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1.
Mol Hum Reprod ; 2022 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-35040999

RESUMO

The maturation of sperms is dependent on the coordinated interactions between sperm and the unique epididymal luminal milieu, which is characterized by high K+ content. This study investigated the involvement of transient receptor potential vanilloid 4 (TRPV4) in the K+ secretion of epididymal epithelium. The expression level and cellular localization of TRPV4 and Ca2+- activated K+ channels (KCa) were analyzed via RT-PCR, real-time quantitative PCR, western blot, and immunofluorescence. The functional role of TRPV4 was investigated using short circuit current (ISC) and intracellular Ca2+ imaging techniques. We found a predominant expression of TRPV4 in the corpus and cauda epididymal epithelium. Activation of TRPV4 with a selective agonist, GSK1016790A, stimulated a transient decrease in the ISC of the epididymal epithelium. The ISC response was abolished by either the TRPV4 antagonists, HC067047 and RN-1734, or the removal of basolateral K+. Simultaneously, the application of GSK1016790A triggered Ca2+ influx in epididymal epithelial cells. Our data also indicated that the big conductance KCa (BK), small conductance KCa (SK), and intermediate conductance KCa (IK) were all expressed in rat epididymis. Pharmacological studies revealed that BK, but not SK and IK, mediated TRPV4-elicited transepithelial K+ secretion. Finally, we demonstrated that TRPV4 and BK were localized in the epididymal epithelium, which showed an increased expression level from caput to cauda regions of rat epididymis. This study implicates that TRPV4 plays an important role in the formation of high K+ concentration in epididymal intraluminal fluid via promoting transepithelial K+ secretion mediated by BK.

2.
Cell Rep ; 38(2): 110205, 2022 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-34982968

RESUMO

Spontaneous mutations introduce uncertainty into coronavirus disease 2019 (COVID-19) control procedures and vaccine development. Here, we perform a spatiotemporal analysis on intra-host single-nucleotide variants (iSNVs) in 402 clinical samples from 170 affected individuals, which reveals an increase in genetic diversity over time after symptom onset in individuals. Nonsynonymous mutations are overrepresented in the pool of iSNVs but underrepresented at the single-nucleotide polymorphism (SNP) level, suggesting a two-step fitness selection process: a large number of nonsynonymous substitutions are generated in the host (positive selection), and these substitutions tend to be unfixed as SNPs in the population (negative selection). Dynamic iSNV changes in subpopulations with different gender, age, illness severity, and viral shedding time displayed a varied fitness selection process among populations. Our study highlights that iSNVs provide a mutational pool shaping the rapid global evolution of the virus.

3.
Int J Mol Sci ; 22(24)2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34948273

RESUMO

The effective and minimally invasive radiation biomarkers are valuable for exposure scenarios in nuclear accidents or space missions. Recent studies have opened the new sight of circulating small non-coding RNA (sncRNA) as radiation biomarkers. The tRNA-derived small RNA (tsRNA) is a new class of sncRNA. It is more abundant than other kinds of sncRNAs in extracellular vesicles or blood, presenting great potential as promising biomarkers. However, the circulating tsRNAs in response to ionizing radiation have not been reported. In this research, Kunming mice were total-body exposed to 0.05-2 Gy of carbon ions, protons, or X-rays, and the RNA sequencing was performed to profile the expression of sncRNAs in serum. After conditional screening and validation, we firstly identified 5 tsRNAs including 4 tRNA-related fragments (tRFs) and 1 tRNA half (tiRNA) which showed a significant level decrease after exposure to three kinds of radiations. Moreover, the radiation responses of these 5 serum tsRNAs were reproduced in other mouse strains, and the sequences of them could be detected in serum of humans. Furthermore, we developed multi-factor models based on tsRNA biomarkers to indicate the degree of radiation exposure with high sensitivity and specificity. These findings suggest that the circulating tsRNAs can serve as new minimally invasive biomarkers and can make a triage or dose assessment from blood sample collection within 4 h in exposure scenarios.

