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This review presents advances in the implementation of high - throughput se quencing and its application to the knowledge of medicinal plants. We conducted a bibliographic search of papers published in PubMed, Science Direct, Google Scholar, Scopus, and Web of Science databases and analyzed the obtained data using VOSviewer (versi on 1.6.19). Given that medicinal plants are a source of specialized metabolites with immense therapeutic values and important pharmacological properties, plant researchers around the world have turned their attention toward them and have begun to examine t hem widely. Recent advances in sequencing technologies have reduced cost and time demands and accelerated medicinal plant research. Such research leverages full genome sequencing, as well as RNA (ribonucleic acid) sequencing and the analysis of the transcr iptome, to identify molecular markers of species and functional genes that control key biological traits, as well as to understand the biosynthetic pathways of bioactive metabolites and regulatory mechanisms of environmental responses. As such, the omics ( e.g., transcriptomics, metabolomics, proteomics, and genomics, among others) have been widely applied within the study of medicinal plants, although their usage in Colombia is still few and, in some areas, scarce. (185)
El extracto de cloroformo (CE) y las fracciones obtenidas de las raíces de Aldama arenaria se evaluaron para determinar su actividad antiproliferativa in vitro contra 10 líneas ce lulares tumorales humanas [leucemia (K - 562), mama (MCF - 7), ovario que expresa un fenotipo resistente a múltiples fármacos (NCI/ADR - RES), melanoma (UACC - 62), pulmón (NCI - H460), próstata (PC - 3), colon (HT29), ovario (OVCAR - 3), glioma (U251) y riñón (786 - 0)]. CE presentó actividad antiproliferativa débil a moderada (log GI 50 medio 1.07), mientras que las fracciones 3 y 4, enriquecidas con diterpenos de tipo pimarane [ent - pimara - 8 (14), ácido 15 - dien - 19 - oico y ent - 8(14),15 - pimaradien - 3 ß - ol], presentaron activid ad moderada a potente para la mayoría de las líneas celulares, con un log GI 50 medio de 0.62 y 0.59, respectivamente. Los resultados mostraron una acción antiproliferativa in vitro prometedora de las muestras obtenidas de A. arenaria , con los mejores resul tados para NCI/ADR - RES, HT29 y OVCAR - 3, y valores de TGI que van desde 5.95 a 28.71 µg.mL - 1, demostrando que los compuestos de esta clase pueden ser prototipos potenciales para el descubrimiento de nuevos agentes terapéuticos
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Plantes médicinales , Séquençage nucléotidique à haut débit , Multi-omique , Médecine traditionnelle , ColombieRÉSUMÉ
La prueba prenatal no invasiva es un método de cribado de aneuploidías fetales y de resultar con riesgo alto debe ser confirmado a través de prueba genética diagnóstica. Es la prueba de detección más sensible y específica para las aneuploidías fetales comunes y minimiza la realización de técnicas invasivas, solo para las gestantes con riesgo elevado. Se debe realizar asesoramiento genético pre- y poscribado. Este estudio tiene como objetivo describir los fundamentos básicos de la prueba prenatal no invasiva mediante el análisis del ácido desoxirribonucleíco libre circulante en plasma materno para cribado de aneuploidías, y de los métodos primordiales y avances en biología molecular incluyendo las tecnologías de secuenciación de nueva generación, que lo han facilitado, considerando sus beneficios y limitaciones al aplicarla en la práctica clínica, en este campo que cambia con tanta rapidez(AU)
The non-invasive prenatal test is a screening method for fetal aneuploidies and if the result is at high risk, it must be confirmed through diagnostic genetic test. It is the most sensitive and specific detection test for common fetal aneuploidies and minimizes the use of invasive techniques, only for pregnant women at high risk. Genetic counseling should be performed before and after screening. This study aims to describe the basic fundamentals of non-invasive prenatal testing by analyzing free circulating deoxyribonucleic acid in maternal plasma for aneuploidy screening, and the primary methods and advances in molecular biology, including next-generation sequencing technologies, which have facilitated it, considering its benefits and limitations when applying it in clinical practice, in this rapidly changing field(AU)
Sujet(s)
Humains , Femelle , Grossesse , Plasma sanguin , ADN , Dépistage de masse , Prévalence , Facteurs de risqueRÉSUMÉ
Glioblastomas are known for their poor clinical prognosis, with recurrent tumors often exhibiting greater invasiveness and faster growth rates compared to primary tumors. To understand the intratumoral changes driving this phenomenon, we employed single-cell sequencing to analyze the differences between two pairs of primary and recurrent glioblastomas. Our findings revealed an upregulation of ferroptosis in endothelial cells within recurrent tumors, identified by the significant overexpression of the NOX4 gene. Further analysis indicated that knocking down NOX4 in endothelial cells reduced the activity of the ferroptosis pathway. Utilizing conditioned media from endothelial cells with lower ferroptosis activity, we observed a decrease in the growth rate of glioblastoma cells. These results highlighted the complex role of ferroptosis within tumors and suggested that targeting ferroptosis in the treatment of glioblastomas requires careful consideration of its effects on endothelial cells, as it may otherwise produce counterproductive outcomes.
