WO2023280243A1 - miR-339-增强子-靶基因网络激活模型及其应用 - Google Patents
miR-339-增强子-靶基因网络激活模型及其应用 Download PDFInfo
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Definitions
- the invention relates to the field of biotechnology, in particular to a miR-339-enhancer-target gene network activation model and its application.
- non-coding RNA is a basic scientific research that has been gradually recognized by scientists in recent years and quickly invested in it, aiming to understand the mystery of life in essence.
- miRNAs microRNAs
- LncRNAs long non-coding RNAs
- miRNAs are small non-coding RNAs with a length of 21-25 nucleotides that regulate gene expression at the post-transcriptional level.
- the first miRNA lin-4 was accidentally discovered more than 30 years ago when studying the developmental regulation of nematodes, and was shown to inhibit protein translation or degrade mRNA by binding to the 3'UTR of lin-14 mRNA in the cytoplasm.
- miRNAs Since then, the negative regulatory mechanism of miRNA has almost become the "golden rule" in the field of miRNA research. Although some miRNAs were later found to be able to promote gene expression or translation under special circumstances, they were basically case studies, limited to phenomenon descriptions and simple mechanism studies, which left follow-up researchers at a loss and lacked the significance of generalization. On the other hand, although miRNAs are involved in most life phenomena and processes, the regulation of miRNAs in vivo is usually considered as a fine-tune, and does not play a decisive "switch" role.
- Enhancer has always been considered as an important DNA sequence cis-regulatory element, which can regulate gene expression in close or long distance.
- H3K4me1 and H3K27ac are important epigenetic marks of enhancers, and H3K27ac is closely related to the activity of enhancers.
- Super-enhancers can be formed when multiple transcriptionally active enhancers enrich transcription factors at high density. Enhancers, especially super-enhancers, can usually drive the expression of genes that control cell identity and cell fate, and play an important role in cell differentiation, tissue development, individual growth and disease pathogenesis.
- Malignant tumors are a global public health problem that endangers human health. As a large developing country, my country has increasingly prominent problems of industrialization, urbanization, and population aging. Unhealthy lifestyles and environmental pollution directly lead to a decline in national health index. Malignant tumors urgently need to wait capture.
- miRNA research has been proven to play an important regulatory role in the development and migration of breast cancer. Relevant research is usually based on the traditional negative regulatory mechanism of miRNA. So far, there has been no substantial breakthrough on how to use miRNA to overcome breast cancer, and there is still a lack of effective therapeutic drugs and treatment options.
- miRNA is a classic nucleic acid molecule. Nucleic acid drugs are considered to be the next generation of drugs after antibody drugs and cellular immunotherapy. They can achieve effects that cannot be replaced by traditional drugs. For example, antibodies mostly function on the cell surface, while nucleic acid drugs can enter cells Internally play a therapeutic role; some nucleic acid drugs can even enter the nucleus to play a precise targeted therapeutic effect.
- Onpattro patisiran
- a new RNAi drug approved by the US FDA in 2018, is a nucleic acid drug.
- the main treatment method is to encapsulate siRNA in lipid nanoparticles and deliver the drug directly to the liver, by targeting and silencing TTR mRNA, hindering the production of targeted TTR protein, thereby reducing the accumulation of amyloid deposits in peripheral nerves, and eventually
- hATTR hereditary transthyretin
- This invention applies the creative "miRNA-enhancer-target gene network activation model” theory for the first time to explain the occurrence and development of breast cancer, that is, miR-339 in the nucleus interacts with enhancers to positively activate target genes to affect tumor growth Proliferation and growth, this theory is completely different from the prior art "negative regulation mechanism of miRNA”.
- This application screened multiple miRNAs located in the enhancer region, respectively overexpressed these miRNAs in different types of cells, and found that multiple genes adjacent to these miRNAs on the genome were transcriptionally activated, and these miRNAs regulated the transcriptional activation of genes Relies on the integrity of the miRNA and its targeting enhancer sequences. Based on this, this application uses the screened miRNAs to reveal the function of miRNAs in the nucleus, providing a new perspective for analyzing the involvement of miRNAs in the occurrence and development of diseases such as tumors.
