to explore the regulatory role of ZNF554 in RNA binding motif 5(RBM5).Results:The expression of ZNF554 was found to be reduced in both UCEC samples and cell lines.Decreased expression of ZNF554 was associated with higher tumor stage,decreased overall survival,and reduced disease-free survival in UCEC.ZNF554 overexpression suppressed cell proliferation,migration,and invasion,while also inducing cell cycle arrest.In contrast,a decrease in ZNF554 expression resulted in the opposite effect.Mechanistically,ZNF554 transcriptionally regulated RBM5,leading to the deactivation of the Wingless(WNT)/β-catenin signaling pathway.Moreover,the findings from rescue studies demonstrated that the inhibition of RBM5 negated the impact of ZNF554 overexpression onβ-catenin and p-glycogen synthase kinase-3β(p-GSK-3β).Similarly,the deliberate activation of RBM5 reduced the increase inβ-catenin and p-GSK-3βcaused by the suppression of ZN展开更多
Breast cancer is a molecularly heterogeneous disease and the most common female malignancy.In recent years,therapy approaches have evolved to accommodate molecular diversity,with a focus on more biologically based the...Breast cancer is a molecularly heterogeneous disease and the most common female malignancy.In recent years,therapy approaches have evolved to accommodate molecular diversity,with a focus on more biologically based therapies to minimize negative consequences.To regulate cell fate in human breast cells,the Hippo signaling pathway has been associated with the alpha subtype of estrogen receptors.This pathway regulates tissue size,regeneration,and healing,as well as the survival of tissue-specific stem cells,proliferation,and apoptosis in a variety of organs,allowing for cell differentiation.Hippo signaling is mediated by the kinases MST1,MST2,LATS1,and LATS2,as well as the adaptor proteins SAV1 and MOB.These kinases phosphorylate the downstream effectors of the Hippo pathway,yes-associated protein(YAP),and transcriptional coactivator with PDZ-binding motif(TAZ),suppressing the expression of their downstream target genes.The Hippo signaling pathway kinase cascade plays a significant role in all cancers.Understanding the principles of this kinase cascade would prevent the occurrence of breast cancer.In recent years,small noncoding RNAs,or microRNAs,have been implicated in the development of several malignancies,including breast cancer.The interconnections between miRNAs and Hippo signaling pathway core proteins in the breast,on the other hand,remain poorly understood.In this review,we focused on highlighting the Hippo signaling system,its key parts,its importance in breast cancer,and its regulation by miRNAs and other related pathways.展开更多
Plant plasmodesmata (PDs) are specialized channels that enable communication between neighboring cells. The intercellular permeability of PDs, which affects plant development, defense, and responses to stimuli, must b...Plant plasmodesmata (PDs) are specialized channels that enable communication between neighboring cells. The intercellular permeability of PDs, which affects plant development, defense, and responses to stimuli, must be tightly regulated. However, the lipid compositions of PD membrane and their impact on PD permeability remain elusive. Here, we report that the Arabidopsis sld1 sld2 double mutant, lacking sphingolipid long-chain base 8 desaturases 1 and 2, displayed decreased PD permeability due to a significant increase in callose accumulation. PD-located protein 5 (PDLP5) was significantly enriched in the leaf epidermal cells of sld1 sld2 and showed specific binding affinity to phytosphinganine (t18:0), suggesting that the enrichment of t18:0-based sphingolipids in sld1 sld2 PDs might facilitate the recruitment of PDLP5 proteins to PDs. The sld1 sld2 double mutant seedlings showed enhanced resistance to the fungal-wilt pathogen Verticillium dahlia and the bacterium Pseudomonas syringae pv. tomato DC3000, which could be fully rescued in sld1 sld2 pdlp5 triple mutant . Taken together, these results indicate that phytosphinganine might regulate PD functions and cell-to-cell communication by modifying the level of PDLP5 in PD membranes.展开更多
Importance:Transient neonatal zinc deficiency(TNZD)occurs in breastfed infants due to abnormally low breast milk zinc levels.Mutations in the solute carrier family 30 member 2(SLC30A2)gene,which encodes the zinc trans...Importance:Transient neonatal zinc deficiency(TNZD)occurs in breastfed infants due to abnormally low breast milk zinc levels.Mutations in the solute carrier family 30 member 2(SLC30A2)gene,which encodes the zinc transporter ZNT2,cause low zinc concentration in breast milk.Objective:This study aimed to provide further insights into TNZD pathophysiology.Methods:SLC30A2 sequencing was performed in three unrelated Japanese mothers,whose infants developed TNZD due to low-zinc milk consumption.The effects of the identified mutations were examined using cell-based assays and luciferase reporter analysis.Results:Novel SLC30A2 mutations were identified in each mother.One harbored a heterozygous missense mutation in the ZNT2 zinc-binding site,which resulted in defective zinc transport.The other two mothers exhibited multiple heterozygous mutations in the SLC30A2 promoter,the first mutations in the SLC30A2 regulatory region reported to date.Interpretation:This report provides new genetic insights into TNZD pathogenesis in breastfed infants.展开更多