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ObjectiveThis study aims to explore the potential mechanism of Danggui Niantongtang in treating knee osteoarthritis （KOA） by regulating the intestinal flora through 16S rDNA analysis. MethodThirty-six C57BL/6J mice were subjected to anterior cruciate ligament transection （ACLT） to establish a KOA model and were randomly divided into the sham surgery group， model group， low-dose Danggui Niantongtang group （0.819 g·kg-1）， medium-dose Danggui Niantongtang group （1.638 g·kg-1）， high-dose Danggui Niantongtang group （3.276 g·kg-1）， and Meloxicam group （0.975 mg·kg-1）， with 6 mice in each group. Except for the treatment groups， the sham surgery group and model group were given normal saline by gavage. After 4 weeks of continuous intervention， feces and intact knee joints of the mice were collected. Hematoxylin-eosin （HE） staining and Safranin O-Fast Green staining were performed to observe the pathological changes in knee joint tissue morphology. The 16S rDNA sequencing was used to analyze changes in the abundance and diversity of intestinal microorganisms before and after treatment， along with corresponding functional predictions. ResultHigh-dose Danggui Niantongtang and Meloxicam significantly relieved pain symptoms in KOA mice， improved the disorder of joint structure， maintained the integrity of knee articular cartilage， increased the expression of type Ⅱ collagen alpha 1 （Col2a1） in articular cartilage， and decreased the expression of matrix metalloproteinase-13 （MMP-13）. The results of 16S rDNA sequencing showed that high-dose Danggui Niantongtang could adjust the abundance and structure of intestinal microbial species. Compared with the sham surgery group， the abundance of Proteobacteria， Actinobacteria， Ruminococcus， and Bacteroides was significantly increased in the model group （P<0.05）， while in the Danggui Niantongtang group， the abundance of these four flora was significantly reduced compared with the model group. Compared with the sham surgery group， the abundance of Verrucomicrobia， Oscillospira， and Akkermansia was significantly decreased in the model group （P<0.05）， while in the Danggui Niantongtang groups， the abundance of these three flora was significantly increased compared with the model group （P<0.05）. Functional pathway prediction of differential genera revealed that species differences among groups mainly involved metabolic pathways with high abundance associated with biosynthesis and precursors， as well as energy production， including amino acid biosynthesis， nucleotide and nucleoside biosynthesis， cofactors， prosthetic groups， electron carriers， and vitamin biosynthesis. ConclusionDanggui Niantongtang can effectively protect articular cartilage and delay the progression of KOA， possibly by regulating the structure of the intestinal flora， promoting probiotics， and inhibiting the growth of harmful pathogenic bacteria.