- miR-339 and the target gene GPER1 tend to be low-expressed in breast cancer clinical tissue samples, and further verification found that miR-339 positively regulates the expression of the GPER1 gene through an enhancer, thereby inhibiting the occurrence and development of breast cancer tumors. If new breast cancer drugs are developed from the perspective of nucleic acid drugs, then miR-339 may bring good news to patients with these diseases.
- the present invention adopts the following technical solutions:
- the first aspect of the present invention discloses a miRNA capable of activating breast cancer-related genes, the position of the gene locus of the miRNA coincides with the histone modification mark H3K4me1 or H3K27ac of the enhancer.
- the breast cancer is Luminal breast cancer and triple-negative breast cancer.
- miRNA means MicroRNAs, which refers to a class of endogenous non-coding RNAs with regulatory functions found in eukaryotes, with a size of about 20-25 nucleotides. Mature miRNAs are produced by a series of nuclease cleavage and processing of longer primary transcripts, and then assembled into RNA-induced silencing complexes, which recognize target mRNAs through complementary base pairing, and according to the degree of complementarity Differently direct the silencing complex to degrade the target mRNA or to repress the translation of the target mRNA.
- nucleotide sequence of the miRNA is as shown in SEQ ID NO: 1, or
- the sequence of the miRNA is 90% homologous and functionally identical to the SEQ ID NO: 1.
- the SEQ ID NO: 1 sequence from 5' ⁇ 3' is: UCCCUGUCCUCCAGGAGCUCACG.
- the breast cancer-related gene is GPER1 (G protein-coupled estrogen receptor 1) gene.
- the second aspect of the present invention discloses a nucleic acid drug, which includes the above-mentioned miRNA or its artificial mimic; preferably, the nucleic acid drug further includes a pharmaceutically acceptable carrier or excipient.
- the pharmaceutical dosage form of nucleic acid includes powder, tablet, granule, capsule, solution, aerosol, injection, emulsion or suspension.
- the fourth aspect of the present invention is a biological material related to the above-mentioned nucleic acid drug, the biological material is selected from one of the following A), B) or C):
- the expression vector includes at least one of pCDH vector, pCMVp-NEO-BAN vector, pEGFP vector, pEGFT-Actin, pSV2 vector, pCDNA vector, pLVX vector, pAAV vector, pET vector and pDsRed vector.
- the step of constructing the recombinant vector comprises: 1) designing primers, PCR amplifying the miRNA sequence; 2) digesting the amplified sequence fragment and the expression vector, and connecting the target sequence fragment and the expression vector; 3) connecting the sequence fragment and the expression vector; The product is transformed into Escherichia coli and cultivated; 4) After identification, the recombinant plasmid is extracted and packaged to obtain the recombinant vector.
- the fifth aspect of the present invention discloses the application of the above-mentioned miRNA or the above-mentioned nucleic acid drug in the diagnosis, prevention and/or treatment of breast cancer.
- the sixth aspect of the present invention discloses a method for screening the aforementioned miRNAs that can activate disease-related genes, comprising the following steps:
- step S2 verifying the relationship between the miRNA screened in step S1 and the target gene within 200kb around it;
- the method for verifying the relationship between the miRNA and its surrounding target genes within 200kb includes: detecting the expression level of the target gene after the miRNA is overexpressed by real-time fluorescent quantitative PCR.
- the seventh aspect of the present invention discloses a model for studying the mechanism of breast cancer, the model is a miRNA-enhancer-target gene network activation model.
- the miRNA interacts with the enhancer to positively activate the target gene to affect the proliferation and growth of the tumor, and the miRNA is miR-339;
- the method for constructing the model includes: screening multiple miRNAs located in the enhancer region, respectively overexpressing the miRNAs in different types of cells, and finding that multiple genes adjacent to the miRNAs on the genome are transcribed Activation; get miRNA-enhancer-target gene network activation model.
- the eighth aspect of the present invention discloses the application of the above model in the field of breast cancer; preferably, the application of the model in the preparation of drugs for treating breast cancer.
