In Silico analysis and linking of metabolism-related genes with the immune landscape in head and neck squamous cell carcinoma

Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma(HNSCC).The integrative analysis of all the metabolismrelated genes(MRGs)in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms.Therefore,this study was designed to establish a prognostic signature based on all the MRGs in HNSCC.Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study.Ultimately 4 prognostic MRGs were selected to construct a model possessing robust prognostic value and accuracy in TCGA cohorts.The favorable reproducibility of this model was confirmed in validation cohorts from GEO databases.The risk score calculated by this model was an independent prognostic factor that further classified these HNSCC patients into high-/low-risk groups.GSEA analyses and somatic mutations indicated the low-risk group could activate several anti-tumor pathways and possessed lower TP53 mutation.The results of ESTIMATE,single-sample GSEA,CIBERSORT,and some immune-related molecules analyses suggested the low-risk group exhibited lower metabolic activities and higher immune characteristics.The Spearman correlation test implied most metabolic pathways with tumor-promoting function were negatively correlated with the immune activity,indicating a plausible approach of combining the anti-metabolism and the immunotherapy drugs in the high-risk group to enhance therapeutic effects than applied separately.In conclusion,this prognostic signature linking MRGs with the immune landscape could promote the individualized treatment for HNSCC patients.

PHOSPHO1 Serves as a Key Metabolism-Related Biomarker in the Tumorigenesis of Diffuse Large B-cell Lymphoma

Objective:Diffuse large B-cell lymphoma(DLBCL)is an aggressive type of non-Hodgkin lymphoma.Due to its genetic heterogeneity and abnormal metabolism,many DLBCL patients have a poor prognosis.This study investigated the key metabolism-related genes and potential mechanisms.Methods:Differentially expressed genes,differentially expressed transcription factors(TFs),and differentially expressed metabolism-related genes(DEMRGs)of glucose and lipid metabolic processes were identified using the edgeR package.Key DEMRGs were screened by Lasso regression,and a prediction model was constructed.The cell type identification by estimating relative subsets of RNA transcripts algorithm was utilized to assess the fraction of immune cells,and Gene Set Enrichment Analysis was used to determine immune-related pathways.A regulatory network was constructed with significant co-expression interactions among TFs,DEMRGs,immune cells/pathways,and hallmark pathways.Results:A total of 1551 DEMRGs were identified.A prognostic model with a high applicability(area under the curve=0.921)was constructed with 13 DEMRGs.Tumorigenesis of DLBCL was highly related to the neutrophil count.Four DEMRGs(PRXL2AB,CCN1,DECR2 and PHOSPHO1)with 32 TF-DEMRG,36 DEMRG-pathway,14 DEMRG-immune-cell,9 DEMRG-immune-gene-set,and 67 DEMRG-protein-chip interactions were used to construct the regulatory network.Conclusion:We provided a prognostic prediction model based on 13 DEMRGs for DLBCL.We found that phosphatase,orphan 1(PHOSPHO1)is positively regulated by regulatory factor X5(RFX5)and mediates MYC proto-oncogene(MYC)targeting the V2 pathway and neutrophils.

Preparation of Superparamagnetic Dextran-coated Iron Oxide Nanoparticles used as a Novel Gene Carrier into Human Bladder Cancer Cells'