The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied ph...The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB‐GRPs distributed on 10 chromosomes were identified in maize（Zea mays L.）, and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified,while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB‐GRPs in maize. Comparative analysis of RB‐GRPs in maize, Arabidopsis（Arabidopsis thaliana L.）, rice（Oryza sativa L.）, and wheat（Triticum aestivum）revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB‐GRPs was significantly regulated by at least two kinds of stresses. In addition, cis‐elements predicted in the promoter regions of the ZmRB‐GRPs also indicated that these ZmRB‐GRPs would be involved in stress response of maize. The preliminary genome‐wide analysis of the RB‐GRPs in maize would provide useful information for further study on the function of the ZmRB‐GRPs.展开更多
Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct gr...Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.展开更多
hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-termi...hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-terminus. To search for its substrates and regulatory components, we screened a two-hybrid library by using the full-length hPFTAIRE1 as a bait. Four 14-3-3 isoforms （β,ε,η,τ） were identified interacting with the hPFTAIRE1. We found a putative 14-3-3 binding consensus motif（RHSSPSS） in the hPFTAIRE 1, which overlapped with its second NLS. Deletion of the RHSSPSS motif or substitution of Ser^119 gwithAla in the conserved binding motif abolished the specific interaction between the hPFTAIRE 1 and the 14-3 -3 proteins. The mutant S 120A hPFTAIRE1 also showed a weak interaction to the 14-3-3 proteins. The results suggested that the Ser^119 is crucial for the interaction between hPFTAIREI and the 14-3-3 proteins. All the hPFTAIRE1 mutants distributed in cytoplasm of Hela cells and human neuroblastoma cells （SH-SY5Y） when fused to the C-terminus of a green fluorescent protein （GFP）, indicating that binding with the 14-3-3 proteins does not contribute to the subcellular localization of the hPFTAIRE1, although the binding may be involved in its signaling regulation.展开更多
The establishment of a landscape of enhancers across human cells is crucial to deciphering the mechanism of gene regulation,cell differentiation,and disease development.High-throughput experimental approaches,which co...The establishment of a landscape of enhancers across human cells is crucial to deciphering the mechanism of gene regulation,cell differentiation,and disease development.High-throughput experimental approaches,which contain successfully reported enhancers in typical cell lines,are still too costly and time-consuming to perform systematic identification of enhancers specific to different cell lines.Existing computational methods,capable of predicting regulatory elements purely relying on DNA sequences,lack the power of cell line-specific screening.Recent studies have suggested that chromatin accessibility of a DNA segment is closely related to its potential function in regulation,and thus may provide useful information in identifying regulatory elements.Motivated by the aforementioned understanding,we integrate DNA sequences and chromatin accessibility data to accurately predict enhancers in a cell line-specific manner.We proposed Deep CAPE,a deep convolutional neural network to predict enhancers via the integration of DNA sequences and DNase-seq data.Benefitting from the well-designed feature extraction mechanism and skip connection strategy,our model not only consistently outperforms existing methods in the imbalanced classification of cell line-specific enhancers against background sequences,but also has the ability to self-adapt to different sizes of datasets.Besides,with the adoption of autoencoder,our model is capable of making cross-cell line predictions.We further visualize kernels of the first convolutional layer and show the match of identified sequence signatures and known motifs.We finally demonstrate the potential ability of our model to explain functional implications of putative disease-associated genetic variants and discriminate diseaserelated enhancers.The source code and detailed tutorial of Deep CAPE are freely available at https://github.com/Shengquan Chen/DeepCAPE.展开更多
