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1.
Cell ; 148(5): 873-85, 2012 Mar 02.
Article in English | MEDLINE | ID: mdl-22385957

ABSTRACT

Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single cells. We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient. The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients.


Subject(s)
Clonal Evolution , Gene Expression Profiling , High-Throughput Nucleotide Sequencing/methods , Janus Kinase 2/genetics , Myeloproliferative Disorders/genetics , Myeloproliferative Disorders/pathology , Single-Cell Analysis/methods , Thrombocythemia, Essential/genetics , Exome , Genome, Human , Humans , Male , Middle Aged , Mutation
2.
Cell ; 148(5): 886-95, 2012 Mar 02.
Article in English | MEDLINE | ID: mdl-22385958

ABSTRACT

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.


Subject(s)
Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Single-Cell Analysis/methods , DNA-Binding Proteins , Exome , Gene Frequency , Humans , Male , Middle Aged , Mutation , Nuclear Proteins/genetics , Phylogeny , Pilot Projects , Principal Component Analysis , Transcription Factors/genetics , Von Hippel-Lindau Tumor Suppressor Protein/genetics
3.
Biochem Biophys Res Commun ; 590: 20-26, 2022 01 29.
Article in English | MEDLINE | ID: mdl-34968780

ABSTRACT

Chondrosarcoma (CHS) is the second most common bone malignant tumor and currently has limited treatment options. We have recently demonstrated that thioredoxin interacting protein (TXNIP) plays a crucial role in the oncogenesis of bone sarcoma, yet its implication in CHS is underdetermined. In the present study, we first found that knockdown of TXNIP promotes the proliferation of CHS cell largely through increasing their glycolytic metabolism, which is well-known as Warburg effect for providing energy. Consistent with our previous report that YAP is fundamental for CHS cell growth, herein we revealed that YAP functioned as an upstream molecule of TXNIP, and that YAP negatively regulated TXNIP mRNA and protein expression both in vitro and in vivo. Mechanistically, although knockdown of YAP upregulated both the nuclear and cytoplasmic TXNIP expression, we did not observe any obvious interaction between YAP and TXNIP; instead, miRNA-524-5p was demonstrated to be required for YAP-regulated TXNIP expression and thus controlling CHS cell growth. Together, our study reveals that TXNIP is a tumor suppressor in terms of CHS, and that the YAP/miRNA-524-5p/TXNIP signaling axis may provide a novel clue for CHS targeted therapy.


Subject(s)
Carrier Proteins/genetics , Chondrosarcoma/genetics , Chondrosarcoma/pathology , MicroRNAs/metabolism , YAP-Signaling Proteins/metabolism , Base Sequence , Binding Sites , Carrier Proteins/metabolism , Cell Line, Tumor , Cell Proliferation/genetics , Gene Knockdown Techniques , Glycolysis/genetics , Humans , MicroRNAs/genetics , Mutation/genetics
4.
Biol Res ; 51(1): 14, 2018 May 30.
Article in English | MEDLINE | ID: mdl-29843798

ABSTRACT

BACKGROUND: Neurokinin1 (NK1) receptor has played a vital role in the development of tumor. However, NKP608 as a NK1 receptor antagonist whether has the effect of the resistance of colorectal cancer is still unclear. Thereby, in this study, we investigated the role of NKP608 on human colorectal cancer and explored the underlying mechanism. METHODS: The cell proliferation of colorectal cancer cells was detected by cell counting kit-8 (CCK8) assay, cell migration and invasion were assessed by transwell assay, the apoptotic ratio of cells was assessed by Annexin V-fluorescein isothiocyanate/propidium iodide stained and flow cytometry. The involvement of molecular mechanisms was examined by western blot. RESULTS: In this study, we found that NKP608 inhibited the proliferation, migration/invasion of HCT116 cells. In addition, NKP608 reduced expressions of Wnt-3a, ß-catenin, Cyclin D1, and (vascular endothelial growth factor) VEGF while induced expression of E-Cadherin. Furthermore, flow cytometry analyzed that NKP608 induced apoptosis of HCT116 cells, consistently, western blotting detecting of apoptosis-related proteins revealed that NKP608 downregulated Bcl-2 while upregulated Bax and Active-Caspase-3. CONCLUSIONS: Taken together, our results demonstrated that NKP608 inhibited colorectal cancer cell proliferation, migration and invasion via suppressing the Wnt/ß-catenin signaling pathway. Therefore, NKP608 might represent a promising therapeutic agent in the treatment of colorectal cancer.