Objective: Application of magnetic nanoparticles as gene carrier in gene therapy has developed quickly. This study was designed to investigate the preparation of superparamagnetic dextran-coated iron oxide nanoparticles (SDION) and the feasibility of SDION used as a novel gene carrier for plasmid DNA in vitro. Methods: SDION were prepared by chemical coprecipitation and separated by gel filtration on Sephacryl S-300HR, characterized by TEM, laser scattering system and Vibrating Sample Magnetometer Signal Processor. The green fluorescent protein (pGFP-C2) plasmid DNA was used as target gene. SDION-pGFP-C2 conjugate compounds were produced by means of oxidoreduction reaction. The connection ratio of SDION and pGFP-C2 DNA was analyzed and evaluated by agarose electrophoresis and the concentration of pGFP-C2 in supernatant was measured. Using liposome as control, the transfection efficiency of SDION and liposome was respectively evaluated under fluorescence microscope in vitro. Results: The diameter of SDION ranges from 3 nm to 8 nm, the effective diameter was 59.2 nm and the saturation magnetization was 0.23 emu/g. After SDION were reasonably oxidized, SDION could connect with pGFP-C2 to a high degree. The transfection efficiency of SDION as gene carrier was higher than that of liposome. Conclusion: The successes in connecting SDION with pGFP-C2 plasmid by means of oxidoreduction reaction and in transferring pGFP-C2 gene into human bladder cancer BIU-87 cells in vitro provided the experimental evidence for the feasibility of SDION used as a novel gene carrier.

FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis

Iron is an essential element for plant growth and development. Iron homeostasis in plants is tightly regulated at both transcriptional and posttranscriptional level. Several bHLH transcription factors involved in iron homeostasis have been identified recently. However, their regulatory mechanisms remain unknown. In this work, we demonstrate that the transcription factor FIT interacted with AtbHLH38 and AtbHLH39 and directly conferred the expression regulation of iron uptake genes for iron homeostasis in Arabidopsis. Yeast two-hybrid analysis and transient expression in Arabidopsis protoplasts showed that AtbHLH38 or AtbHLH39 interacted with FIT, a central transcription factor involved in iron homeostasis in Arabidopsis. Expression of FIT/AtbHLH38 or FIT/AtbHLH39 in yeast cells activated GUS expression driven by ferric chelate reductase （FRO2） and ferrous transporter （IRT1） promoters. Overexpression of FITwith either AtbHLH38 or AtbHLH39 in plants converted the expression of the iron uptake genes FRO2 and IRT1 from induced to constitutive. Further analysis revealed that FRO2 and IRT1 were not regulated at the posttranscriptional level in these plants because IRT1 protein accumulation and high ferric chelate reductase activity were detected in the overexpression plants under both iron deficiency and iron sufficiency. The double overexpression plants accumulated more iron in their shoots than wild type or the plants overexpressing either AtbHLH38, AtbHLH39 or FIT. Our data support that ferric-chelate reductase FRO2 and ferrous-transporter IRT1 are the targets of the three transcription factors and the transcription of FRO2 and IRT1 is directly regulated by a complex of FIT/AtbHLH38 or FIT/AtbHLH39.

Prognostic Biomarkers for Hepatocellular Carcinoma Based on Serine and Glycine Metabolism-related Genes

Background and Aims:Targeted therapy and immunotherapy have emerged as treatment options for hepatocellular carcinoma(HCC)in recent years.The significance of serine and glycine metabolism in various cancers is widely acknowledged.This study aims to investigate their correlation with the prognosis and tumor immune microenvironment(TIME)of HCC.Methods:Based on the public database,different subtypes were identified by cluster analysis,and the prognostic model was constructed through regression analysis.The gene expression omnibus(GEO)data set was used as the validation set to verify the performance of the model.The survival curve evaluated prognostic ability.CIBERSORT was used to evaluate the level of immune cell infiltration,and maftools analyzed the mutations.DsigDB screened small molecule compounds related to prognostic genes.Results:HCC was found to have two distinct subtypes.Subsequently,we constructed a risk score prognostic model through regression analysis based on serine and glycine metabolismrelated genes(SGMGs).A nomogram was constructed based on risk scores and other clinical factors.HCC patients with a higher risk score showed a poor prognosis,and there were significant differences in immune cell infiltration between the high-and low-risk groups.In addition,three potential drugs associated with prognostic genes,streptozocin,norfloxacin,and hydrocotarnine,were identified.Conclusions:This study investigated the expression patterns of SGMGs and their relationship with tumor characteristics,resulting in the development of a novel model for predicting the prognosis of HCC patients.The study provides a reference for clinical prognosis prediction and treatment of HCC patients.