Importance:Pathogenic variants in theRBM20 gene are associated with aggressive dilated cardiomyopathy(DCM).Recently,RBM20 was found to be associated with left ventricular non-compaction cardiomyopathy(LVNC).Thus far,o...Importance:Pathogenic variants in theRBM20 gene are associated with aggressive dilated cardiomyopathy(DCM).Recently,RBM20 was found to be associated with left ventricular non-compaction cardiomyopathy(LVNC).Thus far,only five families with LVNC have been reported to carry variants inRBM20.It remains unknown whether the variants inRBM20 associated with DCM can also cause LVNC.Objective:To elucidate the causativeRBM20 variant in two unrelated patients with both LVNC and DCM,and to identify the clinical characteristics associated with variants inRBM20.Methods:Trio whole-exome sequencing(WES)was performed.Variants were filtered and classified in accordance with the guidelines of the American College of Medical Genetics and Genomics(ACMG).Results:We identified two distinctde novo variants inRBM20(one per patient)in these two patients with LVNC.Both variants have been reported in patients with DCM,without the LVNC phenotype.Patient 1 was an 11-year-old girl who had DCM,LVNC,and heart failure;the ratio of noncompacted-to-compacted myocardium was 2.7:1.Ade novo heterozygous variant c.1907G>A(p.Arg636His)in exon 9 was identified in this patient.Patient 2 was a 13-year-old boy who had clinical phenotypes identical to those of Patient 1;the ratio of noncompacted-to-compacted myocardium was 3.2:1 in this patient.WES revealed ade novo heterozygous variant c.1909A>G(p.Ser637Gly)in exon 9.Both variants were previously characterized as pathogenic,and our study classified them as pathogenic variants based on the ACMG guidelines.Interpretation:We found that two patients with LVNC had variants inRBM20.Our results extended the clinical spectrum of the twoRBM20 variants and illustrated that the same variant inRBM20 can cause DCM,with or without the LVNC phenotype.展开更多
BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band...BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band 1p36.11,contains five noncoding 5 exons,a single 4.9-kb coding exon,and a noncoding 3 exon.CASE SUMMARY In this case report,we diagnosed and treated a 6-mo-old girl with XGS.The primary clinical symptoms included global developmental delay,hypotonia,and mild dysmorphic features.Using high-throughput whole-exosome sequencing to sequence the patient and her parents,and the results showed a novel frameshift mutation of c.1155dupG(p.Arg386Alafs*3)in the AHDC1 gene.The paternal gene was wild type.CONCLUSION This report extends the mutation spectrum of the AHDC1 gene to provide the diagnostic basis for genetic counseling in families with XGS.展开更多
Uncovering conserved 3D protein–ligand binding patterns on the basis of functional groups(FGs)shared by a variety of small molecules can greatly expand our knowledge of protein–ligand interactions.Despite that conse...Uncovering conserved 3D protein–ligand binding patterns on the basis of functional groups(FGs)shared by a variety of small molecules can greatly expand our knowledge of protein–ligand interactions.Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature,large-scale identification and evaluation of FG-based 3D binding motifs are still lacking.Here,we propose a computational method,Automatic FG-based Three-dimensional Motif Extractor(AFTME),for automatic mapping of 3D motifs to different FGs of a specific ligand.Applying our method to 233 naturally-occurring ligands,we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets.Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs.Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities.Finally,we show that our FG–motif map can be used to nominate FGs that potentially bind to specific drug targets,thus providing useful insights and guidance for rational design of small-molecule drugs.展开更多
Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains thr...Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains three continuous zinc finger motifs, which are believed being mctalloprotein structures that interact with DNA. We synthesized the second zine finger fragment of SP1 (SP1-ZF2) and its mutant (SP1-ZF2 / HT. E20→H. R23→T), we also synthesized the Cys-Cys loop (ZF6) and the His-His loop (ZF5) of SPI and linked the twoloops together using a β-turn structure to obtain a finger mimic analogue (ZF-15) by stepwise solid-phase technique. Atomic absorption studies show that SP 1-ZF2 and SP1-ZF2 / HT bind zinc cquimolarly, but ZF-15 docs not bind Zn anyway. The CD experiments demonstrate a significant change in secondary structure in the prescnce or absence of Zn to SP1-ZF2 and SP1-ZF2/ HT, but there is no change about ZF-15. Gcl-retardation clectrophoresis assays indicate that SP1-ZF2 binds to DNA sequence specifically in the presence of Zn, but SP1-ZF2 / HT docs not bind as SP 1-ZF2 did. We observed that a single zine finger like SP1-ZF2 is able to bind DNA sequence specifically.展开更多
基金supported by the National Natural Science Foundation of China(82041015)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB19000000)+1 种基金the Key International Partnership Program of the Chinese Academy of Sciences(153D31KYSB20180055)the National Major Science and Technology Projects of China(2018ZX10301403).