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ObjectiveTo observe the microbial changes in Wistar rats with liver injury caused by the Dictamni Cortex-Flavescens Sophora by high-throughput sequencing technology and investigate the potential mechanism of liver injury caused by the Dictamni Cortex-Flavescens Sophora. MethodFemale Wistar rats were randomly divided into four groups： normal group， as well as low-dose， medium-dose， and high-dose groups of traditional Chinese medicine （TCM）. The rats were gavaged with the Dictamni Cortex-Flavescens Sophora in different doses （4.125， 8.25， 16.5 g·kg-1 of raw drug respectively） for 28 days， and the general condition was recorded. The liver-body weight ratio was calculated， and the biochemical indexes of serum were observed. The Hematoxylin-eosin （HE） staining was used to observe pathological changes in the liver， and 16S rDNA high-throughput sequencing was utilized to detect fecal microbial changes in rats. ResultCompared with the normal group， Dictamni Cortex-Flavescens Sophora increased the liver weights and liver-body weight ratios of Wistar rats. The difference in liver weight between the medium-dose and high-dose groups of TCM was statistically significant （P<0.05）， and the liver-body weight ratios of the low-dose， medium-dose， and high-dose groups of TCM were all statistically significant （P<0.05）. Compared with the normal group， serum albumin and cholesterol levels increased in the medium-dose and high-dose groups of TCM （P<0.05）. The histopathology of the liver in the medium-dose and high-dose groups of TCM showed tiny vacuole-like changes. Compared with the normal group， there were obvious intestinal flora disorders after administration of Dictamni Cortex-Flavescens Sophora， and alpha diversity increased in the medium-dose and high-dose groups of TCM. The principal coordinates analysis showed that species increasingly deviated from the normal group as the administered dose increased. Compared with the normal group， the proportion of Firmicutes and Bacteroidota decreased after the drug administration， and the genus level of Parasutterella， Romboutsia， Turicibacter， Allobaculum， and Dubosiella increased. The genus level of Lachnospiraceae_NK4A136_group， Blautia， Erysipelatoclostridium， Muribaculum， and Ruminococcus_gnavus_group decreased. The correlation analysis showed that Parasutterella， Romboutsia， Turicibacter， Allobaculum， and Dubosiella were positively correlated with serum cholesterol and liver-body weight ratio， and lanchnospiraceae_NK4A136_group， Blautia， Muribaculum， Erysipelatoclostridium， and Ruminococcus_gnavus_group were negatively associated with serum cholesterol and liver-body weight ratio. ConclusionThe liver injury caused by Dictamni Cortex-Flavescens Sophora is manifested as a lipid metabolism disorder， and the mechanism is related to the increase in lipid metabolism-related microorganisms.
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Objective:To delve deeply into the dynamic trajectories of cell subpopulations and the communication network among immune cell subgroups during the malignant progression of glioblastoma(GBM),and to endeavor to unearth key risk biomarkers in the GBM malignancy progression,so as to provide a more profound understanding for the treatment and prognosis of this disease by integrating tran-scriptomic data and clinical information of the GBM patients.Methods:Utilizing single-cell sequencing data analysis,we constructed a cell subgroup atlas during the malignant progression of GBM.The Mono-cle2 tool was employed to build dynamic progression trajectories of the tumor cell subgroups in GBM.Through gene enrichment analysis,we explored the biological processes enriched in genes that significant-ly changed with the malignancy progression of GBM tumor cell subpopulations.CellChat was used to identify the communication network between the different immune cell subgroups.Survival analysis helped in identifying risk molecular markers that impacted the patient prognosis during the malignant pro-gression of GBM.This methodological approach offered a comprehensive and detailed examination of the cellular and molecular dynamics within GBM,providing a robust framework for understanding the disease's progression and potential therapeutic targets.Results:The analysis of single-cell sequencing data identified 6 different cell types,including lymphocytes,pericytes,oligodendrocytes,macrophages,glioma cells,and microglia.The 27 151 cells in the single-cell dataset included 3 881 cells from the pa-tients with low-grade glioma(LGG),10 166 cells from the patients with newly diagnosed GBM,and 13 104 cells from the patients with recurrent glioma(rGBM).The pseudo-time analysis of the glioma cell subgroups indicated significant cellular heterogeneity during malignant progression.The cell interaction analysis of immune cell subgroups revealed the communication network among the different immune sub-groups in GBM malignancy,identifying 22 biologically significant ligand-receptor pairs across 12 key bio-logical pathways.Survival analysis had identified 8 genes related to the prognosis of the GBM patients,among which SERPINE1,COL6A1,SPP1,LTF,C1S,AEBP1,and SAA1L were high-risk genes in the GBM patients,and ABCC8 was low-risk genes in the GBM patients.These findings not only provided new theoretical bases for the treatment of GBM,but also offered fresh insights for the prognosis assessment and treatment decision-making for the GBM patients.Conclusion:This research comprehensively and pro-foundly reveals the dynamic changes in glioma cell subpopulations and the communication patterns among the immune cell subgroups during the malignant progression of GBM.These findings are of significant im-portance for understanding the complex biological processes of GBM,providing crucial new insights for precision medicine and treatment decisions in GBM.Through these studies,we hope to provide more ef-fective treatment options and more accurate prognostic assessments for the patients with GBM.
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Currently, single-cell multi-omics technologies including single-cell DNA sequencing (scDNA-seq) and single-cell RNA sequencing (scRNA-seq) have been used to reveal the heterogeneity of malignant tumor cells, elucidate their pathogenesis, drug resistance and recurrence mechanisms, which provide new strategies for the diagnosis and prognostic assessment of malignant tumors. This article reviews the application of single-cell sequencing technology in the diagnosis and prognostic assessment of acute leukemia based on the progress reported at the 65th American Society of Hematology Annual Meeting.