- the inventors conducted a systematic bioinformatics analysis on 1594 miRNA precursors in different tissue cells in the early stage, and found that the positions of more than 300 miRNA precursors in the genome highly overlapped with the histone modification marks H3K4me1 or H3K27ac of enhancers . It was also found that most of these miRNAs can be localized in the nucleus, and further studies have found that these miRNAs can bind to enhancers, thereby activating gene expression at the genome-wide level. In view of the fact that both enhancer and miRNA are involved in processes such as individual development and disease occurrence, the inventors linked the two to explore their important roles in the occurrence of tumors and other diseases.
- the present invention firstly overexpresses the miRNA miR-339 gene sequence, activates the expression level of surrounding genes, and affects the biological function of the breast cancer cell line.
- the above screening and verification have good application value in the diagnosis and detection of breast cancer and drug development.
- the miR-339 involved in the present invention can activate the expression of genes through enhancers, and is closely related to breast cancer, and its artificially synthesized analogs or inhibitors can be used in the development of nucleic acid drugs.
- the present invention Compared with the prior art, the present invention has the following advantages: the present invention provides that miR-339, which can activate disease-related genes, is related to breast cancer, and provides new strategies and potential drug targets for the diagnosis and treatment of breast cancer and other diseases. Moreover, the present invention applies the theory of "miRNA-enhancer-target gene network activation model" to explain the occurrence and development of breast cancer for the first time, that is, miR-339 in the nucleus interacts with enhancers to positively activate target genes, thereby affecting tumor growth and development. Proliferation and growth, this theory is completely different from the prior art "negative regulation mechanism of miRNA", and overcomes the prejudice of the prior art.
- Figure 2 shows the expression levels of miR-339 and target gene GPER1 in the breast cancer cell line 4175 in Example 2 of the present invention
- Fig. 3 is the dual fluorescein reporter gene experiment detection enhancer sequence activity in the embodiment 3 of the present invention.
- Figure 4 illustrates the effect of the expression of miR-339 on enhancer activity in the double fluorescein reporter gene experiment in Example 3 of the present invention
- FIG. 5 shows that after the ChIP-seq analysis in Example 3 of the present invention overexpressed miR-339, the enrichment of H3K27ac near the position of miR-339 DNA locus was significantly higher than that of the control group;
- Fig. 6 shows that the overexpression of miR-339 in Example 3 of the present invention can activate enhancer activity.
- Figure 7 shows that miR-339 was overexpressed after knocking out the enhancer sequence in Example 3 of the present invention, and the target gene GPER1 could not be reactivated;
- FIG. 8 is a graph showing the proliferation ability of breast cancer cell line 4175 with miR-339 overexpression in Example 3 of the present invention.
- FIG. 9 is a graph showing the proliferation ability of breast cancer cell line T47D with miR-339 overexpression in Example 3 of the present invention.
- Fig. 10 is a diagram of the proliferation ability of breast cancer cell line 4175 after interfering with the expression of GPER1 in Example 3 of the present invention.
- Fig. 11 is a diagram of the proliferation ability of the breast cancer cell line T47D after interfering with the expression of GPER1 in Example 3 of the present invention.
- Figure 12 is a clone formation diagram of breast cancer cell line 4175 overexpressing miR-339 in Example 3 of the present invention.
- Figure 13 is a clone formation diagram of the breast cancer cell line T47D overexpressing miR-339 in Example 3 of the present invention.
- Figure 14 is a diagram of the clone formation of the breast cancer cell line 4175 after interfering with the expression of GPER1 in Example 3 of the present invention.
- Figure 15 is a diagram of the clone formation of the breast cancer cell line T47D after interfering with the expression of GPER1 in Example 3 of the present invention.
- Figure 16 is a diagram of the tumors of three groups of mice in Example 3 of the present invention.
- FIG 17 is a statistical chart of the tumor weights of the three groups of mice in Example 3 of the present invention ("Tumor weight (g)" in the figure refers to "tumor weight”).
- the term "protein” is a general term for different peptides consisting of 25 natural amino acids in different compositions and arrangements, ranging from dipeptides to complex linear and circular structures, and is a multifunctional compound derived from proteins.