文摘Coronavirus disease 2019(COVID-19),caused by the novel human coronavirus SARS-CoV-2,is currently a major threat to public health worldwide.The viral spike protein binds the host receptor angiotensin-converting enzyme 2(ACE2)via the receptor-binding domain(RBD),and thus is believed to be a major target to block viral entry.Both SARS-CoV-2 and SARS-CoV share this mechanism.Here we functionally analyzed the key amino acid residues located within receptor binding motif of RBD that may interact with human ACE2 and available neutralizing antibodies.The in vivo experiments showed that immunization with either the SARS-CoV RBD or SARS-CoV-2 RBD was able to induce strong clade-specific neutralizing antibodies in mice;however,the cross-neutralizing activity was much weaker,indicating that there are distinct antigenic features in the RBDs of the two viruses.This finding was confirmed with the available neutralizing monoclonal antibodies against SARS-CoV or SARS-CoV-2.It is worth noting that a newly developed SARS-CoV-2 human antibody,HA001,was able to neutralize SARS-CoV-2,but failed to recognize SARS-CoV.Moreover,the potential epitope residues of HA001 were identified as A475 and F486 in the SARS-CoV-2 RBD,representing new binding sites for neutralizing antibodies.Overall,our study has revealed the presence of different key epitopes between SARS-CoV and SARSCoV-2,which indicates the necessity to develop new prophylactic vaccine and antibody drugs for specific control of the COVID-19 pandemic although the available agents obtained from the SARS-CoV study are unneglectable.
基金support from the members of the Chilab.We acknowledge the financial support in part by DOD(grant numbers W81XWH-17-1-0143,W81XWH-15-1-0486,W81XWH-19-1-0842)NIH(grant numbers GM124062,1R01NS111588-01A1).
文摘Ferroptosis is a novel form of iron-dependent cell death characterized by lipid per-oxidation.While the importance and disease relevance of ferroptosis is gaining recognition,much remains unknown about various genetic and non-genetic determinants of ferroptosis.Hippo signaling pathway is an evolutionarily conserved pathway that responds to various envi-ronmental cues and controls organ size,cell proliferation,death,and self-renewal capacity.In cancer biology,Hippo pathway is a potent tumor suppressing mechanism and its dysregulation contributes to apoptosis evasion,cancer development,metastasis,and treatment resistance.Hippo dysregulation leads to aberrant activation of YAP and TAZ,the two major transcription co-activators of TEADs,that induce the expression of genes triggering tumor-promoting pheno-types,including enhanced cell proliferation,self-renewal and apoptosis inhibition.The Hippo pathway is regulated by the cell-cell contact and cellular density/confluence.Recently,fer-roptosis has also been found being regulated by the cellular contact and density.The YAP/TAZ activation under low density,while confers apoptosis resistance,renders cancer cells sensitivity to ferroptosis.These findings establish YAP/TAZ and Hippo pathways as novel deter-minants of ferroptosis.Therefore,inducing ferroptosis may have therapeutic potential for YAP/TAZ-activated chemo-resistant and metastatic tumor cells.Reciprocally,various YAP/TAZ-targeting treatments under clinical development may confer ferroptosis resistance,limiting the therapeutic efficacy.