Nonalcoholic steatohepatitis in Asian Indians is neither associated with iron overload nor with HFE gene mutations

AIM: The pathogenesis of occurrence of liver inflammation and fibrosis in patients with nonalcoholic steatohepatitis (NASH) is not completely understood. Other than insulin resistance, iron abnormalities have been thought to be one of the triggering factors. Therefore, our aim was to study the role of iron abnormalities and HFE gene mutations in patients with NASH. METHODS: Thirty-one patients of NASH diagnosed on the basis of clinical examination biochemistry, ultrasonography and liver biopsy (n = 14) were included in the study. Serum iron parameters (n = 23) (iron, ferritin, total iron-binding capacity and transferrin saturation), Perls' iron staining on liver biopsies (n = 14) and HFE gene mutations (C282Y and H63D) (n = 16) were studied in these patients. The association between iron staining, necroinflammatory activity and fibrosis stage on liver biopsies was also determined. RESULTS: Elevated serum iron, ferritin and transferrin saturation above 55% were observed in 4.3% of patients. On histology, 71% of the patients had negative iron staining, 21.4% had 1+ staining, 7.2% had 2+ staining and none had 3+ or 4+ staining. There was no association between the degree of iron staining and necroinflammatory activity (P=0.55) and fibrosis stage (P= 0.09) on histology. None of the patients had C282Y HFE gene mutation and four patients (25%) were found to be heterozygotes for H63D gene mutation. CONCLUSION: Our study does not favor iron overload and HFE gene mutations as major factors in the pathogenesis of NASH in Asian Indians.

Iron overload and HFE gene mutations in Polish patients with liver cirrhosis

BACKGROUND:Increased liver iron stores may contribute to the progression of liver injury and fibrosis,and are associated with a higher risk of hepatocellular carcinoma development.Pre-transplant symptoms of iron overload in patients with liver cirrhosis are associated with higher risk of infectious and malignant complications in liver transplant recipients.HFE gene mutations may be involved in the pathogenesis of liver iron overload and influence the progression of chronic liver diseases of different origins.This study was designed to determine the prevalence of iron overload in relation to HFE gene mutations among Polish patients with liver cirrhosis.METHODS:Sixty-one patients with liver cirrhosis included in the study were compared with a control group of 42 consecutive patients subjected to liver biopsy because of chronic liver diseases.Liver function tests and serum iron markers were assessed in both groups.All patients were screened for HFE mutations (C282Y,H63D,S65C).Thirty-six of 61 patients from the study group and all controls had liver biopsy performed with semiquantitative assessment of iron deposits in hepatocytes.RESULTS:The biochemical markers of iron overload and iron deposits in the liver were detected with a higher frequency (70% and 47% respectively) in patients with liver cirrhosis.There were no differences in the prevalence of all HFE mutations in both groups.In patients with a diagnosis of hepatocellular carcinoma,no significant associations with iron disorders and HFE gene mutations were found.CONCLUSIONS:Iron disorders were detected in patients with liver cirrhosis frequently but without significant association with HFE gene mutations.Only the homozygous C282Y mutation seems to occur more frequently in the selected population of patients with liver cirrhosis.As elevated biochemical iron indices accompanied liver iron deposits more frequently in liver cirrhosis compared to controls with chronic liver disease,there is a need for more extensive studies searching for the possible influence of non-HFE iron homeostasis regulators and their modulation on the course of chronic liver disease and liver cirrhosis.

DDRT-PCR Analysis of Wheat Roots Under Iron-Deficient Condition and Differential Expression of ABC Gene

Differential expression of gene in iron-efficient wheat cultivar Jing411 and iron-inefficient cul-tivar SanshumaiS under iron-deficiency and iron-sufficiency conditions was revealed by differential display reverse transcript PCR (DDRT-PCR) method. Northern blotting was carried out using ATP-binding transporter (ABC) cDNA obtained from DDRT-PCR products of the cultivar Jing411 as probe. Our results suggested that ABC gene expression was suppressed under iron-deficiency condition.