Subject(s)
Cell Movement/drug effects , Cell Proliferation/drug effects , Colorectal Neoplasms/pathology , Neurokinin-1 Receptor Antagonists/pharmacology , Piperidines/pharmacology , Quinolines/pharmacology , Wnt Signaling Pathway/drug effects , Blotting, Western , Cell Line, Tumor , Down-Regulation/drug effects , Flow Cytometry , HCT116 Cells , Humans
5.
Cell Rep ; 42(7): 112700, 2023 07 25.
Article in English | MEDLINE | ID: mdl-37379216

ABSTRACT

How pathogens manipulate host UPRER to mediate immune evasion is largely unknown. Here, we identify the host zinc finger protein ZPR1 as an interacting partner of the enteropathogenic E. coli (EPEC) effector NleE using proximity-enabled protein crosslinking. We show that ZPR1 assembles via liquid-liquid phase separation (LLPS) in vitro and regulates CHOP-mediated UPRER at the transcriptional level. Interestingly, in vitro studies show that the ZPR1 binding ability with K63-ubiquitin chains, which promotes LLPS of ZPR1, is disrupted by NleE. Further analyses indicate that EPEC restricts host UPRER pathways at the transcription level in a NleE-ZPR1 cascade-dependent manner. Together, our study reveals the mechanism by which EPEC interferes with CHOP-UPRER via regulating ZPR1 to help pathogens escape host defense.


Subject(s)
Enteropathogenic Escherichia coli , Escherichia coli Infections , Escherichia coli Proteins , Humans , HeLa Cells , Virulence Factors/metabolism , Enteropathogenic Escherichia coli/metabolism , Escherichia coli Proteins/metabolism
6.
J Gen Psychol ; 149(1): 97-115, 2022.
Article in English | MEDLINE | ID: mdl-33929295

ABSTRACT

Adolescents are believed to be susceptible to eating disorders (EDs) due to their serious fear of appearance evaluation from society. Related to this, low body-esteem has been found to be common among individuals with EDs. The present study mainly aimed to explore how emotional intelligence (EI), gender, and body size influence the relationship between body-esteem and EDs risk among adolescents. 128 middle school students classified as obese and 128 age-and gender-matched normal weight controls were included. All participants were asked to fill out self-report measures of body-esteem, EI, and EDs risk. The results showed that (1) both gender and body size directly influenced body-esteem and EDs risk; (2) EI acted as a moderator between body-esteem and EDs risk; and (3) both gender and body size interacted with EI and body-esteem to influence EDs risk. These findings contribute to our understanding of boundary conditions by which low body-esteem leads to EDs among adolescents, and help us to correspondingly conduct targeted intervention of adolescents' EDs.


Subject(s)
Body Image , Feeding and Eating Disorders , Adolescent , Emotional Intelligence , Humans , Obesity , Self Concept
7.
STAR Protoc ; 3(4): 101882, 2022 12 16.
Article in English | MEDLINE | ID: mdl-36595886

ABSTRACT

Interactions between effectors and their host targets are often weak or transient, making them difficult to identify. We describe a protocol for covalent capture of effector substrates in living cells using genetic code expansion technology. The effector-substrate complexes are captured by the crosslinker and subsequently purified with tandem chromatography. We detail steps for mass spectrum analysis and substrate verification. While the steps here are specific for substrates of enteropathogenic E. coli in HEK293T cells, the protocol has broader applications. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).1.