基金supported by the Science-Technology Foundation for Middle-aged and Young Scientists of Wannan Medical College(No.WK2021F19)the 2023 Wannan Medical College Research Fund(No.WK2023ZZD18).
文摘Objective:Uterine corpus endometrial carcinoma(UCEC),a kind of gynecologic malignancy,poses a significant risk to women’s health.The precise mechanism underlying the development of UCEC remains elusive.Zinc finger protein 554(ZNF554),a member of the Krüppel-associated box domain zinc finger protein superfamily,was reported to be dysregulated in various illnesses,including malignant tumors.This study aimed to examine the involvement of ZNF554 in the development of UCEC.Methods:The expression of ZNF554 in UCEC tissues and cell lines were examined by qRT-PCR and Western blot assay.Cells with stably overexpressed or knocked-down ZNF554 were established through lentivirus infection.CCK-8,wound healing,and Transwell invasion assays were employed to assess cell proliferation,migration,and invasion.Propidium iodide(PI)staining combined with fluorescence-activated cell sorting(FACS)flow cytometer was utilized to detect cell cycle distribution.qRT-PCR and Western blotting were conducted to examine relative mRNA and protein levels.Chromatin immunoprecipitation assay and luciferase reporter assay were used to explore the regulatory role of ZNF554 in RNA binding motif 5(RBM5).Results:The expression of ZNF554 was found to be reduced in both UCEC samples and cell lines.Decreased expression of ZNF554 was associated with higher tumor stage,decreased overall survival,and reduced disease-free survival in UCEC.ZNF554 overexpression suppressed cell proliferation,migration,and invasion,while also inducing cell cycle arrest.In contrast,a decrease in ZNF554 expression resulted in the opposite effect.Mechanistically,ZNF554 transcriptionally regulated RBM5,leading to the deactivation of the Wingless(WNT)/β-catenin signaling pathway.Moreover,the findings from rescue studies demonstrated that the inhibition of RBM5 negated the impact of ZNF554 overexpression onβ-catenin and p-glycogen synthase kinase-3β(p-GSK-3β).Similarly,the deliberate activation of RBM5 reduced the increase inβ-catenin and p-GSK-3βcaused by the suppression of ZN
文摘Breast cancer is a molecularly heterogeneous disease and the most common female malignancy.In recent years,therapy approaches have evolved to accommodate molecular diversity,with a focus on more biologically based therapies to minimize negative consequences.To regulate cell fate in human breast cells,the Hippo signaling pathway has been associated with the alpha subtype of estrogen receptors.This pathway regulates tissue size,regeneration,and healing,as well as the survival of tissue-specific stem cells,proliferation,and apoptosis in a variety of organs,allowing for cell differentiation.Hippo signaling is mediated by the kinases MST1,MST2,LATS1,and LATS2,as well as the adaptor proteins SAV1 and MOB.These kinases phosphorylate the downstream effectors of the Hippo pathway,yes-associated protein(YAP),and transcriptional coactivator with PDZ-binding motif(TAZ),suppressing the expression of their downstream target genes.The Hippo signaling pathway kinase cascade plays a significant role in all cancers.Understanding the principles of this kinase cascade would prevent the occurrence of breast cancer.In recent years,small noncoding RNAs,or microRNAs,have been implicated in the development of several malignancies,including breast cancer.The interconnections between miRNAs and Hippo signaling pathway core proteins in the breast,on the other hand,remain poorly understood.In this review,we focused on highlighting the Hippo signaling system,its key parts,its importance in breast cancer,and its regulation by miRNAs and other related pathways.
基金This research was supported by grants from the National Science and Technology Major Project(2016ZX08010-001)the National Natural Science Foundation of China(31570283).