Evaluation and Application of Two High-Iron Transgenic Rice Lines Expressing a Pea Ferritin Gene

A total of 105 transgenic dce lines independently transformed with a pea ferritin gene （Fer） were previously obtained. After seven generations of selfing and β-glucuronidase （GUS） assisted selection, 82 transgenic lines with stable agronomic traits were got. Among the 82 transgenic lines, two high-iron transgenic rice lines Fer34 and Fer65, with the iron contents in the milled rice being 4.82 and 3.46 times of that of the wild type Xiushui 11, respectively were identified. In the two transgenic lines, the exogenous Fer gene was highly expressed, and inherited as a single locus. The transgene had no negative effect on the agronomic traits of rice plant, other mineral nutritional components, appearance quality and eating quality of the milled rice, indicating that these two lines were elite high-iron breeding lines. Furthermore, the practical application and further studies facilitating utilization of the two elite breeding lines were discussed.

Use of PEI-coated Magnetic Iron Oxide Nanoparticles as Gene Vectors

Summary: To evaluate the feasibility of using polyethyleneimine (PEI) coated magnetic iron oxide nanoparticles (polyMAG-1000) as gene vectors. The surface characteristics of the nanoparticles were observed with scanning electron microscopy. The ability of the nanoparticles to combine with and protect DNA was investigated at different PH values after polyMAG-1000 and DNA were combined in different ratios. The nanoparticles were tested as gene vectors with in vitro transfection models. Under the scanning electron microscope the nanoparticles were about 100 nm in diameter. The nanoparticles could bind and condense DNA under acid, neutral and alkaline conditions, and they could transfer genes into cells and express green fluorescent proteins (GFP). The transfection efficiency was highest (51 %) when the ratio of nanoparticles to DNA was 1:1 (v:w). In that ratio, the difference in transfection efficiency was marked depending on whether a magnetic field was present or not: about 10 % when it was absent but 51 % when it was present. The magnetic iron oxide nanoparticles coated with PEI may potentially be used as gene vectors.

HFE gene in primary and secondary hepatic iron overload

Distinct from hereditary haemochromatosis, hepatic iron overload is a common finding in several chronic liver diseases. Many studies have investigated the prevalence, distribution and possible contributory role of excess hepatic iron in non-haemochromatotic chronic liver diseases. Indeed, some authors have proposed iron removal in liver diseases other than hereditary haemochromatosis. However, the pathogenesis of secondary iron overload remains unclear. The High Fe （HFE） gene has been implicated, but the reported data are controversial. In this article, we summarise current concepts regarding the cellular role of the HFE protein in iron homeostasis. We review the current status of the literature regarding the prevalence, hepatic distribution and possible therapeutic implications of iron overload in chronic hepatitis C, hepatitis B, alcoholic and non- alcoholic fatty liver diseases and porphyria cutanea tarda. We discuss the evidence regarding the role of HFE gene mutations in these liver diseases. Finally, we summarize the common and specific features of iron overload in liver diseases other than haemochromatosis.

Ratio of hemoglobin to mean corpuscular volume: A new index for discriminating between iron deficiency anemia and thalassemia trait

BACKGROUND Iron deficiency anemia(IDA)and thalassemia trait(TT)are the most common microcytic and hypochromic anemias.Differentiation between mild TT and early IDA is still a clinical challenge.AIM To develop and validate a new index for discriminating between IDA and TT.METHODS Blood count data from 126 patients,consisting of 43 TT patients and 83 IDA pa-tients,was retrospectively analyzed to develop a new index formula.This formula was further validated in another 61 patients,consisting of 48 TT patients and 13 IDA patients.RESULTS The new index is the ratio of hemoglobin to mean corpuscular volume.Its sen-sitivity,specificity,accuracy,Youden’s Index,area under the receiver operating characteristic curve,and Kappa coefficient in discriminating between IDA and TT were 93.5%,78.4%,83.3%,0.72,0.97,and 0.65,respectively.CONCLUSION This new index has good diagnostic performance in discriminating between mild TT and early IDA.It requires only two results of complete blood count,which can be a very desirable feature in under-resourced scenarios.