Subject(s)
Escherichia coli , Nucleic Acid Amplification Techniques , Humans , Escherichia coli/genetics , HEK293 Cells , Cloning, Molecular , Mass Spectrometry
8.
Oxid Med Cell Longev ; 2022: 2764940, 2022.
Article in English | MEDLINE | ID: mdl-36742345

ABSTRACT

KIF11 is one of the 45 family members of kinesin superfamily proteins that functions as a motor protein in mitosis. Emerging evidence revealed that KIF11 plays pivotal roles in cancer initiation, development, and progression. However, the prognostic, oncological, and immunological values of KIF11 have not been comprehensively explored in pan-cancer. In present study, we comprehensively interrogated the role of KIF11 in tumor progression, tumor stemness, genomic heterogeneity, tumor immune infiltration, immune evasion, therapy response, and prognosis of cohorts from various cancer types. In general, KIF11 was significantly upregulated in tumors compared with paired normal tissues. KIF11 showed strong relationships with pathological stage, prognosis, tumor stemness, genomic heterogeneity, neoantigens, ESTIMATE, immune checkpoint, and drug sensitivity. The methylation level of KIF11 decreased in most cancers and was correlated with the survival probability in different human cancers. The expression of KIF11 was diverse in different molecular and immune subtypes and remarkably correlated with immune cell infiltration in the tumor microenvironment. Comparative study revealed that KIF11 was a powerful biomarker and associated with immune, targeted, and chemotherapeutic outcomes in various cancers. In addition, KIF11 interaction and coexpression networks mainly participated in the regulation of cell cycle, cell division, p53 signaling pathway, DNA repair and recombination, chromatin organization, antigen processing and presentation, and drug resistance. Our pan-cancer analysis provides a comprehensive understanding of the functions of KIF11 in oncogenesis, progression, and therapy in different cancers. KIF11 may serve as a potential prognostic and immunological pan-cancer biomarker. Moreover, KIF11 could be a novel target for tumor immunotherapy.


Subject(s)
Biomarkers, Tumor , Tumor Microenvironment , Humans , Carcinogenesis , Mitosis , Prognosis , Kinesins/genetics
9.
Elife ; 102021 07 13.
Article in English | MEDLINE | ID: mdl-34254583

ABSTRACT

Autophagy acts as a pivotal innate immune response against infection. Some virulence effectors subvert the host autophagic machinery to escape the surveillance of autophagy. The mechanism by which pathogens interact with host autophagy remains mostly unclear. However, traditional strategies often have difficulty identifying host proteins that interact with effectors due to the weak, dynamic, and transient nature of these interactions. Here, we found that Enteropathogenic Escherichia coli (EPEC) regulates autophagosome formation in host cells dependent on effector NleE. The 26S Proteasome Regulatory Subunit 10 (PSMD10) was identified as a direct interaction partner of NleE in living cells by employing genetically incorporated crosslinkers. Pairwise chemical crosslinking revealed that NleE interacts with the N-terminus of PSMD10. We demonstrated that PSMD10 homodimerization is necessary for its interaction with ATG7 and promotion of autophagy, but not necessary for PSMD10 interaction with ATG12. Therefore, NleE-mediated PSMD10 in monomeric state attenuates host autophagosome formation. Our study reveals the mechanism through which EPEC attenuates host autophagy activity.


Subject(s)
Autophagy/immunology , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Proteasome Endopeptidase Complex/metabolism , Proto-Oncogene Proteins/metabolism , Virulence Factors/genetics , Virulence Factors/metabolism , Autophagy-Related Protein 12 , Autophagy-Related Protein 7 , Enteropathogenic Escherichia coli , Escherichia coli Infections/immunology , Escherichia coli Proteins/chemistry , HeLa Cells , Humans , Interleukin-6 , Lipopolysaccharides , Models, Molecular , Proteasome Endopeptidase Complex/chemistry , Proteasome Endopeptidase Complex/genetics , Protein Conformation , Protein Interaction Domains and Motifs , Proto-Oncogene Proteins/chemistry , Proto-Oncogene Proteins/genetics , Virulence/genetics , Virulence Factors/chemistry
10.
Article in English | MEDLINE | ID: mdl-34899944