文摘Plant plasmodesmata (PDs) are specialized channels that enable communication between neighboring cells. The intercellular permeability of PDs, which affects plant development, defense, and responses to stimuli, must be tightly regulated. However, the lipid compositions of PD membrane and their impact on PD permeability remain elusive. Here, we report that the Arabidopsis sld1 sld2 double mutant, lacking sphingolipid long-chain base 8 desaturases 1 and 2, displayed decreased PD permeability due to a significant increase in callose accumulation. PD-located protein 5 (PDLP5) was significantly enriched in the leaf epidermal cells of sld1 sld2 and showed specific binding affinity to phytosphinganine (t18:0), suggesting that the enrichment of t18:0-based sphingolipids in sld1 sld2 PDs might facilitate the recruitment of PDLP5 proteins to PDs. The sld1 sld2 double mutant seedlings showed enhanced resistance to the fungal-wilt pathogen Verticillium dahlia and the bacterium Pseudomonas syringae pv. tomato DC3000, which could be fully rescued in sld1 sld2 pdlp5 triple mutant . Taken together, these results indicate that phytosphinganine might regulate PD functions and cell-to-cell communication by modifying the level of PDLP5 in PD membranes.
基金supported by a Grant-in-Aid for Scientific Research on Innovative Areas"Integrated Bio-metal Science"(MEXT KAKENHI Grant Number JP19H05768)from the Ministry of Education,Culture,Sports,Science,and Technologya Grant-in-Aid for Scientific Research(B)(JSPS KAKENHI Grant No.JP19H02883)from the Japan Society for the Promotion of Science(to Taiho Kambe).
文摘Importance:Transient neonatal zinc deficiency(TNZD)occurs in breastfed infants due to abnormally low breast milk zinc levels.Mutations in the solute carrier family 30 member 2(SLC30A2)gene,which encodes the zinc transporter ZNT2,cause low zinc concentration in breast milk.Objective:This study aimed to provide further insights into TNZD pathophysiology.Methods:SLC30A2 sequencing was performed in three unrelated Japanese mothers,whose infants developed TNZD due to low-zinc milk consumption.The effects of the identified mutations were examined using cell-based assays and luciferase reporter analysis.Results:Novel SLC30A2 mutations were identified in each mother.One harbored a heterozygous missense mutation in the ZNT2 zinc-binding site,which resulted in defective zinc transport.The other two mothers exhibited multiple heterozygous mutations in the SLC30A2 promoter,the first mutations in the SLC30A2 regulatory region reported to date.Interpretation:This report provides new genetic insights into TNZD pathogenesis in breastfed infants.
基金financially supported by the National Natural Science Foundation of China (31171565 and 31371635)
文摘The RNA‐binding glycine‐rich protein（RB‐GRP）family is characterized by the presence of a glycine‐rich domain arranged in（Gly）n‐X repeats and an RNA‐recognition motif（RRM）. RB‐GRPs participate in varied physiological and biochemical processes especially in the stress response of plants. In this study, a total of 23 RB‐GRPs distributed on 10 chromosomes were identified in maize（Zea mays L.）, and they were divided into four subgroups according to their conserved domain architecture. Five pairs of paralogs were identified,while none of them was located on the same chromosomal region, suggesting that segmental duplication is predominant in the duplication events of the RB‐GRPs in maize. Comparative analysis of RB‐GRPs in maize, Arabidopsis（Arabidopsis thaliana L.）, rice（Oryza sativa L.）, and wheat（Triticum aestivum）revealed that two exclusive subgroups were only identified in maize. Expression of eight ZmRB‐GRPs was significantly regulated by at least two kinds of stresses. In addition, cis‐elements predicted in the promoter regions of the ZmRB‐GRPs also indicated that these ZmRB‐GRPs would be involved in stress response of maize. The preliminary genome‐wide analysis of the RB‐GRPs in maize would provide useful information for further study on the function of the ZmRB‐GRPs.
基金supported by Project for the Biological Information and Information Processing Properties of Biological Systems from the Academy of Finland(No.122973)Project for the Structure-dynamics Relationships in Biological Network from the Academy of Finland(No.132877)Finnish Funding Agency for Technology and Innovation Finland Distinguished Professor program(No.1480/31/09)
文摘Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.