葡萄IRT基因的克隆、鉴定及其对氨基酸-铁复合肥的响应特征

为揭示葡萄铁素吸收与转运的分子机制,明确铁调节转运蛋白编码基因VvIRT在葡萄果实不同发育时期的表达差异及其对叶面喷施氨基酸-铁复合肥的响应特征,本研究以烟酿1号为材料,分离并克隆葡萄铁调节转运蛋白编码基因IRT,分析IRT基因分布、结构及其编码蛋白质的保守基序等特征;设置叶面喷施氨基酸-铁复合肥处理,利用实时荧光定量PCR分析烟酿1号IRT基因在果实不同发育时期的表达差异及其对叶面喷施处理的响应特征。结果表明:在葡萄基因组中克隆得到10个VvIRT基因(VvIRT1~VvIRT10),分布在7条染色体上。其编码蛋白质均含有Fe^(2+)转运蛋白或锌/铁转运体(PF02535),属于典型的铁调节蛋白。VvIRT1、VvIRT2、VvIRT4、VvIRT5、VvIRT8等基因编码的蛋白质属于碱性蛋白质,而其他5个蛋白质属于酸性蛋白质。VvIRT5蛋白和VvIRT8蛋白属于不稳定蛋白,其他8个蛋白为稳定蛋白。VvIRT7蛋白主要定位于液泡膜,其他蛋白质均主要定位于细胞质膜。VvIRT7在葡萄果实不同发育时期各组织中的整体表达水平都是最高的,其次为VvIRT9和VvIRT6,而VvIRT1、VvIRT3、VvIRT5、VvIRT8和VvIRT10在葡萄果实发育过程中均无表达。叶面喷施铁肥处理下,韧皮部中VvIRT7表达量和果实及韧皮部中VvIRT9表达量在花后35 d(幼果期)至70 d(转色期)明显增加,而在花后85 d(第2次膨大期)至115 d(成熟期),韧皮部和叶片中VvIRT7和VvIRT9表达量明显减少。因此,葡萄VvIRT基因对叶面喷施铁肥的响应特征与果实发育时期及器官类型密切相关,VvIRT7、VvIRT9基因编码蛋白质是葡萄果实发育过程中2个重要的铁调节转运蛋白。