ABSTRACT

OBJECTIVE: This study aimed to investigate the possible mechanism of the Zhishi and Baizhu herb pair in the treatment of gastric cancer by means of network pharmacology and molecular docking and to provide a theoretical basis for experiments and clinical application of traditional Chinese medicine for treating gastric cancer. METHODS: The main active chemical components of Zhishi and Baizhu were screened through Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and selected by using the thresholds of oral bioavailability ≥30% and drug-likeness ≥18%. The targets of Zhishi and Baizhu were obtained from TCMSP, Therapeutic Targets Database (TTD), and the DrugBank database. The corresponding genes of the targets were retrieved from the UniProt database, and the gastric cancer targets were obtained from the GeneCards database and TTD. Subsequently, the networks were built between the main drug components, drug targets, and gastric cancer targets. Then, the enrichment analyses of GO and KEGG were applied to predict the potential roles of gastric cancer pathogenesis via the R package clusterProfiler. Finally, molecular docking was used to determine the affinity between the targets and components. RESULTS: Twenty-seven main active components were predicted from the Zhishi-Baizhu herb pair, and a total of 120 intersection genes were screened from 303 potential medicine genes and 1,839 disease genes. The enrichment included the PI3K-Akt and IL-17 signaling pathways, and the network analysis showed that the Zhishi-Baizhu herb pair acted on seven key targets, namely, AKT1, MMP9, IL-6, CCND1, BCL2, MTOR, and MDM2 (where they played a role in treating gastric cancer). Molecular docking showed that luteolin and naringenin could stably bind to the targets. CONCLUSION: The possible mechanisms of the components of the Zhishi-Baizhu herb pair in treating gastric cancer might be related to luteolin and naringenin, which intervened with the targets AKT1, MMP9, IL-6, CCND1, BCL2, MTOR, and MDM2, and are linked with the PI3K-Akt and IL-17 signaling pathways. This knowledge will lay a solid foundation for further experimental and clinical studies.

11.
Biosci Rep ; 38(5)2018 10 31.
Article in English | MEDLINE | ID: mdl-30177520

ABSTRACT

Disc nucleus pulposus (NP) cell experiences periodic osmolarity alterations during daily activities, which has been proved to affect cell biology in vitro The present study was aimed to investigate the effects of cartilage-derived morphogenetic protein-2 (CDMP-2) on NP cell apoptosis under the hyperosmolarity culture and the potential mechanism. Isolated rat NP cells were cultured in the in situ-osmolarity medium or hyperosmolarity medium for 3 days. CDMP-2 was added into the hyperosmolarity medium to investigate its effects on NP cell apoptosis. Cell apoptosis rate, caspase-3 activity, gene expression of Bcl-2, Bax, and caspase-3, and protein expression of Bcl-2, Bax, and cleaved caspase-3 were analyzed to evaluate NP cell apoptosis. Additionally, the intracellular reactive oxygen species (ROS) and the total superoxide dismutase (SOD) activity were analyzed to investigate the potential role of oxidative damage in this process. In the hyperosmolarity culture, NP cells showed a significantly increased cell apoptosis rate and caspase-3 activity, an up-regulated expression of Bax and caspase-3/cleaved-caspase-3 and a down-regulated expression of Bcl-2. However, CDMP-2 partly inhibited these effects of hyperosmolarity culture on NP cells. Additionally, the hyperosmolarity culture significantly increased ROS content and decreased the total SOD activity compared with the in situ-osmolarity culture, whereas exogenous CDMP-2 partly decreased the ROS content and increased the total SOD activity in the hyperosmolarity culture. In conclusion, CDMP-2 is effective in attenuating hyperosmolarity environment-induced NP cell apoptosis, and this process may be mediated through inhibiting oxidative stress damage. The present study indicates that CDMP-2 may be helpful to retard hyperosmolarity niche-mediated disc degeneration.


