BLV-miRNA跨界调控人类靶基因预测及生物信息学分析

doi:10.3864/j.issn.0578-1752.2021.03.019

Abstract

Abstract:

【Objective】To assess risk of regulation of human-derived genes by miRNAs derived from bovine leukemia virus (BLV), the prospective research on the possible food safety problems and the possible impact on human health caused by BLV-miRNA were carried out, which would lay the foundation for the necessary research on the implementation of Enzootic Bovine Leukosis (EBL) prevention and control measures in actual production in the future, and provide theoretical guidance for the study of the relationship between BLV and human diseases.【Method】 In this study, the mature sequence of BLV miRNAs was first queried using mirbase website, and the miRanda software was used to predict target genes. The predictive 10 miRNAs (BLV-miR-B1-3P,5P, BLV-miR-B2-3P, 5P, BLV-miR-B3-3P,5P, BLV-miR-B4-3P,5P, and BLV-miR-B5-3P,5P) were encoded by BLV. The top 10 candidate target genes of each BLV-miRNA score were selected for functional analysis, including a total of 88 duplicated genes. The candidate target genes co-regulated by multiple BLV miRNAs were verified by secondary prediction using RNAhybrid software, and their functions were analyzed. 【Result】The ten miRNAs encoded by BLV were predicted to obtain 1 630-16 383 target genes, respectively. After functional analysis of eighty-eight candidate target genes in the top ten, it was found that eighteen of them had no relevant functional reports. Thirty-six candidate target genes were related to the occurrence and development of neoplastic diseases. Two candidate target genes could regulate cell cycle. Sixteen candidate target genes were involved in the regulation of cell signal transduction. Fourteen candidate target genes played a role in the formation of structure/cytoskeleton proteins. The function of cell proliferation and apoptosis showed an antagonistic relationship and the genes that often promoting proliferation could also suppress apoptosis. A total of thirteen genes played a regulatory role in cell proliferation and apoptosis. Interestingly, the regulation of the thirteen candidate target genes on cell proliferation and apoptosis was bidirectional. However, it was not clear whether the regulation of BLV miRNA towards cells was more prone to proliferation or apoptosis, so further studies were still needed to discuss in depth. Two candidate target genes could regulate cell differentiation. The sixteen candidate target genes played a role in regulating cell migration/invasion function, again suggesting that BLV miRNA might have a more important correlation with neoplastic diseases. The seven candidate target genes might play an important role in the differentiation, migration and invasion of breast cells, suggesting that the study on the correlation between BLV and human breast cancer could be further discussed from the perspective of BLV miRNA. Two candidate target genotypes of BLV-B4-3P, Collagen 1 chain gene (COL1A1), had a regulatory effect on human acute lymphoblastic leukemia (ALL). In addition, candidate target genes that could be co-targeted by multiple BLV miRNAs belong to the mucin family (MUC5B, MUC12 and MUC16), and be expressed in the colon, influencing the formation of colon mucosa.【Conclusion】Exogenous BLV miRNA might transboundary regulate cell cycle signal transduction structure/cytoskeleton proliferation apoptosis differentiation migration/invasion related cell function related genes and destroy cell structure. The correlation between BLV miRNA and human breast cancer might be shown in the process of differentiation, migration and invasion of human breast cancer cells. BLV-miR-B4-3p shared a seed sequence with miR 29a, which might affect the occurrence and development of human acute lymphoblastic leukemia. Exogenous BLV miRNA had the target of inhibiting the expression of mucin genes, such as MUC5B, MUC12, and MUC16, through the destruction of intestinal mucosa formation to achieve transboundary regulation of human gene risk.

Key words: bioinformatics, bovine leukemia virus, transboundary regulation, human-derived genes, miRNA

WANG Yong,LI SiYan,HE SiRui,ZHANG Di,LIAN Shuai,WANG JianFa,WU Rui. Prediction and Bioinformatics Analysis of BLV-miRNA Transboundary Regulation of Human Target Genes[J].Scientia Agricultura Sinica, 2021, 54(3): 662-674.