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Objective:To explore the characteristics and patterns of gene mutations in tyrosine kinase inhibitor (TKI)-resistant chronic myeloid leukemia (CML) patients and their relationship with TKI-resistant CML.Methods:A retrospective case series study was performed. Clinical data and next-generation sequencing results from TKI-resistant CML patients in Nanfang Hospital of Southern Medical University and Yuebei People's Hospital of Shantou University Medical College from August 2018 to November 2022 were retrospectively analyzed, and the gene mutations of the patients in general and at different disease stages were analyzed.Results:Sixty patients were enrolled, with the age [ M ( Q1, Q3)] of 41.5 years old (32 years old, 53 years old); 38 cases (63.33%) were male and 22 cases (36.67%) were female; 43 cases were in the chronic stage, and 17 cases were in the progression stage (3 cases were in the accelerated stage and 14 cases were in the blast stage). non-ABL1 mutations were detected in 30 patients (50.00%) including 45 times of 15 non-ABL1 genes. The number of non-ABL1 mutation gene was 1 (0, 2) in 60 patients. Of the 60 patients, 21 (35.00%) had ASXL1 mutations, 5 (8.33%) had DNMT3A mutations, 5 (8.33%) had RUNX1 mutations, and 3 (5.00%) had SETBP1 mutations; the proportions of patients with 1 and ≥2 non-ABL1 mutations were 33.33% (20/60) and 16.67% (10/60), respectively. The total detection rates of non-ABL1 mutations were 52.94% (9/17) and 48.84% (21/43), and the detection rates of ≥2 non-ABL1 mutations were 23.53% (4/17) and 13.95% (6/43) in patients with progression and patients with chronic disease, and the differences were not statistically significant ( χ2 = 0.08, P = 0.774; χ2 = 0.80, P = 0.370). Seventeen of 60 patients (28.33%) had mutations in the ABL1 kinase region, of which 14 (82.35%) had non-ABL1 mutations; of these 17 cases, 6 patients with progressive disease all had non-ABL1 mutations, in 11 patients with chronic disease, 8 patients had non-ABL1 mutations, and the difference was not statistically significant ( P = 0.452). Conclusions:Patients with TKI-resistant CML have high frequencies of non-ABL1 mutations, and there is a trend for higher mutation rates in patients with progressive disease than in patients with chronic disease, and these may be related to the abnormal activation of ABL1 kinase by BCR-ABL1 fusion gene in patients with drug-resistant CML, which leads to the genome-level and epigenome-level mutations, and driving disease progression from chronic phase to accelerated or blast phase.
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With the great progress of precise medicine for lymphatic malignancies, minimal residual diseases (MRD) play an increasingly important role in their evaluation of treatment response, prognosis judgement, treatment decision guidance, and recurrence prediction. At present, nearly a thousand articles on hematological malignancies related to MRD detection are published annually. At the 65th American Society of Hematology annual meeting in 2023, nearly 500 articles on the application of MRD detection in the diagnosis and treatment of lymphatic malignancies cover a wide and rich range of content. This paper reviews the oral reports of MRD detection in acute lymphocytic leukemia, chronic lymphocytic leukemia, multiple myeloma and lymphoma.
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Objective To explore the clinical value of ultrasound bronchoscopy combined with met-agenomic next-generation sequencing(mNGS)in the etiological diagnosis of pneumonia with poor absorption and dissipation.Methods The clinical data of the patients with pneumonia with poor absorption and dissipa-tion in this hospital from January 2022 to February 2023 were retrospectively collected.Among them,73 cases received the endobronchial ultrasound guided tranbronchial needle aspiration(EBUS-TBNA)and 36 cases re-ceived endobronchial ultrasound transbronchial lung biopsy using guide sheath(EBUS-GS-TBLB).The distri-bution of causes and incidence of examination related complications were analysed.Results The results of ul-trasound bronchoscopy combined with mNGS examination showed that the benign lesions accounted for 33.03％,mainly chronic inflammation(9.17％)and infectious disease(20.18％),and tuberculosis was the main cause of infectious diseases(7.34％).The malignant lesions accounted for 57.80％,mainly adenocarcinoma(28.44％).The diagnostic positive rate was 90.83％,and no definite diagnosis accounted for 9.17％.There was no statistically significant difference in the diagnostic positive rate between the patients receiving EBUS-TBNA combined with mNGS examination and the patients receiving EBUS-GS-TBLB combined with mNGS examination(94.52％vs.83.33％,P＞0.05),and there was no statistically significant difference in the inci-dence rates of complications such as less bleeding,anoxia,pneumothorax and delayed resuscitation.No serious complications such as mediastinal emphysema,large vessel injury,shock and death were observed in all pa-tients.Conclusion Ultrasound bronchoscopy combined with mNGS has the characteristics of high diagnostic positive rate and few complications in the etiological diagnosis of pneumonia with poor absorption and dissipa-tion.It can help clinical physicians clarify the diagnosis as soon as possible,and may become a new method for diagnosing respiratory system diseases in recent years.