4.
Open Life Sci ; 16(1): 1278-1292, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34966852

RESUMO

We performed polyacrylamide gel electrophoresis of human proteins with sodium dodecyl sulfate, isolated proteins at multiple positions, and then used liquid chromatography and tandem mass spectrometry (LC-MS/MS) to determine the protein identities. Although beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are 41.7 and 36 kDa proteins, respectively, LC-MS/MS identified their peptides at all the positions studied. The National Center for Biotechnology Information (USA) database lists only one ACTB mRNA but five GAPDH mRNAs and one noncoding RNA. The five GAPDH mRNAs encode three protein isoforms, while our bioinformatics analysis identified a 17.6 kDa isoform encoded by the noncoding RNA. All LC-MS/MS-identified GAPDH peptides at all positions studied are unique, but some of the identified ACTB peptides are shared by ACTC1, ACTBL2, POTEF, POTEE, POTEI, and POTEJ. ACTC1 and ACTBL2 belong to the ACT family with significant similarities to ACTB in protein sequence, whereas the four POTEs are ACTB-containing chimeric genes with the C-terminus of their proteins highly similar to the ACTB. These data lead us to conclude that GAPDH and ACTB are poor reference genes for determining the protein loading in such techniques as Western blotting, a leading role these two genes have been playing for decades in biomedical research.

5.
Nucleic Acids Res ; 49(20): 11596-11613, 2021 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-34723322

RESUMO

Using the programmable RNA-sequence binding domain of the Pumilio protein, we FLAG-tagged Xist (inactivated X chromosome specific transcript) in live mouse cells. Affinity pulldown coupled to mass spectrometry was employed to identify a list of 138 candidate Xist-binding proteins, from which, Ssb (also known as the lupus autoantigen La) was validated as a protein functionally critical for X chromosome inactivation (XCI). Extensive XCI defects were detected in Ssb knockdown cells, including chromatin compaction, death of female mouse embryonic stem cells during in vitro differentiation and chromosome-wide monoallelic gene expression pattern. Live-cell imaging of Xist RNA reveals the defining XCI defect: Xist cloud formation. Ssb is a ubiquitous and versatile RNA-binding protein with RNA chaperone and RNA helicase activities. Functional dissection of Ssb shows that the RNA chaperone domain plays critical roles in XCI. In Ssb knockdown cells, Xist transcripts are unstable and misfolded. These results show that Ssb is critically involved in XCI, possibly as a protein regulating the in-cell structure of Xist.

6.
Scand J Gastroenterol ; : 1-12, 2021 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-34738858

RESUMO

BACKGROUND AND OBJECTIVES: The association between abdominal obesity and reflux esophagitis (RE) has been extensively evaluated, but the current findings are mixed and more convincing epidemiological evidence urgently needs to be established. To thoroughly explore this relationship, we summarized the latest studies, performed an updated meta-analysis, and examined the dose-response relationship. METHODS: We performed a systematic search of PubMed, Web of Science, and Embase up to 28 March 2021, using prespecified terms to identify studies investigating the association between abdominal obesity and RE. Odds ratios (ORs) with 95% confidence intervals (CIs), mean differences (MDs) or standardized mean differences (SMDs) with 95% CIs were taken as effect-size estimates. RESULTS: Forty-two observational studies, including 11 cohort studies, were meta-analyzed. Overall, a statistically significant association was observed between abdominal obesity and RE, by both the pooled OR (adjusted OR = 1.51, 95% CI: 1.37-1.66, p < .001) and the pooled SMD (SMD = 0.36, 95% CI: 0.30-0.42, p < .001). Moreover, this significant relationship persisted with subgroup stratification. In subgroup analyses, we found that study design, abdominal obesity measurement, adjustment for covariates and sex were possible sources of between-study heterogeneity. For the dose-response analyses, the risk of RE increased with the degree of abdominal obesity, and the increasing trend accelerated when waist circumference (WC) reached 87.0 cm. CONCLUSION: This meta-analysis indicated a significant association between abdominal obesity and RE, and the risk of RE increased with abdominal obesity especially when the WC was over 87.0 cm.