基金grants from National Natural Science Foundation of China （Nos. 30400073 ,30330010）.
文摘hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-terminus. To search for its substrates and regulatory components, we screened a two-hybrid library by using the full-length hPFTAIRE1 as a bait. Four 14-3-3 isoforms （β,ε,η,τ） were identified interacting with the hPFTAIRE1. We found a putative 14-3-3 binding consensus motif（RHSSPSS） in the hPFTAIRE 1, which overlapped with its second NLS. Deletion of the RHSSPSS motif or substitution of Ser^119 gwithAla in the conserved binding motif abolished the specific interaction between the hPFTAIRE 1 and the 14-3 -3 proteins. The mutant S 120A hPFTAIRE1 also showed a weak interaction to the 14-3-3 proteins. The results suggested that the Ser^119 is crucial for the interaction between hPFTAIREI and the 14-3-3 proteins. All the hPFTAIRE1 mutants distributed in cytoplasm of Hela cells and human neuroblastoma cells （SH-SY5Y） when fused to the C-terminus of a green fluorescent protein （GFP）, indicating that binding with the 14-3-3 proteins does not contribute to the subcellular localization of the hPFTAIRE1, although the binding may be involved in its signaling regulation.
基金partially supported by the National Key R&D Program of China(Grant No.2018YFC0910404)the National Natural Science Foundation of China(Grant Nos.61873141,61721003,61573207,71871019,71471016,71531013,and 71729001)the Tsinghua-Fuzhou Institute for Data Technology,China。
文摘The establishment of a landscape of enhancers across human cells is crucial to deciphering the mechanism of gene regulation,cell differentiation,and disease development.High-throughput experimental approaches,which contain successfully reported enhancers in typical cell lines,are still too costly and time-consuming to perform systematic identification of enhancers specific to different cell lines.Existing computational methods,capable of predicting regulatory elements purely relying on DNA sequences,lack the power of cell line-specific screening.Recent studies have suggested that chromatin accessibility of a DNA segment is closely related to its potential function in regulation,and thus may provide useful information in identifying regulatory elements.Motivated by the aforementioned understanding,we integrate DNA sequences and chromatin accessibility data to accurately predict enhancers in a cell line-specific manner.We proposed Deep CAPE,a deep convolutional neural network to predict enhancers via the integration of DNA sequences and DNase-seq data.Benefitting from the well-designed feature extraction mechanism and skip connection strategy,our model not only consistently outperforms existing methods in the imbalanced classification of cell line-specific enhancers against background sequences,but also has the ability to self-adapt to different sizes of datasets.Besides,with the adoption of autoencoder,our model is capable of making cross-cell line predictions.We further visualize kernels of the first convolutional layer and show the match of identified sequence signatures and known motifs.We finally demonstrate the potential ability of our model to explain functional implications of putative disease-associated genetic variants and discriminate diseaserelated enhancers.The source code and detailed tutorial of Deep CAPE are freely available at https://github.com/Shengquan Chen/DeepCAPE.
文摘Importance:Pathogenic variants in theRBM20 gene are associated with aggressive dilated cardiomyopathy(DCM).Recently,RBM20 was found to be associated with left ventricular non-compaction cardiomyopathy(LVNC).Thus far,only five families with LVNC have been reported to carry variants inRBM20.It remains unknown whether the variants inRBM20 associated with DCM can also cause LVNC.Objective:To elucidate the causativeRBM20 variant in two unrelated patients with both LVNC and DCM,and to identify the clinical characteristics associated with variants inRBM20.Methods:Trio whole-exome sequencing(WES)was performed.Variants were filtered and classified in accordance with the guidelines of the American College of Medical Genetics and Genomics(ACMG).Results:We identified two distinctde novo variants inRBM20(one per patient)in these two patients with LVNC.Both variants have been reported in patients with DCM,without the LVNC phenotype.Patient 1 was an 11-year-old girl who had DCM,LVNC,and heart failure;the ratio of noncompacted-to-compacted myocardium was 2.7:1.Ade novo heterozygous variant c.1907G>A(p.Arg636His)in exon 9 was identified in this patient.Patient 2 was a 13-year-old boy who had clinical phenotypes identical to those of Patient 1;the ratio of noncompacted-to-compacted myocardium was 3.2:1 in this patient.WES revealed ade novo heterozygous variant c.1909A>G(p.Ser637Gly)in exon 9.Both variants were previously characterized as pathogenic,and our study classified them as pathogenic variants based on the ACMG guidelines.Interpretation:We found that two patients with LVNC had variants inRBM20.Our results extended the clinical spectrum of the twoRBM20 variants and illustrated that the same variant inRBM20 can cause DCM,with or without the LVNC phenotype.