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Objective To analyze the clinical outcomes of early invasive fungal disease(IFD)in patients after allogenetic hematopoietic stem cell transplantation(allo-HCST)with metagenomic next-generation sequencing(mNGS).Methods A retrospective analysis was conducted on patients undergoing allo-HCST in our Bone Marrow Transplantation Center between July 2021 and October 2022.These patients experienced one of the following conditions within 100 d after transplantation:① Patients with persistent fever and negative blood culture after empiric antimicrobial therapy for 72 h or longer;② Hyperpyrexia of unknown origin occurred again after effective anti-infection in the past;③ Symptoms in lower respiratory tract associated with lung lesions on CT scan,and empiric anti-infective therapy was ineffective.Peripheral blood or bronchoscopic alveolar lavage fluid were tested with mNGS,and overall survival(OS)and non-relapse mortality(NRM)were analyzed.Results There were 60 patients enrolled in this study.For the peripheral blood samples of 47 cases and bronchoalveolar lavage fluid samples of 13 cases,mNGS found that 19 cases were negative to pathogens,30 cases were non-fungal positive,and 11 case were fungal positive,including 3 cases of aspergillus,5 cases of mucor,2 cases of Candida tropicalis,and 1 case of Trichosporon asahii.Of the 11 patients with fungal positive,8 achieved complete remission after antifungal therapy according to the mNGS results.The 1-year OS and NRM of the 60 patients were 70.0％(95％CI:64.1％～75.9％)and 20.0％(95％CI:11.9％～32.5％),respectively,while those of the fungal infection patients were 54.5％(95％CI:49.5％～69.5％)and 36.4％(95％ CI:15.5％～70.3％),respectively.No significant differences were seen in 1-year OS(P=0.487)and 1-year NRM(P=0.358)among the negative,fungal infection and non-fungal infection patients,neither OS(P=0.238)and NRM(P=0.154)between the fungal infection and the non-fungal infection patients.Conclusion mNGS can rapidly diagnose the early IFD after allo-HSCT,which is helpful for timely and effective treatment and improves the prognosis of patients.
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Objective To establish and forensically verify a 42 microhaplotypes(mircohaps,MHs)mul-tiplex assay system based on next-generation sequencing(NGS),and to explore the application value of this system in the practice of forensic genetics.Methods A total of 42 highly polymorphic MHs were selected from previous studies,and sequenced by the MiSeq FGxTM platform to verify the repeata-bility,sensitivity,specificity,stability,and mixture analysis ability of the detection system.Through population genetic investigation of 102 unrelated Chinese Han individuals in Liyang City,Jiangsu Province,China,the application value of this system in forensic genetics was evaluated.Results The sequencing repeatability of the 42-plex MHs assay was 100%and the sensitivity was as low as 0.062 5 ng.The system had the ability to withstand the interference of indigo(≤2 500 ng/μL),humic acid(≤9 ng/μL),hemoglobin(≤20 μmol),and urea(≤200 ng/μL)and to detect mixtures of 2 people(1∶19),3 people(1∶1∶9)and 4 people(1∶1∶1∶9).Based on 102 individual data,the combined power of discrimination and the combined power of exclusion were 1-3.45×10-30 and 1-3.77×10-11,respectively,and the average effect value of alleles was 2.899.Conclusion The 42-plex MHs assay was successfully established in this study and this system has high repeatability and sensitivity,good anti-jamming ability and mixture analysis ability.The 42 MHs are highly polymorphism and have good application value in individual identification and paternity testing.