铁蓄积大鼠食管黏膜组织差异表达基因的筛选及生物学功能分析

目的筛选铁蓄积大鼠食管黏膜组织差异表达基因,并分析差异表达基因的生物学功能。方法12只6周龄雄性SD大鼠随机分为铁蓄积组和对照组,每组6只,铁蓄积组隔天腹腔注射蔗糖铁溶液制备铁蓄积模型,对照组注射等量生理盐水,14周后取血和食管、肝等组织,应用血清学、组织学方法鉴定铁蓄积造模是否成功;剥离两组食管黏膜组织,采用转录组测序技术筛选差异表达基因,并对差异表达基因进行基因本体(GO)功能富集分析及真核生物蛋白相邻类的聚簇(KOG)分类富集分析。结果筛选出9个差异表达基因,5个上调基因包括昼夜相关转录抑制因子(Ciart)、液泡蛋白质分选因子25(Vps25)、甲状腺激素应答蛋白(Thrsp)、UDP-N-乙酰氨基葡萄糖焦磷酸化酶1(Uap1)、血清解整合素—金属蛋白酶33(Adam33),4个下调基因包括过氧化物酶基因(Pxdn)、硫酸乙酰肝素蛋白多糖基因2(Hspg2)、中心体相关蛋白2(Cep2)、G蛋白信号转导调节因子4(Rgs4)。GO功能富集分析显示,上调基因的生物过程(BP)集中在节律过程、代谢过程、行为、生物过程调节、特定位置运动、生物过程的负调控、生物调节、定位、细胞过程、多细胞生物过程;细胞组成(CC)主要集中在膜封闭腔、细胞器部分、细胞器、膜、细胞外区域部分、膜部分、细胞部分、细胞;分子功能(MF)主要集中在结合、结构分子活性、催化活性。下调基因的BP主要集中在解毒、刺激反应、细胞组成或生物形成、信号、生物过程的负调控、生物过程的正调节、发育过程、细胞过程、生物过程调节、生物调节、代谢过程;CC主要集中在细胞外基质、细胞外基质组成、细胞外区域部分、细胞外区域、细胞器、膜、细胞部分、细胞;MF主要集中在酶调节活性、抗氧化活性、分子功能调节剂、受体调节活性、结构分子活性、结合、催化活性。KOG分类富集分析显示,表达上调的基因中有3个获得功能注释,Uap1被注释到细胞壁/膜/包膜生物形成,Adam33被注释到翻译后修饰,蛋白质折叠和伴侣蛋白,Vps25被注释到功能预测。表达下调的基因中有2个获得功能注释,Rgs4被注释到信号转导机制,Hspg2被注释到翻译后修饰,蛋白质折叠和伴侣蛋白。结论铁蓄积大鼠食管黏膜组织中共筛选出9个差异表达基因,包括5个表达上调基因和4个表达下调基因。GO功能富集分析显示差异表达基因主要参与的BP包括节律过程、代谢过程、细胞过程、生物过程调节等,主要参与的CC包括细胞器、膜、细胞外区域部分等,主要参与的MF包括结合、催化活性、结构分子活性。有5个差异基因获得KOG功能注释,包括翻译后修饰、蛋白质折叠和伴侣蛋白、信号转导等,主要参与细胞周期、细胞代谢、细胞增殖及氧化应激等通路。

17α-乙炔雌二醇胁迫下零价铁对硝化污泥中抗性基因的影响

采用硝化污泥序批式反应器去除17α-乙炔雌二醇(EE2),基于宏基因组测序技术考察了零价铁(ZVI)对硝化污泥去除17α-乙炔雌二醇(EE2)过程中抗生素抗性基因(ARGs)的影响,结合菌群结构分析了其潜在影响机制.结果表明,硝化污泥处理EE2过程中ARGs丰度提高了724.42TPM(每百万转录本中来自于某基因的转录本数目),但ZVI削减了此过程中的ARGs丰度增长趋势,EE2及ZVI改变了ARGs亚型的分布,但对ARGs类型及亚型种类无明显影响.EE2使得硝化污泥中属于高风险等级(Q1及Q2)的ARGs丰度增加了555.75TPM及151.08TPM,ZVI降低了硝化污泥中的抗性风险.多重耐药是硝化污泥中丰度占比最大的高风险(Q1和Q2等级)ARGs类型,占比高达49.23%.微生物群落是硝化污泥中ARGs的重要驱动因子,鞘脂单胞菌属(Sphingopyxis)等菌属与多种ARGs显著正相关,可能是多种ARGs的共同潜在宿主.

Expression of Ferric Chelate Reductase Gene in Citrus junos and Poncirus trifoliataTissues

It has been hypothesized that under iron stress high ferric chelate reductase (FCR) activity in the absorptive root of plants tolerant to iron_deficiency will be induced and result in subsequent Fe 2+ transport across the plasmalemma. The activity of FCR and expression of FCR gene (FRO2) in Citrus junos Sieb. ex Tanaka tolerant to iron_deficiency and Poncirus trifoliata (L.) Raf. susceptible to iron_deficiency were determined to elucidate the physiological difference which causes the different tolerance of the two citrus rootstocks to iron stress. The activity of FCR was detectable in excised roots and was stimulated about 20_times in C. junos and only about 3_times in P. trifoliata under iron deficiency for four weeks. The FRO2 of Arabidopsis was used as a probe, the tissue print technique was used to ascertain the expression of the FCR gene in C. junos and P. trifoliata under iron stress. High_level transcripts were observed in the absorptive root, young green stem as well as new leaf of C. junos under iron stress for two weeks, and the transcripts were accumulated only slightly in P. trifoliata at the same time. The results showed that the obvious increase of FCR activity was an important reason for the tolerance of C. junos to iron_deficiency, and the regulation of FCR activity seemed to be at the transcriptional level, and the expression of FRO2 occurred in the root, stem and leaf.