基金Supported by National Administration of Traditional Chinese Medicine,No.2019XZZX-EK002.
文摘BACKGROUND Xia–Gibbs syndrome(XGS,OMIM:615829),caused by mutations within the ATHook DNA-binding motif-containing protein 1(AHDC1)gene(OMIM:615790),located on the short arm of chromosome 1 within the cytogenetic band 1p36.11,contains five noncoding 5 exons,a single 4.9-kb coding exon,and a noncoding 3 exon.CASE SUMMARY In this case report,we diagnosed and treated a 6-mo-old girl with XGS.The primary clinical symptoms included global developmental delay,hypotonia,and mild dysmorphic features.Using high-throughput whole-exosome sequencing to sequence the patient and her parents,and the results showed a novel frameshift mutation of c.1155dupG(p.Arg386Alafs*3)in the AHDC1 gene.The paternal gene was wild type.CONCLUSION This report extends the mutation spectrum of the AHDC1 gene to provide the diagnostic basis for genetic counseling in families with XGS.
基金supported by the National Natural Science Foundation of China(Grant No.31621002)the Ministry of Science and Technology of China(Grant No.2017YFA0504903 to LN)the Hefei National Science Center Pilot Project Funds,China(in part)。
文摘Uncovering conserved 3D protein–ligand binding patterns on the basis of functional groups(FGs)shared by a variety of small molecules can greatly expand our knowledge of protein–ligand interactions.Despite that conserved binding patterns for a few commonly used FGs have been reported in the literature,large-scale identification and evaluation of FG-based 3D binding motifs are still lacking.Here,we propose a computational method,Automatic FG-based Three-dimensional Motif Extractor(AFTME),for automatic mapping of 3D motifs to different FGs of a specific ligand.Applying our method to 233 naturally-occurring ligands,we define 481 FG-binding motifs that are highly conserved across different ligand-binding pockets.Systematic analysis further reveals four main classes of binding motifs corresponding to distinct sets of FGs.Combinations of FG-binding motifs facilitate the binding of proteins to a wide spectrum of ligands with various binding affinities.Finally,we show that our FG–motif map can be used to nominate FGs that potentially bind to specific drug targets,thus providing useful insights and guidance for rational design of small-molecule drugs.
文摘Transcription factor SPI is a protcin present in mammalian cells that binds to GC box promoter clements of Gene and selectively activates mRNA synthesis. The gene contains functional recognition sites. It contains three continuous zinc finger motifs, which are believed being mctalloprotein structures that interact with DNA. We synthesized the second zine finger fragment of SP1 (SP1-ZF2) and its mutant (SP1-ZF2 / HT. E20→H. R23→T), we also synthesized the Cys-Cys loop (ZF6) and the His-His loop (ZF5) of SPI and linked the twoloops together using a β-turn structure to obtain a finger mimic analogue (ZF-15) by stepwise solid-phase technique. Atomic absorption studies show that SP 1-ZF2 and SP1-ZF2 / HT bind zinc cquimolarly, but ZF-15 docs not bind Zn anyway. The CD experiments demonstrate a significant change in secondary structure in the prescnce or absence of Zn to SP1-ZF2 and SP1-ZF2/ HT, but there is no change about ZF-15. Gcl-retardation clectrophoresis assays indicate that SP1-ZF2 binds to DNA sequence specifically in the presence of Zn, but SP1-ZF2 / HT docs not bind as SP 1-ZF2 did. We observed that a single zine finger like SP1-ZF2 is able to bind DNA sequence specifically.