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Objective To compare the categorical agreement between drug susceptibility testing(DST)and whole genome sequencing(WGS)for the detection of drug resistance in Mycobacterium tuberculosis(MTB),and to explore the characteristics of WGS for MTB drug resistance detection.Methods A total of 71 MTB clinical isolates retained in West China Hospital of Sichuan University from 2018 to 2020 were included in this study.The MTB strains were tested for resistance to 14 anti-tuberculosis drugs,including Isoniazid(INH),Rifampicin(RIF),Rifabutin(RFB),Ethambutol(EMB),Streptomycin(SM),Moxifloxacin(MFX),Ofloxacin(OFX),Levofloxacin(LFX),Amikacin(AMK),Kanamycin(KAN),Capreomycin(CPM),Para-aminosalicylic acid(PAS),Ethionamide(ETH)and Clofazimine(CLO),using both DST(colorimetric redox indicator meth-od)and WGS methods.Kappa test was performed to analyze the results of drug resistance detection for both methods.Results Based on DST and WGS methods to detect anti-tuberculosis drug resistance in seventy-one MTB clinical isolates,the results showed that the agreement rate of RIF,RFB,SM,MFX,OFX and LFX ex-ceeded 90.00％,and the kappa values were all greater than 0.80,with near perfect agreement;The agreement rates of INH and EMB were 84.51％and 81.69％,and Kappa values were 0.68 and 0.54,respectively,with fair agreement.No more than two drug resistant MTB strains of AMK and KAN were detected by both meth-ods,and the resistance rate was less than 3.00％.The agreement rates of CPM,ETH,PAS,and CLO ranged from 61.97％to 91.55％,and the Kappa values were less than 0.40,with slight or fair agreement.Conclusion There are differences in the ability of WGS to detect resistance to various anti-tuberculosis drugs,and it is more effective in detecting resistance to six anti-tuberculosis drugs,including RIF,RFB,SM,MFX,OFX and LFX,while there are still certain differences in detecting resistance to other anti-tuberculosis drugs compared with DST.It is necessary to further clarify the detailed resistance mechanisms of relevant anti-tu-berculosis drugs and to explore the standardization of WGS for drug resistance detection.
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Objective:To explore the effects of acupuncture combined with Buyang Huanwu Decoction on intestinal flora in cerebral blood flow hypo perfusion model rats with carotid artery stenosis.Methods:Totally 40 rats were randomly divided into sham-operation group, model group, TCM treatment group and acupuncture and drug combination treatment group, with 10 rats in each group. Except the sham-operation group, the other groups were prepared cerebral ischemia model by needle control and thread embolism method. TCM treatment group received Buyang Huanwu Decoction 100 mg/kg for gavage, once a day, and the intervention lasted for 2 weeks. In the acupuncture and drug combination group, based on the TCM treatment group, Baihui and its left and right sides of 2 mm were selected for acupuncture, once a day, and continuous intervention was performed for 2 weeks. Neurological function evaluation and behavioral function score were performed 7 and 14 days after administration, respectively. 16S rRNA sequencing was used to comprehensively characterize the structure and composition of fecal microflora of rats in each group. Linear discriminant analysis Effect Size (LEfSe) was used to analyze the difference of intestinal bacteria among groups.Result:On the 7th and 14th day after administration, compared with the model group, the neurological function score in the TCM treatment group and the acupuncture and drug combination group decreased ( P<0.05), and the behavioral function score increased ( P<0.05). Compared with model group, the Shannon index of TCM treatment group and acupuncture and drug combination group increased ( P<0.05). The abundance of Firmicutes increased ( P<0.05), and the abundance of Bacteroidetes and Proteobacteria decreased ( P<0.05); the abundance of Clostridia increased ( P<0.05), and the abundance of Gammaproteobacteria decreased ( P<0.05). The abundance of Escherichia-Shigella and Bacteroides decreased ( P<0.05); the abundance of lactobacillus significantly increased ( P<0.05). Conclusion:Acupuncture combined with Buyang Huanwu Decoction can improve the symptoms of cerebral hypoperfusion model rats with carotid artery stenosis, and the mechanism may be to increase the abundance of probiotics.
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Objective:Study on the correlation between the active components of Salviea Miltiorrhizae Radix et Rhizoma screened by high-throughput sequencing and the regulation of lncRNA-mRNA in human lung adenocarcinoma A549 cells.Methods:A549 cells were cultured, and the IC 50 dose of cryptotanshinone and tanshinone ⅡA was confirmed according to the cell proliferation experiment. A549 cells were randomly divided into blank control group, cryptotanshinone group, and tanshinone IIA group using a random number table method. After 24 hours of intervention, the cell cycle was detected by flow cytometry. High-throughput sequencing technique was used to detect the expressions of lncRNA and mRNA in A549 cells in intervention group and non-intervention group. By analyzing the expression profiles of differential genes related to cryptotanshinone and tanshinone ⅡA, the obtained differential genes were analyzed by GO and KEGG. Results:The cell cycle results showed that the proportion of G0/G1 phase cells in cryptotanshinone and Tanshinone ⅡA was increased ( P<0.01), the proportion of S phase cells was decreased ( P<0.01), and the proportion of G2/M phase cells in cryptotanshinone was decreased ( P<0.01). The results of high-throughput screening showed that cryptotanshinone could up-regulate 4 698 lncRNA, down-regulate 1 557 lncRNA, up-regulate 4 810 mRNA and down-regulate 5 644 mRNA. Tanshinone ⅡA could up-regulate 1 348 lncRNA, down-regulate 1 299 lncRNA, up-regulate 4646 mRNA and down-regulate 4 741 mRNA. The function and pathway enrichment analysis of differential lncRNA and mRNA showed that the differentially expressed genes of cryptotanshinone and tanshinone ⅡA were mainly related to cell cycle, autophagy, AMPK signaling pathway, FoxO signaling pathway and EGFR signaling pathway. GAS5 may be one of the targets for the inhibitory effects of cryptotanshinone and tanshinone ⅡA. Conclusion:Cryptotanshinone and tanshinone ⅡA have certain inhibitory effects on A549 cells, and there are differentially expressed genes of lncRNA-mRNA, which are closely related to cell cycle and signal pathway.