- Active peptides have a variety of human metabolism and physiological regulation functions, are easy to digest and absorb, and have the functions of promoting immunity, hormone regulation, antibacterial, antiviral, lowering blood pressure, and lowering blood fat. They are extremely safe to eat and are currently the most popular in the international food industry. Research topics and highly promising functional factors.
- the term "cloning” refers to duplication, copying and doubling, that is, to produce the same copy from the prototype, whose appearance and genetic genes are exactly the same as the prototype.
- sequencing refers to a method for determining the sequence of a gene.
- This embodiment is the construction of miR-339 overexpression vector, and its steps mainly include:
- the DNA sequence information of pri-miR-339 was obtained from the UCSC database and the miRbase database, and the relevant primer sequences were designed using Primer 5.0 software, and then the applicability of the primers was tested by BLAST.
- the primers were synthesized by Shanghai Sonny Biotechnology Co., Ltd.
- the final designed primers are: PCDH339-EcoRI-F and PCDH339-BamHI-R.
- PCDH339-EcoRI-F GAAGATTCTAGAGCTAGCGAATTCGGCCACAGGCAGGTGCCACC (SEQ ID NO: 2);
- PCDH339-BamHI-R GCAGATCCTTCGCGGCCGCGGATCCACACCAGTGGAACATCCCATGC (SEQ ID NO: 3).
- KODFX High Fidelity Enzyme was purchased from TOYOBO Company, product number KFX-101.
- PCR products were detected by 1% agarose gel electrophoresis, and the target fragment was recovered using a common agarose gel DNA recovery kit (Tiangen Biochemical Technology Co., Ltd.).
- Enzyme digestion and purification refers to the enzyme digestion system on the NEB website, which is digested overnight at 37°C, and then purified and recovered using a PCR product recovery kit (Tiangen Biochemical Technology Co., Ltd.).
- the digested PCR product was ligated with the digested pCDH vector, and ligated overnight at 16°C.
- 2 ⁇ Taq Master Mix was purchased from lifetech company.
- the miR-339 sequence was overexpressed in breast cancer cells T47D and 4175, and the expression levels of surrounding genes were detected.
- Encapsulation of lentivirus by liposome method According to molecular cloning, the plasmid pCDH-miR339 obtained in Example 1, the virus packaging plasmid psPAX2 and the capsid plasmid pMD2.G-VSVG were transferred into 293T cells. The supernatant was collected once after 48h and 72h respectively, and the collected supernatant was filtered through a 0.45 ⁇ m filter to obtain the lentivirus stock solution.
- Infected cells spread the cells to be infected in 6cm culture dishes at a rate of ⁇ 200,000 per dish in advance, and perform the first infection after the cells adhere to the wall on the second day, and repeat the infection once on the third day; on the fourth day The cells were allowed to recover for one day without any stimulation; on the fifth day, drug screening was carried out on the corresponding drug-killing markers carried by the plasmids.
- Takara (D2680A) reverse transcription PCR kit was used for reverse transcription.
- Reverse transcription PCR conditions 42°C for 10 minutes, 95°C for 2 minutes.
- Takara real-time fluorescent quantitative PCR kit was used to detect the expression of the target gene at the transcriptional level.
- the miR-339 expression plasmid (PSR-339) and the pGL 3-p-339 vector inserted into the miR-339 locus were simultaneously transfected into 293T cells for a double-fluorescein reporter gene experiment.
- the results showed that after cotransfection of miR-339 expression plasmid (PSR-339) and pGL3-p-339 vector inserted into miR-339 locus, the reporter gene activity was significantly higher than that of the control group transfected only with pGL3-p-339 vector The activity was higher, suggesting that the enhancer activity was enhanced by miR-339 (Fig. 4-a,b).
- H3K27ac ChIP-purified DNA from the experimental group and control group that overexpressed miR-339 in 293T cells, and the qualified library was analyzed by high-throughput sequencing to determine whether the enhancer near miR-339 was overexpressed by miR -339 activated.
- H3K27ac ChIP-seq data analysis results ( Figure 5) and QPCR results ( Figure 6) showed that, compared with the control cells, a DNA sequence located about 60 kb upstream of the GPER1 gene was significantly enriched in H3K27ac after miR-339 overexpression set, suggesting that this region is an enhancer activated by miR-339, and this location coincides with the miR-339 locus.