Subject(s)
Bone Morphogenetic Proteins/metabolism , Intervertebral Disc Degeneration/drug therapy , Nucleus Pulposus/drug effects , Oxidative Stress/drug effects , Animals , Apoptosis/drug effects , Bone Morphogenetic Proteins/pharmacology , Caspase 3/genetics , Gene Expression Regulation/genetics , Humans , Intervertebral Disc Degeneration/genetics , Intervertebral Disc Degeneration/pathology , Nucleus Pulposus/metabolism , Nucleus Pulposus/pathology , Osmolar Concentration , Osmotic Pressure/drug effects , Proto-Oncogene Proteins c-bcl-2/genetics , Rats , Reactive Oxygen Species/chemistry , Superoxide Dismutase-1/genetics , bcl-2-Associated X Protein/genetics
12.
Asian Pac J Trop Med ; 10(5): 498-502, 2017 May.
Article in English | MEDLINE | ID: mdl-28647188

ABSTRACT

OBJECTIVE: To study whether miR-200a and miR-200b target PTEN gene expression to regulate the endometrial cancer cell growth in vitro. METHODS: Endometrial cancer cells ECC-1 were cultured and transfected with the miR-200a and miR-200b mimics and inhibitors as well as the negative control mimics and inhibitors, and then the cell proliferation activity as well as the expression of PTEN and downstream genes in cells was determined; after transfection of miR-200a and miR-200b mimics as well as PTEN-3'UTR luciferase report gene plasmids, the fluorescence activity of luciferase reporter gene was determined. RESULTS: 12 h, 24 h and 48 h after transfection, the cell proliferation activity of miR-200a mimics group and miR-200b mimics group were significantly higher than those of NC mimics group while the cell proliferation activity of miR-200a inhibitor group and miR-200b inhibitor group were significantly lower than those of NC inhibitor group; 48 h after transfection, PTEN expression in cells and PTEN-3'UTR luciferase reporter gene fluorescence activity of miR-200a mimics group and miR-200b mimics group were significantly lower than those of NC mimics group while p-PI3K and p-Akt expression were significantly higher than those of NC mimics group; PTEN expression in cells and PTEN-3'UTR luciferase reporter gene fluorescence activity of miR-200a inhibitor group and miR-200b inhibitor group were significantly higher than those of NC inhibitor group while p-PI3K and p-Akt expression were significantly lower than those of NC inhibitor group. CONCLUSION: miR-200a and miR-200b can promote the endometrial cancer cell growth in vitro by targeted inhibition of PTEN gene expression.

13.
Asian Pac J Trop Med ; 9(6): 567-71, 2016 Jun.
Article in English | MEDLINE | ID: mdl-27262068

ABSTRACT

OBJECTIVE: To study the effect of hypoxia on the expression of placental trophoblast cells SATB1 and ß-catenin and its correlation with the pathogenesis of preeclampsia. METHODS: Trophoblastic cell lines HRT8/SVneo were cultured, SATB1 and ß-catenin expression and cell biological behavior were determined after hypoxia reoxygenation treatment; cell biological behavior and the expression of related genes were determined after the transfection of SATB1 and ß-catenin siRNA; preeclampsia placenta and normal placenta tissues were collected and the expression of SATB1 and ß-catenin were determined. RESULTS: OD value, cell migration rate, mRNA contents of SATB1 and ß-catenin of H/R group were significantly lower than those of Nor group, cell apoptosis rate was higher than that of Nor group and the number of invasive cells was less than that of Nor group; OD value and bcl-2 mRNA content of SATB1-siRNA group were lower than those of NC group; cell apoptosis rate as well as Bax, Caspase-3, Caspase-6 and Caspase-9 mRNA contents were higher than those of NC group; cell migration rate as well as CTSB, CTSD, MMP2 and MMP9 mRNA contents of ß-catenin-siRNA group were lower than those of NC group; the number of invasive cells was less than that of NC group; the expression levels of SATB1 and ß-catenin in preeclampsia placenta tissue were significantly lower than those in normal placenta tissue. CONCLUSIONS: Hypoxia can inhibit the expression of SATB1 and ß-catenin in the pathogenesis of preeclampsia, which can affect the proliferation, apoptosis, migration and invasion of cells.