7.
Int J Radiat Biol ; 97(12): 1731-1740, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34597255

RESUMO

BACKGROUND: Ionizing radiation, especially heavy ion (HI) beams, has been widely used in biology and medicine. However, the mechanism of membrane damage by such radiation remains primarily uncharacterized. PURPOSE: Transcriptomic profiles of Escherichia coli (E. coli) treated with HI illustrated the response mechanisms of the membrane, mainly ABC transporters, related genes regulated by antibiotics treatment through enrichment analyses of GO and KEGG. The networks of protein-protein interactions indicated that LsrB was the crucial one among the ABC transporters specially regulated by HI through the calculation of plugins MCODE and cytoHubba of Cytoscape. Finally, the expression pattern, GO/KEGG enrichment terms, and the interaction between nine LuxS/AI-2 quorum sensing system members were investigated. CONCLUSIONS: Above all, results suggested that HI might perform membrane damage through regulated material transport, inhibited LuxS/AI-2 system, finally impeded biofilm formation. This work provides further evidence for the role of ABC transporters, especially LsrB, in membrane damage of E. coli to HI. It will provide new strategies for improving the precise application of HI.

8.
Inorg Chem ; 60(21): 16266-16272, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34672549

RESUMO

A tricoordinate borenium ion has received considerable attention in recent years for its applications in Lewis acid catalysis. Over the years, asymmetric catalysis mediated by a chiral borenium ion has also been developed. To stabilize the electron-deficient boron atom, a series of chloroborane masked borenium ions featuring the symmetrical [B-Cl-B]+ linkage are prepared and utilized as the catalyst for the enantioselective Diels-Alder cycloaddition of cyclopentadiene and 2,2,2-trifluoroethyl acrylate. The presence of a Cp* ligand is critical in realizing the cyclic diboron compounds, and the stability of the resulting [B-Cl-B]+ cation is dependent on the steric bulkiness of the oxazolidinone moiety. The stereoselectivity of the Diels-Alder cycloaddition is controlled by the substituents of the chiral oxazolidinone ligand and could be further improved via the coordination of SnCl4 at the bridging chloride of the [B-Cl-B]+ cation.

9.
Cell Death Dis ; 12(11): 1029, 2021 10 29.
Artigo em Inglês | MEDLINE | ID: mdl-34716300

RESUMO

Breast cancer is a major threat to women's health and estrogen receptor-positive (ER+) breast cancer exhibits the highest incidence among these cancers. As the primary estrogen, estradiol strongly promotes cellular proliferation and radiotherapy, as a standard treatment, exerts an excellent therapeutic effect on ER+ breast cancer. Therefore, we herein wished to explore the mechanism(s) underlying the inhibitory effects of radiation on the proliferation of ER+ breast cancer cells. We used the ER+ breast cancer cell lines MCF7 and T47D, and their complementary tamoxifen-resistant cell lines in our study. The aforementioned cells were irradiated at different doses of X-rays with or without exogenous estradiol. CCK8 and clone-formation assays were used to detect cellular proliferation, enzyme-linked immunosorbent assay (ELISA) to determine estradiol secretion, western immunoblotting analysis and quantitative real-time PCR to evaluate the expression of proteins, and immunofluorescence to track endoplasmic reticulum stress-related processes. Finally, BALB/C tumor-bearing nude mice were irradiated with X-rays to explore the protein expression in tumors using immunohistochemistry. We found that ionizing radiation significantly reduced the phosphorylation of estrogen receptors and the secretion of estradiol by ER+ breast cancer cells. CYP19A (aromatase) is an enzyme located in the endoplasmic reticulum, which plays a critical role in estradiol synthesis (aromatization), and we further demonstrated that ionizing radiation could induce endoplasmic reticulum stress with or without exogenous estradiol supplementation, and that it downregulated the expression of CYP19A through ER-phagy. In addition, ionizing radiation also promoted lysosomal degradation of CYP19A, reduced estradiol synthesis, and inhibited the proliferation of tamoxifen-resistant ER+ breast cancer cells. We concluded that ionizing radiation downregulated the expression of CYP19A and reduced estradiol synthesis by inducing endoplasmic reticulum stress in ER+ breast cancer cells, thereby ultimately inhibiting cellular proliferation.