Figures/Tables 13

Table 1

Fig. 1

Table 2

Table 3

Candidate target genes involved in cell signal transduction"

序号 Number	基因名称 Gene name	miRNA miRNA	评分 Score	与信号转导关系 Relationship with signal transduction
1	NOTCH3	BLV-miR-B1-3p	600	编码果蝇I型膜蛋白缺口的人类同源物,建立细胞间信号传导途径,其在神经发育中起关键作用 The human homologues encoding gaps in Drosophila type I membrane proteins, establishing intercellular signal transduction pathways, which play a key role in neural development
2	MUC12	BLV-miR-B1-5p	4260	编码膜糖蛋白,在细胞内信号传导中发挥作用/黏液素在上皮表面形成的保护性黏液屏障中起重要作用 It encodes membrane glycoproteins and plays a role in intracellular signaling, and mucin plays an important role in the protective mucus barrier formed by the epithelial surface
3	MUC21	BLV-miR-B1-5p	3738	膜结合糖蛋白,在上皮表面形成保护性黏膜屏障中起重要作用,也在细胞内信号传导中起作用 Membrane-bound glycoproteins play an important role in the formation of a protective mucosal barrier on the epithelial surface and in intracellular signaling
4	ATF3	BLV-miR-B2-5p	180	编码哺乳动物激活转录因子;参与细胞应激反应 Encode mammalian activation transcription factors and participate in cellular stress response
5	NR2C2	BLV-miR-B2-5p	179	该基因编码属于核激素受体家族的蛋白质,该家族的成员充当配体激活的转录因子 The gene encodes proteins belonging to the nuclear hormone receptor family, members of which act as ligand-activated transcription factors
6	OR14I1	BLV-miR-B2-5p	187	负责识别和G蛋白介导的气味信号转导 Responsible for recognition and G protein-mediated odor signal transduction
7	POU3F3	BLV-miR-B2-3p	444	该基因编码含有POU结构域的蛋白质,该蛋白质起着转录因子的作用 The gene encodes a protein containing a POU domain, which acts as a transcription factor
8	TIAL1-201	BLV-miR-B2-5p	180	该基因编码的蛋白质是RNA结合蛋白家族的成员,调节各种活动,包括翻译控制,剪接和凋亡 The gene encodes proteins that are members of the RNA-binding protein family and regulate various activities including translation control, splicing, and apoptosis
9	TXNL1-204	BLV-miR-B2-5p	175	TXNL1- XRCC1是一种新型的调控途径,氧化还原传感器TXNL1在液相内吞中起调节作用^[21] TXNL1- XRCC1 is a new regulatory approach, and the redox sensor TXNL1 plays a regulatory role in liquid phase endocytosis
10	MUC12	BLV-miR-B3-3p	1893	编码膜糖蛋白,在细胞内信号传导中发挥作用/黏液素在上皮表面形成的保护性黏液屏障中起重要作用 It encodes membrane glycoproteins and plays a role in intracellular signaling, and mucin plays an important role in the protective mucus barrier formed by the epithelial surface
11	AHNAK2	BLV-miR-B3-5p	6265	编码的蛋白质可通过与钙通道蛋白结合而在钙信号传导中起作用 The encoded protein can play a role in calcium signaling by binding to calcium channel proteins
12	EPN1	BLV-miR-B4-5p	1506	促进囊泡的内吞作用^[22] Promoting endocytosis of vesicles
13	TSPAN14	BLV-miR-B4-5p	1052	作为跨膜蛋白,可调节内质网出口^[23] As a transmembrane protein, it can regulate the export of endoplasmic reticulum
14	MUC12	BLV-miR-B4-5p	1045	编码膜糖蛋白,在细胞内信号传导中发挥作用/黏液素在上皮表面形成的保护性黏液屏障中起重要作用 It encodes membrane glycoproteins and plays a role in intracellular signaling, and mucin plays an important role in the protective mucus barrier formed by the epithelial surface
15	MUC12	BLV-miR-B5-3p	506	编码膜糖蛋白,在细胞内信号传导中发挥作用/黏液素在上皮表面形成的保护性黏液屏障中起重要作用 It encodes membrane glycoproteins and plays a role in intracellular signaling, and mucin plays an important role in the protective mucus barrier formed by the epithelial surface
16	MUC12	BLV-miR-B5-5p	3373	编码膜糖蛋白,在细胞内信号传导中发挥作用/黏液素在上皮表面形成的保护性黏液屏障中起重要作用 It encodes membrane glycoproteins and plays a role in intracellular signaling, and mucin plays an important role in the protective mucus barrier formed by the epithelial surface

Table 3

Table 4

Candidate target genes involved in the synthesis of cell structure / skeleton protein"