14.
Microbes Infect ; 7(5-6): 882-9, 2005 May.
Article in English | MEDLINE | ID: mdl-15878679

ABSTRACT

A novel coronavirus, the severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), was identified as the causative agent of SARS. The profile of specific antibodies to individual proteins of the virus is critical to the development of vaccine and diagnostic tools. In this study, 13 recombinant proteins associated with four structural proteins (S, E, M and N) and five putative uncharacterized proteins (3a, 3b, 6, 7a and 9b) of the SARS-CoV were prepared and used for screening and monitoring their specific IgG antibodies in SARS patient sera by protein microarray. Antibodies to proteins S, 3a, N and 9b were detected in the sera from convalescent-phase SARS patients, whereas those to proteins E, M, 3b, 6 and 7a were undetected. In the detectable specific antibodies, anti-S and anti-N were dominant and could persist in the sera of SARS patients until week 30. Among the rabbit antisera to recombinant proteins S3, N, 3a and 9b, only anti-S3 serum showed significant neutralizing activity to the SARS-CoV infection in Vero E6 cells. The results suggest (1) that anti-S and anti-N antibodies are diagnostic markers and in particular that S3 is immunogenic and therefore is a good candidate as a subunit vaccine antigen; and (2) that, from a virus structure viewpoint, the presence in some human sera of antibodies reacting with two recombinant polypeptides, 3a and 9b, supports the hypothesis that they are synthesized during the virus cycle.


Subject(s)
Antibodies, Viral/immunology , Neutralization Tests , Severe acute respiratory syndrome-related coronavirus/immunology , Viral Proteins/immunology , Animals , Antibodies, Viral/biosynthesis , Humans , Immunoglobulin G/immunology , Rabbits
15.
Exp Ther Med ; 9(6): 2225-2228, 2015 Jun.
Article in English | MEDLINE | ID: mdl-26136964

ABSTRACT

The aim of the present study was to observe the myocardial expression of members of the histone deacetylase (HDAC) family (HDAC2, HDAC5 and HDAC9) in rats with or without myocardial hypertrophy (MH) in the presence and absence of the angiotensin II receptor blocker valsartan. Adult male Wistar rats were randomly divided into three groups (n=6/group): Sham-operated control rats, treated with distilled water (1 ml/day) through gavage; rats with MH (established through aortic constriction), treated with distilled water (1 ml/day) through gavage; and MH + valsartan rats, treated with 20 mg/kg/day valsartan through gavage. Treatments commenced one day after surgery and continued for eight weeks. Body weight (BW), heart weight (HW) and plasma atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) levels were determined, and the myocardial expression of HDAC2, HDAC5 and HDAC9 was analyzed through a reverse transcription semi-quantitative polymerase chain reaction. The BWs of the rats in the three groups were similar at baseline; however, after eight weeks the BW of the rats in the MH + valsartan group was significantly reduced compared with that of the MH rats. Furthermore, the HW/BW ratio and plasma ANP and BNP levels were increased, the myocardial HDAC2 expression was significantly upregulated and the HDAC5 and HDAC9 expression was significantly downregulated in the MH rats compared with those in the control rats; however, these changes were significantly attenuated by valsartan. Modulation of myocardial HDAC5, HDAC9 and HDAC2 expression may therefore be one of the anti-hypertrophic mechanisms of valsartan in this rat MH model.