10.
Natl Sci Rev ; 8(4): nwab006, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-34676097

RESUMO

After a short recovery period, COVID-19 reinfections could occur in convalescent patients, even those with measurable levels of neutralizing antibodies. Effective vaccinations and protective public health measures are recommended for the convalescent COVID-19 patients.

11.
Sci Rep ; 11(1): 20929, 2021 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-34686717

RESUMO

The research is executed to analyze the connection between genomic instability-associated long non-coding RNAs (lncRNAs) and the prognosis of cervical cancer patients. We set a prognostic model up and explored different risk groups' features. The clinical datasets and gene expression profiles of 307 patients have been downloaded from The Cancer Genome Atlas database. We established a prognostic model that combined somatic mutation profiles and lncRNA expression profiles in a tumor genome and identified 35 genomic instability-associated lncRNAs in cervical cancer as a case study. We then stratified patients into low-risk and high-risk groups and were further checked in multiple independent patient cohorts. Patients were separated into two sets: the testing set and the training set. The prognostic model was built using three genomic instability-associated lncRNAs (AC107464.2, MIR100HG, and AP001527.2). Patients in the training set were divided into the high-risk group with shorter overall survival and the low-risk group with longer overall survival (p < 0.001); in the meantime, similar comparable results were found in the testing set (p = 0.046), whole set (p < 0.001). There are also significant differences in patients with histological grades, FIGO stages, and different ages (p < 0.05). The prognostic model focused on genomic instability-associated lncRNAs could predict the prognosis of cervical cancer patients, paving the way for further research into the function and resource of lncRNAs, as well as a key approach to customizing individual care decision-making.

12.
Hum Immunol ; 2021 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-34556350

RESUMO

Hepatitis C virus (HCV) infection is a global health problem. Several previous studies have addressed the role of host single-nucleotide polymorphisms (SNPs) in HCV infection. SNPs in the regulatory region of the human leukocyte antigen G (HLA-G) gene play an important role in several diseases. The objective of this study is to determine the association of HLA-G 3'untranslated region (UTR) polymorphisms with the susceptibility to chronic hepatitis C infection in the Chinese population. HLA-G 3' UTR polymorphisms, which include 14-bp Ins/Del (rs371194629), +3003T/C (rs1707), +3010C/G (rs1710), +3027 A/C (rs17179101), +3035C/T (rs17179108), +3142 G/C (rs1063320), +3187 A/G (rs9380142) and + 3196C/G (rs1610696), were analyzed in 246 patients with chronic hepatitis C infection and 294 healthy individuals. The alleles, genotypes, and haplotypes were compared between chronic hepatitis C-infected subjects and controls using chi-square tests and logistic regression models. After a correction of multiple comparisons by the false discovery rate (FDR), the allele frequency of + 3196C, genotype frequencies of + 3187 AA and + 3196CC and frequency of the UTR-3 haplotype were significantly higher in the patients than in the control group (P < 0.05), whereas the frequencies of UTR-1 and UTR-2 haplotypes were significantly lower in the patients than in the control group (P < 0.05). After a correction of multiple comparisons by FDR, UTR-2 and UTR-3 maintained significant associations with chronic hepatitis C. This study indicates that HLA-G 3'UTR polymorphisms are associated with the susceptibility to chronic hepatitis C infection in the Chinese population. HLA-G 3'UTR may play an important role in risk modulation toward HCV infection.