序号 Number	基因名称 Gene name	miRNA miRNA	评分 Score	与结构/骨架关系 Relationship with structure / skeleton
1	MYO19	BLV-miR-B1-3p	596	肌球蛋白,为肌肉收缩,胞质分裂和细胞器运输等过程提供动力^[24] It is myosin that powers muscle contraction, cytokinesis and organelle transport
2	BSN	BLV-miR-B1-5p	2197	编码的tau蛋白是神经细胞的骨架成分 The encoded tau protein is a skeleton component of nerve cells
3	KLC1	BLV-miR-B1-5p	2308	与肌动蛋白重链结合、参与了囊泡、线粒体和高尔基体等物质的结合 It binds to actin heavy chains and is involved in the binding of vesicles, mitochondria and golgi bodies
4	OBSCN	BLV-miR-B1-5p	2921	该基因编码的Obscurins蛋白可作为巨噬细胞的骨架蛋白[^25] Obscurins encoded by this gene can be regarded as the cytoskeleton protein of macrophages
5	EPPK1	BLV-miR-B3-5p	920	在细胞骨架结构中起作用^[26] It plays a role in the cytoskeletal structure
6	CDC42	BLV-miR-B4-5p	925	细胞骨架结构中发挥作用^[20] It plays a role in the cytoskeletal structure
7	LTBP3	BLV-miR-B4-5p	1074	编码的蛋白质与转化生长因子β（TGF-β）形成复合物,在细胞外基质中发挥结构作用 The encoded protein forms a complex with transforming growth factor β (TGF-β) and plays a structural role in the extracellular matrix
8	DNAJC14	BLV-miR-B5-3p	316	是一种热休克蛋白,有助于Hsp70介导的蛋白质折叠^[27] Is a heat shock protein that helps Hsp70-mediated protein folding
9	OBSCN	BLV-miR-B5-5p	1061	该基因编码的Obscurins蛋白可作为巨噬细胞的骨架蛋白^[25] Obscurins encoded by this gene can be regarded as the cytoskeleton protein of macrophages
10	FNBP1L	BLV-miR-B2-5p	1469	该基因编码的蛋白质与CDC42和N-WASP结合,通过激活N-WASP-WIP复合物来促进CDC42诱导的肌动蛋白聚合 The protein encoded by this gene binds to CDC42 and N-WASP, and promotes CDC42-induced actin polymerization by activating the N-WASP-WIP complex
11	GAS2L1-208	BLV-miR-B2-5p	178	该蛋白结合细胞骨架的成分,并可能参与介导微管和微丝之间的相互作用;GAS2L1,一种微管和肌动蛋白结合蛋白,参与中心粒动力学和中心体分离^[28];Gas2是一种生长停滞特异性蛋白,是微丝网络系统的组成部分^[29] The protein binds to cytoskeletal components and is involved in mediating the interaction between microtubules and microfilaments. GAS2L1, a microtubule and actin binding protein, involved in centrosome dynamics and centrosome separation. Gas2 is a growth stagnation specific protein and a component of the microfilament network system
12	CLEC16A	BLV-miR-B2-3p	439	该基因编码包含C型凝集素结构域的家族的成员 The gene encodes a member of a family that contains the type C lectin domain
13	HERC5-201	BLV-miR-B2-5p	175	该基因是泛素连接酶HERC家族的成员,编码具有HECT结构域和5个RCC1重复序列的蛋白质 The gene is a member of the ubiquitin ligase HERC family that encodes proteins with HECT domains and five RCC1 repeats
14	MAST1	BLV-miR-B2-3p	304	该基因是微管相关丝氨酸/苏氨酸激酶（MAST）家族的成员。由该基因编码的蛋白质具有N端丝氨酸/苏氨酸激酶结构域 This gene is a member of the microtubule-associated serine/threonine kinase (MAST) family, and the protein encoded by this gene has an N-terminal serine/threonine kinase domain

Table 4

Table 5

Candidate target genes involved in cell proliferation"