16.
J Virol Methods ; 119(1): 17-23, 2004 Jul.
Article in English | MEDLINE | ID: mdl-15109816

ABSTRACT

Severe acute respiratory syndrome (SARS) is an acute newly emerged infectious respiratory illness. The etiologic agent of SARS was named 'SARS-associated coronavirus' (SARS-CoV) that can be detected with reverse transcription-polymerase chain reaction (RT-PCR) assays. In this study, 12 sets of nested primers covering the SARS-CoV genome have been screened and showed sufficient sensitivity to detect SARS-CoV in RNA isolated from virus cultured in Vero 6 cells. To optimize further the reaction condition of those nested primers sets, seven sets of nested primers have been chosen to compare their reverse transcribed efficiency with specific and random primers, which is useful to combine RT with the first round of PCR into a one-step RT-PCR. Based on the sensitivity and simplicity of results, the no. 73 primer set was chosen as the candidate primer set for clinical diagnoses. To specify the amplicon to minimize false positive results, a Taqman RT-nested PCR system of no. 73 nested primer set was developed. Through investigations on a test panel of whole blood obtained from 30 SARS patients and 9 control persons, the specificity and sensitivity of the Taqman RT-nested PCR system was found to be 100 and 83%, respectively, which suggests that the method is a promising one to diagnose SARS in early stages.


Subject(s)
Reverse Transcriptase Polymerase Chain Reaction/methods , Severe Acute Respiratory Syndrome/diagnosis , Severe Acute Respiratory Syndrome/virology , Severe acute respiratory syndrome-related coronavirus/genetics , Severe acute respiratory syndrome-related coronavirus/isolation & purification , Adolescent , Adult , Aged , Base Sequence , Child , China , DNA Primers/genetics , DNA, Viral/genetics , Female , Genome, Viral , Humans , Male , Middle Aged , Reverse Transcriptase Polymerase Chain Reaction/statistics & numerical data , Sensitivity and Specificity , Virology/methods , Virology/statistics & numerical data
17.
Genomics Proteomics Bioinformatics ; 1(4): 304-9, 2003 Nov.
Article in English | MEDLINE | ID: mdl-15629059

ABSTRACT

Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GF=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.


Subject(s)
Asian People/genetics , DNA Mutational Analysis/methods , HLA-A Antigens/genetics , Polymorphism, Genetic/genetics , Alleles , China , Gene Frequency , Genotype , HLA-A Antigens/blood , Humans , Sensitivity and Specificity , Sequence Analysis, DNA , Serology
18.
Genomics Proteomics Bioinformatics ; 1(2): 108-17, 2003 May.
Article in English | MEDLINE | ID: mdl-15626341

ABSTRACT

The corona-like spikes or peplomers on the surface of the virion under electronic microscope are the most striking features of coronaviruses. The S (spike) protein is the largest structural protein, with 1,255 amino acids, in the viral genome. Its structure can be divided into three regions: a long N-terminal region in the exterior, a characteristic transmembrane (TM) region, and a short C-terminus in the interior of a virion. We detected fifteen substitutions of nucleotides by comparisons with the seventeen published SARS-CoV genome sequences, eight (53.3%) of which are non-synonymous mutations leading to amino acid alternations with predicted physiochemical changes. The possible antigenic determinants of the S protein are predicted, and the result is confirmed by ELISA (enzyme-linked immunosorbent assay) with synthesized peptides. Another profound finding is that three disulfide bonds are defined at the C-terminus with the N-terminus of the E (envelope) protein, based on the typical sequence and positions, thus establishing the structural connection with these two important structural proteins, if confirmed. Phylogenetic analysis reveals several conserved regions that might be potent drug targets.


Subject(s)
Antigens, Viral/immunology , Membrane Glycoproteins/genetics , Mutation/genetics , Phylogeny , Severe acute respiratory syndrome-related coronavirus/genetics , Viral Envelope Proteins/genetics , Amino Acid Sequence , Base Composition , Computational Biology , Enzyme-Linked Immunosorbent Assay , Molecular Sequence Data , Protein Structure, Tertiary , Severe acute respiratory syndrome-related coronavirus/immunology , Sequence Analysis, DNA , Sequence Homology , Spike Glycoprotein, Coronavirus , Viral Envelope Proteins/metabolism
19.
Zhonghua Yi Xue Za Zhi ; 84(4): 294-8, 2004 Feb 17.
Article in Zh | MEDLINE | ID: mdl-15059511