13.
Front Immunol ; 12: 694573, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34484191

RESUMO

Inclusion membrane proteins (Incs) play an important role in the structure and stability of chlamydial inclusion and the interaction between Chlamydia spp. and their hosts. Following Chlamydia infection through the respiratory tract, human polymorphonuclear neutrophils (hPMN) not only act as the primary immune cells reaching the lungs, but also serve as reservoir for Chlamydia. We have previously identified a Chlamydia psittaci hypothetical protein, CPSIT_0556, as a medium expressed inclusion membrane protein. However, the role of inclusion membrane protein, CPSIT_0556 in regulating hPMN functions remains unknown. In the present study, we found that CPSIT_0556 could not only inhibit hPMN apoptosis through the PI3K/Akt and NF-κB signaling pathways by releasing IL-8, but also delays procaspase-3 processing and inhibits caspase-3 activity in hPMN. Up-regulating the expression of anti-apoptotic protein Mcl-1 and down-regulating the expression of pro-apoptotic protein Bax could also inhibit the translocalization of Bax in the cytoplasm into the mitochondria, as well as induce the transfer of p65 NF-κB from the cytoplasm to the nucleus. Overall, our findings demonstrate that CPSIT_0556 could inhibit hPMN apoptosis through PI3K/Akt and NF-κB pathways and provide new insights towards understanding a better understanding of the molecular pathogenesis and immune escape mechanisms of C. psittaci.

14.
Stem Cells Dev ; 30(20): 1028-1036, 2021 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-34486378

RESUMO

Inflammation, the main factor in the progression of osteoarthritis (OA), impairs the chondrogenesis of bone mesenchymal stem cells (BMSCs), which is an appealing process to target to regenerate impaired articular cartilage. This article aimed to investigate whether SP600125, a competitive ATP-specific inhibitor of the JNK pathway, could promote the chondrogenesis of BMSCs by enhancing their anti-inflammatory capacity. Chondrogenic differentiation was assessed by Alcian blue staining, immunofluorescence staining, and Western blot. The inflammation level was associated with the expression of matrix metalloproteinases (Mmp), evaluated by Western blot. Intra-articular injection of BMSCs pretreated with or without SP600125 was carried out on C57BL/6 mice after inducing OA by surgical destabilization of the medial meniscus. Safranin O-fast green (SO) and hematoxylin-eosin staining were employed to evaluate the cartilage destruction and immunohistochemical analysis was adopted to detect the expression of Col2 and Mmp-13 proteins in the mouse knee joint. We showed that SP600125 could inhibit inflammation induced by tumor necrosis factor-α (TNF-α) and promote the chondrogenesis of BMSCs. In the presence of TNF-α, the expression of aggrecan (Agc) and collagen type II alpha 1 (Col2) was significantly decreased compared with that in the control group and increased with the addition of SP600125. Moreover, the expression of Mmp-1, Mmp-3, and Mmp-13 was increased in BMSCs treated only with TNF-α and downregulated in SP600125-treated BMSCs. In vivo study showed that SP600125 could enhance protective effects of BMSCs on OA mice. Our results indicated that SP600125 rescued the chondrogenesis of BMSCs by inhibiting inflammation induced by TNF-α, which provides a theoretical basis for solving the problem of cartilage repair under inflammatory conditions.