序号 Number	基因名称 Gene name	miRNA miRNA	评分 Score	与增殖关系 Relationship with proliferation
1	RPS6KA5	BLV-miR-B1-3p	618	抑制细胞增殖^[30] Inhibiting of cell proliferation
2	SHPRH	BLV-miR-B1-3p	590	抑制细胞增殖^[31] Inhibiting of cell proliferation
3	EVC	BLV-miR-B1-5p	2266	该基因发生突变可能通过下调Hh途径活性导致心肌细胞的增殖能力降低^[32]。心肌细胞的抗细胞凋亡能力降低^[32] Mutation of this gene may reduce the proliferation of cardiomyocytes by down-regulating Hh pathway activity. The anti-apoptotic ability of cardiomyocytes was decreased
4	BIRC6	BLV-miR-B2-3p	908	诱导细胞增殖^[33]。抑制凋亡^[34] Inducing cell proliferation and inhibiting apoptosis
5	EGFR	BLV-miR-B2-3p	1049	诱导细胞增殖 Inducing cell proliferation
6	COL16A1	BLV-miR-B3-5p	1031	通过上调内皮受体VEGFR1,VEGFR2和uPAR触发血管生成^[35] Angiogenesis is triggered by upregulation of endothelial receptors VEGFR1, VEGFR2, and uPAR
7	KMT2D	BLV-miR-B3-5p	1203	下调抑制胃癌的增殖^[36]。诱导其凋亡^[36] Down-regulating gastric cancer proliferation and inducing apoptosis
8	TET3	BLV-miR-B4-3p	1691	细胞增殖^[37] Cell proliferation
9	CDC42	BLV-miR-B4-5p	925	促进肿瘤生长^[20] Promoting tumor growth
4	TRO	BLV-miR-B4-3p	1374	通过PKC-δ诱导人子宫内膜上皮细胞的凋亡 Apoptosis of human endometrial epithelial cells was induced by PKC-δ
5	COL1A2	BLV-miR-B4-3p	2543	通过PI3K-Akt信号通路抑制胃癌细胞凋亡^[38] The apoptosis of gastric cancer cells was inhibited by pi3K-Akt signaling pathway
6	COL3A1	BLV-miR-B4-3p	2098	拮抗细胞凋亡功能^[19] Antagonizing apoptosis
7	TIAL1-201	BLV-miR-B2-5p	180	该基因编码的蛋白质是RNA结合蛋白家族的成员,调节各种活动,包括翻译控制,剪接和凋亡 The gene encodes proteins that are members of the RNA-binding protein family and regulate various activities, including translation control, splicing, and apoptosis

Table 5

Table 6

Table 7

Candidate target genes involved in cell migration / invasion"

序号 Score	基因名称 Gene name	miRNA miRNA	评分 Score	与迁移关系 Relationship with migration
1	NOTCH3	BLV-miR-B1-3p	600	促进转移^[41] Promoting metastasis
2	RICTOR	BLV-miR-B1-3p	592	促癌细胞转移^[42] Promoting metastasis of cancer cells
3	TNXB	BLV-miR-B1-3p	747	具有抗黏附作用
4	RPS6KA5	BLV-miR-B1-3p	618	肿瘤侵袭有关^[30] Relating to tumor invasion
5	FOCAD	BLV-miR-B3-3p	446	FOCAD编码一种在胶质瘤中具有肿瘤抑制功能的粘着斑蛋白^[43] FOCAD encodes a focal adhesion proteins of an tumor inhibitory function in glioma
6	PLEKHG3	BLV-miR-B3-3p	444	激活细胞前端的肌动蛋白丝来增强极化细胞迁移^[44] Activating the actin filaments at the cell front for enhancing the polarized migration of cells
7	EPPK1	BLV-miR-B3-5p	920	在伤口愈合期间加速角质形成细胞迁移 Promoting keratinocyte migration during wound healing
8	COL16A1	BLV-miR-B3-5p	1031	COL16A1在炎症晚期时在肠上皮下肌成纤维细胞（ISEMF）表面表达增加,导致细胞扩散^[45] COL16A1 expression increasing in cell surface which led to cell diffusion
9	COL1A2	BLV-miR-B4-3p	2543	促进胃癌细胞迁移和侵袭^[38] Promoting cell migration and invasion in gastric cancer cells
10	TRO	BLV-miR-B4-3p	1374	介导滋养细胞和子宫内膜上皮细胞之间的细胞黏附 It mediates cell adhesion between endometrial epithelial cells and trophoblast
11	CDC42	BLV-miR-B4-5p	925	影响细胞间黏附、肿瘤细胞形成过程的细胞迁移和侵袭^[20] Affecting cell adhesion and cell migration and invasion during the tumor cell formation
12	EPN1	BLV-miR-B4-5p	1506	可能降低癌细胞稳定性 It may have decreased cancer cells stability
13	LTBP3	BLV-miR-B4-5p	1074	促进癌细胞传播过程中的早期转移^[46] Promoting metastasis in cancer cells of early phase
14	DNAH17	BLV-miR-B5-3p	320	DNAH17编码动力蛋白轴索重链,参与细胞运动^[47] DNAH17 encodes a dynein heavy chain motor protein and participates in cell motility
15	ATP11A	BLV-miR-B2-3p	563	编码的蛋白质是完整的膜,是结直肠癌异时转移的独立预测因子^[48] The protein encoded was an independent predictor of colorectal cancer metastasis
16	ENPP7	BLV-miR-B2-3p	580	编码的蛋白质锚定在细胞膜中,它可能起到保护肠黏膜免受炎症和肿瘤发生的作用 It protects the intestinal mucosa against injuries inflammation and tumorigenesis to encoding protein which is anchored to the inner face of cellular membrane