ABSTRACT

OBJECTIVE: To detect BRCA1 and BRCA2 gene germline mutation in the Chinese breast cancer families. METHODS: Samples of peripheral blood were collected to prepare genomic DNA by conventional techniques from 15 inherited breast cancer patients from 14 breast cancer families, 76 sporadic breast cancer patients, and 100 healthy controls based on informed consent. Exons 4, 8, 11 and 18 - 20 of BRCA1, and exons 1 - 14, 17 - 24 and 27 of BRCA2, were analyzed using DNA direct sequencing. RESULTS: Six single nucleotide polymorphisms (SNPs) were found on the exon 11 of BRCA1, 2 being silent changes without change of amino acid coding, and 4 with change of amino acid coding among which 2 were polymorphic amino acid alterations and 2 were pathogenic SNPs, i.e. mutational sites. One novel BRCA1 mutation, C1196T (Pro 359 Leu), was identified in a family breast cancer patients, who was diagnosed at the age of 37. Another BRCA1 mutation, Trp 372 stop was found in a breast cancer patient who was diagnosed at the age 29. Eight SNPs were found on the exon3, 10 and 11 of BRCA2, among which 5 were silent changes and 3 were polymorphic amino acid alterations. A1093C (Asn289His) in exon 10 and A 3199G (Asn991Asp) in exon 11 being found simultaneously in the patients of 2 families but not appearing in pool DNA sample, and Asn 371 His appearing as A/C heterozygote in pool DNA sample. CONCLUSION: Two pathogenic SNPs have been found in BRCA1 and may be related to early-onset breast cancer. One of them may be a novel mutation characterized of familial breast cancer in China.


Subject(s)
Breast Neoplasms/genetics , Genes, BRCA1 , Genes, BRCA2 , Germ-Line Mutation/genetics , Base Sequence , China , DNA Mutational Analysis , DNA, Neoplasm/chemistry , DNA, Neoplasm/genetics , Exons , Family Health , Female , Humans , Polymorphism, Single Nucleotide
20.
Biol. Res ; 51: 14, 2018. graf
Article in English | LILACS | ID: biblio-950900

ABSTRACT

BACKGROUND: Neurokinin1 (NK1) receptor has played a vital role in the development of tumor. However, NKP608 as a NK1 receptor antagonist whether has the effect of the resistance of colorectal cancer is still unclear. Thereby, in this study, we investigated the role of NKP608 on human colorectal cancer and explored the underlying mechanism. METHODS: The cell proliferation of colorectal cancer cells was detected by cell counting kit-8 (CCK8) assay, cell migration and invasion were assessed by transwell assay, the apoptotic ratio of cells was assessed by Annexin V-fluorescein isothiocyanate/propidium iodide stained and flow cytometry. The involvement of molecular mechanisms was examined by western blot. RESULTS: In this study, we found that NKP608 inhibited the proliferation, migration/invasion of HCT116 cells. In addition, NKP608 reduced expressions of Wnt-3a, ß-catenin, Cyclin D1, and (vascular endothelial growth factor) VEGF while induced expression of E-Cadherin. Furthermore, flow cytometry analyzed that NKP608 induced apoptosis of HCT116 cells, consistently, western blotting detecting of apoptosis-related proteins revealed that NKP608 downregulated Bcl-2 while upregulated Bax and Active-Caspase-3. CONCLUSIONS: Taken together, our results demonstrated that NKP608 inhibited colorectal cancer cell proliferation, migration and invasion via suppressing the Wnt/ß-catenin signaling pathway. Therefore, NKP608 might represent a promising therapeutic agent in the treatment of colorectal cancer.


Subject(s)
Humans , Piperidines/pharmacology , Quinolines/pharmacology , Colorectal Neoplasms/pathology , Cell Movement/drug effects , Cell Proliferation/drug effects , Wnt Signaling Pathway/drug effects , Neurokinin-1 Receptor Antagonists/pharmacology , Down-Regulation/drug effects , Blotting, Western , Cell Line, Tumor , HCT116 Cells , Flow Cytometry
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