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Objective To investigate the effect of cisplatin treatment on the transcriptional level of human liver cancer cells by conducting transcriptome sequencing analysis after treating human liver cancer cell lines with differ-ent concentrations of cisplatin(CDDP).Methods Liver cancer cell lines HepG2 and Huh7 were incubated with cisplatin at different final concentrations of 0,20,50,100 and 200 μmol/L.After 12 hours,cell viability,immuno-fluorescence and RNA-sequencing(RNA-seq)were performed.Differential gene expression analysis(DEG),KEGG pathway analysis,and protein-protein interaction network analysis were conducted.Results Cisplatin de-creased cell viability and increased DNA damage in HepG2,Huh7 cells.Among the genes regulated after cisplatin treatment at different concentrations,59 genes were commonly up-regulated in both HepG2 and Huh7 cells,while 81 genes were commonly down-regulated.The commonly upregulated genes were mainly enriched in cancer initiation and progression pathways.The 81 commonly down-regulated genes were mainly enriched in Rap1 signaling pathway,Ras signaling pathway,signaling pathways regulating pluripotency of stem cells,axon guidance,and cell adhesion-related pathways.Survival analysis of key nodes in the protein-protein interaction network of commonly up-regulated and downregulated genes revealed a significant correlation between high expression of Jun proto-oncogene,AP-1 transcription factor subunit(JUN)and prolonged patient survival and a significant correlation between low ex-pression of growth arrest and DNA damage inducible alpha(GADD45A)and prolonged patient survival.Conclu-sions The study revealed common transcriptional changes in liver cancer cells under cisplatin treatment.Differential expression of JUN and GADD45A is a potential core mechanism to explain drug resistance.This conclusion provides some important prognostic indicators for clinical treatment.
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Objective To explore the role and possible molecular mechanism of Isocitrate dehydrogenase 1(IDH1)gene in proliferation and migration of intrahepatic cholangiocarcinoma(iCCA)cell HuCCT1.Methods HuCCT1 cells with IDH1 gene knockout(HuCCT1IDH1-/-)were constructed by CRISPR/Cas9 gene editing technology.To investigate the capacities of proliferation,migration and invasion of HuCCT1WT(HuCCT1 cells with wild-type IDH1 gene)and HuCCT1IDH1-/-cells,assays of CCK-8,clone formation,scratch and transwell were performed.Western blotting was used to detect the expression levels of epithelial-mesenchymal transition(EMT)associated proteins E-cadherin,N-cadherin,Vimentin,MMP-9,Wnt3a and β-catenin in two groups of cells.The transcriptome sequencing data of HuCCT1WT and HuCCT1IDH1-/-cells were analyzed by bioinformatics methods,Western blotting was used to verify the expression of signaling pathway-related proteins.Results Compared with HuCCT1WT cells,HuCCT1IDH1-/-cells showed the number of proliferation and clone formation significantly reduced(P<0.05),the proportion of cells blocked in G2/M phase was significantly increased(P<0.01),the rate of scratch healing was significantly decreased(P<0.01),and the number of migrated cells(P<0.001)and invaded cells(P<0.05)was significantly reduced.qRT-PCR assay showed that the expression levels of IDH1,Vimentin,MMP-9 and genes related to the regulation of G2/M cycle proliferation,Cyclin A2,Cyclin B1 and CDK1 mRNA were down-regulated in HuCCT1IDH1-/-cells(P<0.05),and the expression of CDH1 mRNA encoding E-cadherin was up-regulated(P<0.01);Western blotting assay showed that the expression level of E-cadherin in HuCCT1IDH1-/-cells was significantly increased(P<0.05),and the expression level of N-cadherin,Vimentin and MMP-9 protein was significantly decreased(P<0.05)than that in HuCCT1WT cells.Data of transcriptome sequencing revealed 1476 differentially expressed genes(DEGs)between two groups of HuCCT1 cells.Go enrichment analysis showed the DEGs were significantly enriched in cell biological processes associated with inflammatory response,cell signaling and cell metabolism.Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis suggested that the DEGs may be involved in some signaling pathways such as Wnt,MAPK,Rap1,Hippo and TNF,which are closely related to the regulation of proliferation and invasion of tumor cells.Western blotting verification results showed that compared with HuCCT1WT cells,the relative expression of Wnt3a and β-catenin proteins of HuCCT1IDH1-/-cells was significantly decreased(P<0.05).Conclusions IDH1 gene may participate in the control of biological functions of HuCCT1 cells,including cell proliferation,migration,invasion and epithelial mesenchymal transition.The mechanism may be related to the activation of the Wnt/β-catenin signaling pathway.