二氢卟吩铁调控辣椒对高温胁迫的耐性及相关基因的表达

为评估高温胁迫下二氢卟吩铁(Iron chlorine e6,ICE6)缓解辣椒幼苗高温伤害效应及对耐高温胁迫相关基因表达量的影响。本研究以艳椒465为供试品种,探究高温胁迫下,二氢卟吩铁对辣椒幼苗相对电导率、可溶性糖含量、抗氧化酶活性、脯氨酸含量等生理生化指标和耐高温相关基因表达的影响。试验结果表明,高温胁迫下,与清水对照比,喷施0.2μg/ml二氢卟吩铁可提高辣椒叶片中可溶性糖、脯氨酸、还原型谷胱甘肽含量,增强超氧化物歧化酶、过氧化物酶活性,降低相对电导率及丙二醛含量;二氢卟吩铁能提高CaWRKY19、CaWRKY55和CaWRKY40耐高温胁迫相关基因的表达。由此可见,用0.2μg/ml二氢卟吩铁处理可显著提高辣椒耐高温胁迫能力。

基于生物信息学对骨关节炎铁超载关键基因的筛选与验证

背景:铁超载是指体内铁积累过多的情况,可引起各种组织的病理改变。目前,对于骨关节炎中铁超载相关的分子机制和潜在基因靶点,仍有待进一步的研究和探索。目的:通过生物信息学手段分析骨关节炎铁超载关键基因,并利用动物实验加以验证,以期为铁超载角度防治骨关节炎提供新的思路。方法:使用GEO数据库和GeneCards数据库筛选出与骨关节炎相关的基因和铁超载相关的基因。然后,取两者的交集,得到骨关节炎和铁超载共同相关的基因集合。采用GO和KEGG富集分析筛选这些基因的功能和通路。为了进一步研究这些基因之间的相互作用,构建PPI网络,并利用Cytoscape软件的5种计算方法来识别骨关节炎铁超载的关键基因(Hub基因)。将12只雄性SD大鼠分为骨关节炎组与对照组(正常大鼠),每组6只,骨关节炎组大鼠采用改良Hulth方法建立膝骨关节炎模型,并使用PCR检测Hub基因在两组大鼠膝关节组织中的表达情况。结果与结论:①共获得51个骨关节炎铁超载基因,GO富集分析表明其主要参与细胞因子受体结合、趋化因子受体结合、细胞因子活性、生长因子受体结合及寡糖结合等过程;②KEGG富集分析表明骨关节炎铁超载基因主要参与肿瘤坏死因子信号通路、脂质和动脉粥样硬化等信号通路;③构建蛋白质-蛋白质相互作用网络,进一步分析获得细胞间黏附分子1(intercellular cell adhesion molecule-1,ICAM-1)、肿瘤坏死因子配体超家族成员11(tumor necrosis factor superfamily member 11,TNFSF11)、骨髓瘤细胞癌基因(myelocytomatosis oncogene,MYC)、Janus激酶2(janus kinase 2,JAK2)及白细胞介素6,5个骨关节炎铁超载Hub基因,动物实验证实其在对照组与骨关节炎组大鼠膝关节组织中的表达有显著差异(P<0.05);④结果显示,ICAM-1,TNFSF11,MYC,JAK2及白细胞介素6可作为骨关节炎铁超载的关键基因,有望成为防治骨关节炎的新靶点。