- Example 3 miR-339 inhibits the proliferation of breast cancer cells by targeting and activating the target gene GPER1
- Example 2 On the basis of Example 2, further detect and evaluate the proliferation ability of breast cancer cell lines 4175 and T47D stably expressing miR-339 constructed by lentivirus through the proliferation of CCK8.
- each group was set up as a control group: breast cancer cell lines 4175 and T47D transfected with empty virus fluid.
- Example 2 further detect and evaluate the proliferation ability of breast cancer cell lines 4175 and T47D stably expressing miR-339 constructed by lentivirus through the proliferation of clone formation.
- each group was set up as a control group: breast cancer cell lines 4175 and T47D transfected with empty virus fluid.
- Figure 16 is a graph of tumors in each group
- Figure 17 is a statistical graph of tumor weight.
- the nude mice tumors in the experimental group overexpressing miR-339 were significantly smaller than those in the control group, suggesting that miR-339 has the potential to inhibit the occurrence and development of breast cancer tumors; after overexpressing miR-339 and re-knocking down GPER1, the nude mice formed tumors The size is larger than that of nude mice in the experimental group overexpressing miR-339, indicating that GPER1 can inhibit tumor growth in nude mice.
- miR-339 is located on chromosome 7 of the human genome.
- Current research focuses on the involvement of miR-339 in tumor development and metastasis through negative regulation of target genes.
- the present application first finds that miR-339 is a key factor in the occurrence and development of breast cancer through bioinformatics analysis.
- exogenous miR-339 was overexpressed in Luminal breast cancer and triple-negative breast cancer cell lines T47D and 4175, respectively, and the results showed that after overexpression of miR-339, the expression of tumor suppressor gene GPER1 in these two breast cancer cells Both of them were up-regulated, and their proliferation and clonogenic ability were significantly inhibited.
- GPER1 is a G protein-coupled receptor, which has been reported many times as a tumor suppressor gene to be down-regulated or inactivated in estrogen-related cancers, and is associated with poor prognosis of tumors.
- the research results of this application suggest that miR-339 analogs or mimics can be used as a potential strategy for the treatment of triple-negative breast cancer.
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Abstract
Description
Claims (11)
- 一种可激活乳腺癌相关基因的miRNA,其特征在于,所述miRNA的基因座位置与增强子的组蛋白修饰标志H3K4me1或H3K27ac重合。
- 根据权利要求1所述的miRNA,其特征在于,所述miRNA的核苷酸序列如SEQ ID NO:1所示,或所述miRNA的序列为与所述SEQ ID NO:1具有90%同源性且功能相同的序列。
- 根据权利要求1所述的miRNA,其特征在于,所述乳腺癌相关基因为GPER1基因。
- 一种核酸药物,其特征在于,所述核酸药物包括权利要求1-3任一项所述的miRNA或其人工模拟物;优选的,所述核酸药物还包括药学上可接受的载体或赋形剂。