Table 7

Table 8

Table 9

Fig. 2

Fig. 3

Fig. 4

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miRNA名称 miRNA name	成熟序列 Mature sequence
BLV-miR-B1-3P	UCAGUGUACCAUCACAAGCCUCU
BLV-miR-B1-5P	AGGCUGUGGUGGUGCACUGGCUU
BLV-miR-B2-3P	UGCGUGUCGCUCAGUCAUUUU
BLV-miR-B2-5P	AUGACUGAGUGUAGCGCAGAGA
BLV-miR-B3-3P	UAACGCUGACGGGGGCGAUUUCU
BLV-miR-B3-5P	AUCCCCCUGCCAGCGUUGGUC
BLV-miR-B4-3P	UAGCACCACAGUCUCUGCGCCUUU
BLV-miR-B4-5P	GCGGGAGGCUCUGGUGCUGG
BLV-miR-B5-3P	CUCGAGCCGCAACCUCCCUUUCU
BLV-miR-B5-5P	AGGAAGGUUGUGGCUCAGAGGU

Prediction and Bioinformatics Analysis of BLV-miRNA Transboundary Regulation of Human Target Genes

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序号 Number	基因名称 Gene name	miRNA	评分 Score	与细胞周期关系 Relationship with cell cycle
1	MGRN1	BLV-miR-B2-3p	308	MGRN1介导的α-微管蛋白在细胞间期起泛素化作用^[19] MGRN1-mediated α-tubulin ubiquitination in the intercellular phase
2	CDC42	BLV-miR-B4-5p	925	调控细胞周期^[20] Regulating of cell cycle

序号 Number	基因名称 Gene name	miRNA miRNA	评分 Score	与分化关系 Relationship with differentiation
1	MYO19	BLV-miR-B1-3p	596	确保细胞在分裂期间的彻底隔离^[39] Ensure complete isolation of cells during division
2	RPS6KA5	BLV-miR-B1-3p	618	控制分化^[40] Control of differentiation

序号 Score	基因名称 Gene name	miRNA miRNA	评分 Score	与白血病关系 Relationship with leukemia
1	COL1A1	BLV-miR-B4-3p	2603	ALL患者的骨骼发育异常与Col1A1 Sp1结合位点基因多态性存在相关性^[49] There is a correlation between ALL patients have dysfunctional bone development and Col1A1 Sp1 binding site gene polymorphism
2	BCR	BLV-miR-B4-3p	320	ALL的融合转录本^[50] The fusion transcripts of ALL

序号 Score	基因名称 Gene name	miRNA miRNA	评分 Score	与乳腺癌关系 Relationship with breast cancer
1	NOTCH3	BLV-miR-B1-3p	600	在癌症转移过程中起作用^[41] Playing a vital role in cancer metastasis
2	RICTOR	BLV-miR-B1-3p	592	在癌症转移过程中起作用^{[42, 51]} Playing a vital role in cancer metastasis
3	RPS6KA5	BLV-miR-B1-3p	618	调节乳腺癌中腔细胞分化和转移性休眠,增加骨归巢和生长能力,与肿瘤侵袭有关^[40] It regulates the differentiation of luminal cells and metastatic dormancy in breast cancer, increases bone homing and growth capacity and is related to tumor invasion
4	OBSCN	BLV-miR-B1-5p	2921	OBSCN缺失会导致细胞间接触被破坏,在体内外均会导致肿瘤的发生,迁移和侵袭^[25] These cells contacts are disrupted by OBSCN defecting and leaded to cancer cell migration and invasion in vivo and in vitro
5	COL1A1	BLV-miR-B4-3p	2603	癌症来源的miR-218通过调控COL1A1在血液水平上乳腺癌向骨的转移过程起作用^[49] MiR-218 of cancer work in transfer process with breast cancer metastasis to bone at the blood level by regulatory COL1A1
6	OBSCN	BLV-miR-B5-5p	1061	OBSCN缺失会导致细胞间接触被破坏,在体内外均会导致肿瘤的发生,迁移和侵袭^[25] These cells contacts are disrupted by OBSCN defecting and leaded to cancer cell migration and invasion in vivo and in vitro
7	ATF3	BLV-miR-B2-5p	180	乳腺癌期间的病理状况下,已经观察到ATF3的持续和延长表达^[52] ATF3 will prolonge and sustaine expression under pathological situations in breast cancer

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