15.
Biomed Environ Sci ; 34(8): 650-655, 2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34474727

RESUMO

Epstein-Barr virus (EBV) and cytomegalovirus (CMV), two of the most prevalent human herpesviruses, cause a wide spectrum of diseases and symptoms and are associated with serious health problem. In this study, we developed an internal control reference recombinase-aided amplification (ICR-RAA) assay for the rapid detection of EBV and CMV within 30 min. The assay had a sensitivity of 5 and 1 copies/test for EBV and CMV, respectively, with no cross reaction with other pathogens. In comparison with those of the commercial quantitative polymerase chain reaction (qPCR), the sensitivity of the EBV and CMV ICR-RAAs using extracted DNA was 93.33% and 84.84%, respectively; the specificity was 98.75% and 100.00%, respectively; and the Kappa values were 0.930 and 0.892 ( P < 0.05), respectively. In comparison with those of qPCR, the sensitivity of the EBV and CMV ICR-RAAs using the DNA by thermal lysis was 72.22% and 80.00%, respectively; the specificity was 100.00%; and the Kappa values were 0.764 and 0.878 ( P < 0. 05), respectively. Thus, rapid and specific detection of EBV and CMV is possible using ICR-RAA assays.


Assuntos
Citomegalovirus/genética , DNA Viral/análise , Herpesvirus Humano 4/genética , Técnicas de Amplificação de Ácido Nucleico , Recombinases/genética , Adolescente , Adulto , Criança , Pré-Escolar , Infecções por Citomegalovirus/diagnóstico , Infecções por Citomegalovirus/virologia , Infecções por Vírus Epstein-Barr/diagnóstico , Infecções por Vírus Epstein-Barr/virologia , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Adulto Jovem
17.
Front Cell Dev Biol ; 9: 687769, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34395420

RESUMO

Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) represent an infinite cell source for cardiovascular disease modeling, drug screening and cell therapy. Despite extensive efforts, current approaches have failed to generate hPSC-CMs with fully adult-like phenotypes in vitro, and the immature properties of hPSC-CMs in structure, metabolism and electrophysiology have long been impeding their basic and clinical applications. The prenatal-to-postnatal transition, accompanied by severe nutrient starvation and autophagosome formation in the heart, is believed to be a critical window for cardiomyocyte maturation. In this study, we developed a new strategy, mimicking the in vivo starvation event by Earle's balanced salt solution (EBSS) treatment, to promote hPSC-CM maturation in vitro. We found that EBSS-induced starvation obviously activated autophagy and mitophagy in human embryonic stem cell-derived cardiomyocytes (hESC-CMs). Intermittent starvation, via 2-h EBSS treatment per day for 10 days, significantly promoted the structural, metabolic and electrophysiological maturation of hESC-CMs. Structurally, the EBSS-treated hESC-CMs showed a larger cell size, more organized contractile cytoskeleton, higher ratio of multinucleation, and significantly increased expression of structure makers of cardiomyocytes. Metabolically, EBSS-induced starvation increased the mitochondrial content in hESC-CMs and promoted their capability of oxidative phosphorylation. Functionally, EBSS-induced starvation strengthened electrophysiological maturation, as indicated by the increased action potential duration at 90% and 50% repolarization and the calcium handling capacity. In conclusion, our data indicate that EBSS intermittent starvation is a simple and efficient approach to promote hESC-CM maturation in structure, metabolism and electrophysiology at an affordable time and cost.

18.
Front Cell Infect Microbiol ; 11: 577236, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34307184

RESUMO

Gut microbiota is regarded as the second human genome and forgotten organ, which is symbiotic with the human host and cannot live and exist alone. The gut microbiota performs multiple physiological functions and plays a pivotal role in host health and intestinal homeostasis. However, the gut microbiota can always be affected by various factors and among them, it is radiotherapy that results in gut microbiota dysbiosis and it is often embodied in a decrease in the abundance and diversity of gut microbiota, an increase in harmful bacteria and a decrease in beneficial bacteria, thereby affecting many disease states, especially intestine diseases. Furthermore, gut microbiota can produce a variety of metabolites, among which short-chain fatty acids (SCFAs) are one of the most abundant and important metabolites. More importantly, SCFAs can be identified as second messengers to promote signal transduction and affect the occurrence and development of diseases. Radiotherapy can lead to the alterations of SCFAs-producing bacteria and cause changes in SCFAs, which is associated with a variety of diseases such as radiation-induced intestinal injury. However, the specific mechanism of its occurrence is not yet clear. Therefore, this review intends to emphasize the alterations of gut microbiota after radiotherapy and highlight the alterations of SCFAs-producing bacteria and SCFAs to explore the mechanisms of radiation-induced intestinal injury from the perspective of gut microbiota and its metabolite SCFAs.