- 一种与权利要求4所述的核酸药物相关的生物材料,其特征在于,所述生物材料选自下述A)、B)或C)中的一种:A)与权利要求1-3任一项所述的miRNA的核苷酸序列互补配对的干扰RNA分子或者抑制剂;B)包含有权利要求1-3任一项所述miRNA的核苷酸序列的表达载体或重组载体;C)包含有B)中所述的表达载体或重组载体的细胞或微生物。优选的,所述表达载体包括pCDH载体、pCMVp-NEO-BAN载体、pEGFP载体、pEGFT-Actin、pSV2载体、pCDNA载体、pLVX载体、pAAV载体、pET载体和pDsRed载体中的至少一种。优选的,所述重组载体构建步骤包括:1)设计引物,PCR扩增所述miRNA序列;2)将扩增的序列片段和表达载体酶切,连接目的序列片段和表达载体;3)将连接产物转化大肠杆菌,培养;4)鉴定后提取重组质粒并进行包装即得到重组载体。
- 权利要求1-3任一项所述的miRNA或权利要求4所述的核酸药物在诊断、预防和/或治疗乳腺癌中的应用。
- 一种筛选权利要求1-3任一项所述的可激活疾病相关基因的miRNA的方法,其特征 在于,包括以下步骤:S1、通过生物信息学分析,筛选基因座位置与H3K4me1或H3K27ac重合的miRNA;S2、验证步骤S1筛选的miRNA与其周围200kb范围内的靶基因的关系;S3、获取S2中与所述靶基因具有相关性的miRNA,即为可激活疾病相关基因的miRNA。
- 根据权利要求7所述的方法,其特征在于,步骤S2中,验证miRNA与其周围200kb范围内的靶基因的关系的方法包括:实时荧光定量PCR检测过表达所述miRNA后所述靶基因的表达量。
- 一种用于研究乳腺癌机制的模型,其特征在于,所述模型为miRNA-增强子-靶基因网络激活模型。
- 根据权利要求9所述的模型,其特征在于,miRNA与增强子互相作用进而正向激活靶基因从而影响肿瘤的增殖生长,所述miRNA为miR-339;优选的,所述模型的构建方法包括:筛选位于增强子区域的多个miRNA,分别将所述miRNA在不同种类的细胞中过表达,发现在基因组上与所述miRNA邻近的多个基因被转录激活;得到miRNA-增强子-靶基因网络激活模型。
- 根据权利要求9-10所述的模型在乳腺癌领域中的应用;优选的,所述模型在制备治疗乳腺癌药物中的应用。
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| CN119799702A (zh) * | 2025-01-06 | 2025-04-11 | 河南农业大学 | miR-31-5p模拟物在增强金龟子绿僵菌对烟粉虱杀伤效果中的应用 |
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| CN105586401A (zh) * | 2015-12-14 | 2016-05-18 | 常州杰傲医学检验所有限公司 | 一种用于乳腺癌诊断的miRNA标志物、其应用及诊断试剂盒 |
| CN113528522A (zh) * | 2021-07-09 | 2021-10-22 | 复旦大学 | miR-339-增强子-靶基因网络激活模型及其应用 |
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| CN107488735B (zh) * | 2017-10-10 | 2019-11-05 | 广州医科大学附属第二医院 | miR-339-5p在抑制前列腺癌骨转移及TGF-β信号通路中的应用 |
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| CN105586401A (zh) * | 2015-12-14 | 2016-05-18 | 常州杰傲医学检验所有限公司 | 一种用于乳腺癌诊断的miRNA标志物、其应用及诊断试剂盒 |
| CN113528522A (zh) * | 2021-07-09 | 2021-10-22 | 复旦大学 | miR-339-增强子-靶基因网络激活模型及其应用 |
Non-Patent Citations (3)
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| DATABASE NUCLEOTIDE 3 March 2015 (2015-03-03), ANONYMOUS : "TPA: Homo sapiens microRNA hsa-miR-339-5p", XP093021164, retrieved from NCBI Database accession no. LM379269.1 * |
| WANG YAN: "The Screening of Invasion-related miRNAs in Breast Cancer Cell and the Preliminary Study on Biological Function of hsa-miR-339-5p", MEDICINE AND HEALTH SCIENCES, CHINA MASTER'S THESES/DOCTORAL DISSERTATIONS FULL-TEXT DATABASE (MASTER), no. 1, 15 January 2011 (2011-01-15), XP093021144 * |
| WU YAN, WENYU GAO, SUPING GAO, ZHIHONG LI: "Application value of serum miR-196a-5p and miR-339-5p expression levels in diagnosis of breast cancer", ZHONGGUO PUTONG WAIKE ZAZHI = CHINESE JOURNAL OF GENERAL SURGERY, ZHONGNAN DAXUE, CENTRAL SOUTH UNIVERSITY, CN, vol. 30, no. 5, 31 May 2021 (2021-05-31), CN , pages 551 - 557, XP093021146, ISSN: 1005-6947, DOI: 10.7659/j.issn.1005-6947.2021.05.007 * |
Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN119799702A (zh) * | 2025-01-06 | 2025-04-11 | 河南农业大学 | miR-31-5p模拟物在增强金龟子绿僵菌对烟粉虱杀伤效果中的应用 |
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