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Objective To investigate the clinical and genetic characteristics of a family with hypokalemic periodic paralysis(HOKPP).Methods The clinical data of one HOKPP family were retrospectively analyzed.Results The proband presented with periodic paralysis,limb weakness and decreased serum potassium(1-2 mmol/L).The proband's father and cousin had similar symptoms.A heterozygous missense variant c.2006G＞A(p.R669H)in SCN4A gene was identified in the proband,his father,younger aunt and cousin using gene detection.However,the variant was absent in his elder aunt and younger uncle.Conclusions The family shows irregular dominant inheritance.The severity,frequency and age of onset of male heterozygotes were different,while female heterozygotes had no clinical phenotype.The study first confirms that the R669H variant in SCN4A gene causes complete penetrance in males and carriers in females in Asian populations.
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Objective To investigate the clinical features of rhino-orbital-cerebral mucormycosis(ROCM)with bilateral cranial nerve palsies as the clinical manifestation.Methods The related clinical data about ROCM with bilateral cranial nerve palsy as a clinical manifestation was collected,analyzed as well as discussed in the manuscript.And the relevant literatures were reviewed.Results This patient was a healthy young man with new-onset diabetes and diabetic ketoacidosis.The patient developed rapidly with acute onset,bilateral blindness,blepharoptosis and extraocular muscle paralysis.The presence of mucormycosis was confirmed by CSF second-generation sequencing,fungal fluorescent staining and culture.Although effective antifungal therapy was performed early,but the patient quickly presented with cerebral hemorrhage and herniation.Eventually,the patient died after discharge.Conclusions ROCM is a rare and high-mortality infectious disease.This case indicated that the clinicians should consider the presence of ROCM in patients with diabetes/diabetic ketoacidosis when the bilateral cranial nerves paralysis are the clinical symptom,whicn can not be explained by other lesions.CSF next-generation sequencing is helpful for rapid diagnosis.
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Purpose To explore the clinicopathological characteristics of tonsil squamous cell carcinoma(TSCC),and to explore the whole exome mutations and tumor mutational bur-den(TMB)in TSCC cases.Methods Ten patients with clini-cally and histopathologically confirmed TSCC and their clinico-pathological characteristics were collected,The expression of CK(AE1/AE3),CK5/6,p63,p40,p16 and Ki67 were meas-ured by two steps of EnVision,and the whole exome sequencing(WES)and TMB were conducted in 3 of them.Results A-mong the 10 patients,there were 6 females and 4 males which aged from 43 to 76 years old.Microscopically,the cancer cells infiltrated into the subdermis of crypts in the form ofnests and irregular cord,accompanied by comedo like necrosis,intercellu-lar bridges,and varying degrees of keratinization.Obvious atyp-ia and mitotic figures were easily seen.Follow-up was available in all cases,ranging from 6 to 45 months.Nine cases had sur-vived.Immunohistochemistry staining showed that all cases were positive for CK(AE1/AE3),CK5/6,p63,p40,and p16 was positively expressed in three cases,and the proliferation index Ki67 ranged from 40％to 90％.The WES of three cases showed that ARID1B and LRP6 were common cancer susceptibility genes,and WDFY4,ZFHX4 exhibited higher mutation rates,which were both 3/3.The TMB analysis showed that one out of three cases was＞9 mut/Mb.Conclusion The early symptoms of TSCC are not obvious that lead to easily missed and misdiag-nosed.The WES analyses suggest that WDFY4 and ZFHX4 had a higher mutation rate.The TMB analysis suggests that some TSCC patients may benefit from immunotherapy.