Assuntos
Microbioma Gastrointestinal , Bactérias , Disbiose , Ácidos Graxos Voláteis , Humanos , Intestinos
19.
Artigo em Inglês | MEDLINE | ID: mdl-34214662

RESUMO

Klebsiella pneumoniae (K. pneumoniae) is an important pathogen that can cause severe hospital- and community-acquired infections. To systematically investigate its methylation features, we determined the whole genome sequences of 14 K. pneumoniae strains covering varying serotypes, multilocus sequence typing (MLST), clonal groups (CGs), viscosity/virulence, and drug resistance. Their methylomes were further characterised using PacBio-SMRT and bisulfite technologies. We identified 15 methylation motifs (13 N6-methyladenine (6mA) and two 5-methylcytosine (5mC) motifs), among which eight were novel. Their corresponding DNA methylases (MTases) were also validated. Additionally, we analysed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distributive patterns of some hemi/un-methylated GATC motifs, which tend to be located within intergenic regions (IGRs). Specifically, we characterised the in vivo methylation kinetics at single base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalysed re-methylation. The slower methylation rates of the GATC motifs in the replication origins (oriC) and IGRs implicate an epigenetic mechanism in the regulation of replication initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumoniae at single base resolution, and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.

20.
Aging (Albany NY) ; 13(12): 16445-16470, 2021 06 18.
Artigo em Inglês | MEDLINE | ID: mdl-34148032

RESUMO

Acute myeloid leukemia (AML) is a group of heterogeneous hematological malignancies. We identified key genes as ITGAM and lncRNA ITGB2-AS1 through different bioinformatics tools. Furthermore, qPCR was performed to verify the expression level of essential genes in clinical samples. Retrospective research on 179 AML cases was used to investigate the relationship between the expression of ITGAM and the characteristics of AML. The critical gene relationship with immune infiltration in AML was estimated. The clinical validation and prognostic investigation showed that ITGAM, PPBP, and ITGB2-AS1 are highly expressed in AML (P < 0.001) and significantly associated with the overall survival in AML. Moreover, the retrospective research on 179 clinical cases showed that positive expression of ITGAM is substantially related to AML classification (P < 0.001), higher count of white blood cells (P < 0.01), and poor chemotherapy outcome (P < 0.05). Furthermore, based on grouping ITGAM as the high and low expression in TCGA-LAML profile, we found that genes in the highly expressed ITGAM group are mainly involved in immune infiltration and inflammation-related signaling pathways. Finally, we discovered that the expression level of ITGAM and lncRNA ITGB2-AS1 are not just closely related to the immune score and stromal score (P < 0.001) but also significantly positively correlated with various Immune signatures in AML (P < 0.001), indicating the association of these genes with immunosuppression in AML. The prediction of candidate drugs indicated that certain immunosuppressive drugs have potential therapeutic effects for AML. The critical genes could be used as potential biomarkers to evaluate the survival and prognosis of AML.


Assuntos
Perfilação da Expressão Gênica , Regulação Leucêmica da Expressão Gênica , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/imunologia , Feminino , Ontologia Genética , Redes Reguladoras de Genes , Genes Essenciais , Humanos , Leucemia Mieloide Aguda/tratamento farmacológico , Masculino , Pessoa de Meia-Idade , Prognóstico , Mapas de Interação de Proteínas/genética , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Curva ROC , Reprodutibilidade dos Testes , Transdução de Sinais/genética , Transcriptoma/genética , Resultado do Tratamento , Microambiente Tumoral/genética
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