苗药紫金牛、铁扫帚组方干预慢性阻塞性肺疾病大鼠气道Wnt通路RhoA基因与TGF-β_(1)、MMP-9的相关性研究

目的研究苗药紫金牛、铁扫帚组方干预COPD大鼠气道Wnt通路RhoA基因与TGF-β_(1)、MMP-9的相关性,从而探讨苗药紫金牛、铁扫帚配方干预COPD大鼠气道重塑的调控机制。方法构建COPD大鼠模型,进行气道成纤维细胞的培养,采用ELISA检测气道成纤维细胞上清液中TGF-β_(1)、MMP-9细胞因子的含量,并运用Westernblot方法检测气道成纤维细胞中RhoA基因蛋白的表达,从而研究RhoA基因表达与TGF-β_(1)、MMP-9细胞因子的相关性及苗药紫金牛、铁扫帚的影响。结果与正常组相比,COPD大鼠模型组气道成纤维细胞上清液中TGF-β_(1)、MMP-9的含量升高,同时RhoA基因在也是表达增高。经苗药紫金牛、铁扫帚治疗后,细胞因子TGF-β_(1)、MMP-9与RhoA基因的表达则降低,从而得出TGF-β_(1)、MMP-9细胞因子与RhoA基因呈正相关。结论COPD大鼠气道成纤维细胞上清液中TGF-β_(1)、MMP-9细胞因子是COPD大鼠气道重建中成纤维细胞增殖的关键因子。而RhoA基因对组织纤维化有关,且能调控细胞因子TGF-β_(1)、MMP-9。苗药紫金牛、铁扫帚能够抑制炎性因子TGF-β_(1)、MMP-9的表达及WNT通路的RhoA基因的增殖,从而寻求苗药紫金牛、铁扫帚配方干预COPD气道重塑的机制。

施硅水平对水稻根表铁膜和体内Cd累积分布的影响

稻田镉(Cd)污染治理是中国当前亟需解决的重大科学问题;根表铁膜是水稻根系吸收Cd的重要屏障,施硅(Si)调控水稻根系抗氧化酶和乙烯合成酶活性影响根表铁膜对Cd的吸附,并改变水稻体内Cd的累积和分布,但不同施Si水平对水稻根表铁膜和体内Cd累积分布的影响尚未完全清楚。采用水稻盆栽试验,探讨高、低两种施Si水平条件下,水稻成熟期不同组织器官中Cd的含量、分布规律和水稻体内Cd的转运能力,以及抽穗期根表铁膜的Cd含量、形貌特征与根系抗氧化酶和乙烯合成酶基因的表达,试图揭示不同施Si水平对水稻根表铁膜Cd吸附和体内Cd累积分布的影响。结果表明,施Si会减少成熟期水稻茎中Cd的含量,增大根系中Cd的分布比例,而高Si水平(0.66 g·kg^(-1))还会进一步降低茎节和糙米中Cd的含量和分布比例,抑制根系转运Cd至糙米的能力。此外,施Si可以增强抽穗期水稻根系超氧化物歧化酶基因(OsSOD-Cu/Zn和OsSOD-Fe)、过氧化氢酶基因(OsCATa和OsCATb)以及乙烯合成酶基因(OsACS1)的表达,高Si水平(0.66 g·kg^(-1))能够显著增加根表铁膜中的DCB-Fe和DCB-Cd含量,增大根表铁膜的表面粗糙度,并且进一步增强根系OsSOD-Fe和OsACS1的表达。研究结果证实施Si水平是影响水稻根表铁膜和体内Cd累积分布的关键因素,高水平Si能够更显著地促进水稻根系抗氧化酶基因的表达,增强铁膜形成及其对Cd的吸附,并且抑制根系Cd向糙米的转运和茎节中Cd的分布,从而降低糙米中Cd的累积。该研究成果可为解决中国稻田Cd污染治理难题提供理论依据。