METTL3-modified RNASEH1-AS1 regulates the malignant biological behaviors of colorectal cancer SW480 cells through the BUD13/ANXA2/Wnt/β-catenin axis / 中国肿瘤生物治疗杂志

@#[摘 要] 目的：探究甲基转移酶样蛋白3（METTL3）修饰的RNASEH1-AS1通过BUD13/膜联蛋白A2/ Wnt/β-连环蛋白（BUD13/ANXA2/Wnt/β-catenin）轴调控结直肠癌细胞SW480恶性生物学行为的分子机制。方法：选取2022年6月至2022年11月间在复旦大学附属中山医院厦门医院手术治疗的24例CRC患者，收集患者的CRC组织和对应的癌旁组织，用qPCR法检测其中METTL3、RNASEH1-AS1、BUD13、ANXA2、β-catenin、GSK-3β mRNA的表达，用Pearson法分析CRC组织中RNASEH1-AS1表达分别与METTL3和BUD13表达的相关性。常规培养结直肠癌细胞SW480，分为sh-NC组、sh-RNASEH1-AS1组、NC组、sh-METTL组、si-NC组、si-BUD13组、sh-RNASEH1-AS1+pc-NC组、sh-RNASEH1-AS1+pc-ANXA2组、sh-METTL+pc-NC组、sh-METTL+pc-ASEH1-AS1组，用Lipofectamine® 2000转染试剂将sh-NC、sh-RNASEH1-AS1、sh-NC、sh-METTL、si-NC、si-BUD13、sh-RNASEH1-AS1+pc-NC、sh-RNASEH1-AS1+pc-ANXA2、sh-METTL+pc-NC、sh-METTL+pc-ASEH1-AS1分别转染SW480细胞，用qPCR法检测后SW480细胞中METTL3、RNASEH1-AS1、BUD13、ANXA2的表达，细胞克隆形成实验检测转染后各组SW480细胞的增殖能力，FCM术检测转染后各组SW480细胞的凋亡情况，细胞划痕实验检测转染后各组SW480细胞的迁移能力，WB法检测转染后各组SW480细胞中ANXA2、β-catenin、p-β-catenin、GSK-3β、p-GSK-3β、c-Myc、cyclinD1蛋白表达，RNA免疫沉淀（RIP）法检测RNASEH1-AS1与BUD1、BUD1与ANXA2的靶向关系。结果：数据库CRC数据分析和中国人CRC组织和癌旁组织的qPCR法检测结果均显示，与癌旁组织相比CRC组织中METTL3、RNASEH1-AS1、BUD13、ANXA2、β-catenin、GSK-3β均呈明显高表达（均P<0.01），且RNASEH1-AS1表达与METTL3（r=0.698，P<0.01）、BUD13（r=0.784，P<0.01）的表达呈正相关。在结直肠癌各细胞中METTL3、RNASEH1-AS1、BUD13、ANXA2 mRNA均呈高表达（均P<0.05）；敲减RNASEH1-AS1或METTL3后SW480细胞中RNASEH1-AS1、BUD13、ANXA2表达显著降低（均P<0.05），而过表达RNASEH1-AS1后上述分子表达明显上调（均P<0.05）；敲减RNASEH1-AS1或METTL3可抑制SW480的增殖、迁移和p-β-catenin、p-GSK-3β、c-Myc、cyclinD1蛋白的表达，促进其凋亡（均P<0.05），而过表达RNASEH1-AS1则可促进SW480增殖、迁移和p-β-catenin、p-GSK-3β、c-Myc、cyclinD1蛋白的表达和抑制其凋亡（均P<0.05）；RNASEH1-AS1通过招募BUD13靶向促进ANXA2的表达（均P<0.05）；过表达ANXA2可部分逆转敲减RNASEH1-AS1对SW480细胞的影响（均P<0.05）。结论：METTL3修饰的RNASEH1-AS1通过BUD13/ANXA2/Wnt/β-catenin轴调控SW480细胞的恶性生物学行为。

Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features.

PURPOSE: In this study we aimed to identify the molecular genetic cause of a progressive multisystem disease with prominent lipodystrophy. METHODS: In total, 5 affected individuals were investigated using exome sequencing. Dermal fibroblasts were characterized using RNA sequencing, proteomics, immunoblotting, immunostaining, and electron microscopy. Subcellular localization and rescue studies were performed. RESULTS: We identified a lipodystrophy phenotype with a typical facial appearance, corneal clouding, achalasia, progressive hearing loss, and variable severity. Although 3 individuals showed stunted growth, intellectual disability, and died within the first decade of life (A1, A2, and A3), 2 are adults with normal intellectual development (A4 and A5). All individuals harbored an identical homozygous nonsense variant affecting the retention and splicing complex component BUD13. The nucleotide substitution caused alternative splicing of BUD13 leading to a stable truncated protein whose expression positively correlated with disease expression and life expectancy. In dermal fibroblasts, we found elevated intron retention, a global reduction of spliceosomal proteins, and nuclei with multiple invaginations, which were more pronounced in A1, A2, and A3. Overexpression of both BUD13 isoforms normalized the nuclear morphology. CONCLUSION: Our results define a hitherto unknown syndrome and show that the alternative splice product converts a loss-of-function into a hypomorphic allele, thereby probably determining the severity of the disease and the survival of affected individuals.

CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13.

BACKGROUND: Prostate cancer (PCa) belongs to an epithelial malignancy that occurs in the prostate gland and is the most common malignancy of the male genitourinary system. Referring to related literature, circSERPINA3 has been reported to be up-regulated in PCa. However, its biological function remains unclear. PURPOSE: This study aimed to reveal the specific role and relevant molecular mechanism of circSERPINA3 in PCa. METHODS: RT-qPCR was used to examine gene expression and functional analyses were conducted to verify the effect of circSERPINA3 on cell apoptosis, autophagy and aerobic glycolysis in PCa cells. Mechanism assays were applied to evaluate the relationship among circSERPINA3/miR-653-5p/SERPINA3/BUD13. RESULTS: CircSERPINA3 was verified to be up-regulated in PCa cells and to inhibit cell apoptosis while promoting aerobic glycolysis and autophagy in PCa cells. CircSERPINA3 and SERPINA3 were also testified to bind to miR-653-5p through a line of mechanism experiments. Moreover, it was discovered that circSERPINA3 could stabilize SERPINA3 mRNA via recruiting BUD13. Additionally, SERPINA3 was verified to inhibit cell apoptosis, while promoting aerobic glycolysis and autophagy in PCa cells. CONCLUSIONS: Our study suggested that circSERPINA3 regulated apoptosis, autophagy and aerobic glycolysis of PCa cells by competitively binding to miR-653-5p and recruiting BUD13.

Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex.

Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.

Long non-coding RNA DBH-AS1 promotes cancer progression in diffuse large B-cell lymphoma by targeting FN1 via RNA-binding protein BUD13.

Diffuse large B-cell lymphoma (DLBC) is a subtype of lymphoma with the worst prognosis. Existing treatment methods are not effective enough due to its high occurrence of metastasis. Therefore, identification of effective therapeutic targets is becoming increasingly important. In this research, long non-coding RNA dopamine ß hydroxylase antisense RNA 1 (DBH-AS1) was found to be upregulated in DLBC tissues and cells. Knockdown of DBH-AS1 suppressed the proliferation, migration, and invasion of cancer cells. Afterwards, RNA-binding protein BUD13 homolog (BUD13) was found to be upregulated in cancer tissues and cells while binding to DBH-AS1. Fibronectin 1 (FN1) was the downstream messenger RNA (mRNA) of BUD13. FN1 was upregulated in DLBC and was positively correlated with DBH-AS1. Further rescue assays proved that DBH-AS1 mediated FN1 expression by recruiting BUD13. In the meantime, BUD13 stabilized FN1 mRNA to promote FN1 expression. In this way, DBH-AS1/BUD13/FN1 axis was confirmed. A set of rescue assays proved that DBH-AS1 regulated DLBC progression via BUD13 and FN1. The function and mechanism of DBH-AS1 were investigated for the first time in DLBC. DBH-AS1 might become a therapeutic target in lymphoma treatment in the future.

Interaction of polymorphisms in APOA4-APOA5-ZPR1-BUD13 gene cluster and sleep duration on 5-year lipid changes in middle aged and older Chinese.

STUDY OBJECTIVES: Lipid profiles are influenced by both genetic and environmental factors. Genetic variants in the APOA4-APOA5-ZPR1-BUD13 gene cluster and aberrant sleep duration were independently identified to be associated with lipids in previous studies. We aimed to investigate whether sleep duration modified the genetic associations with longitudinal lipids changes. METHODS: Four single nucleotide polymorphisms (SNPs), rs17119975, rs651821, rs7396835, and rs964184 in the APOA4-APOA5-ZPR1-BUD13 gene cluster were genotyped among 8648 apparently healthy subjects from the Dongfeng-Tongji (DFTJ) cohort. Information on sleep duration was obtained by questionnaires. Changes in total cholesterol, triglyceride, high-density lipoprotein cholesterol (HDL-c), low-density lipoprotein cholesterol (LDL-c), were evaluated from baseline to 5-year follow-up. RESULTS: After multivariate adjustments, we found that rs651821 and weighted genetic risk score (GRS) were significantly associated with increased triglyceride, and the genetic association with triglyceride change consistently strengthened across sleep duration categories. The differences in triglyceride changes per increment of risk allele for rs651821 were 0.028 (SE = 0.017, p = 0.112), 0.051 (SE = 0.009, p < 0.001), and 0.064 (SE = 0.016, p < 0.001) in individuals with sleep duration ≤7, >7-<9, and ≥9 h, respectively (p interaction = 0.031). The GRS also showed a significant interaction with sleep duration categories for triglyceride change (p interaction = 0.010). In addition, all of the four SNPs and GRS were inversely related to HDL-c changes. CONCLUSIONS: Longer sleep duration might exacerbate the adverse effects of SNPs in APOA4-APOA5-ZPR1-BUD13 gene cluster on 5-year triglyceride changes.

BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7.

Intron retention (IR) has emerged as an important mechanism of gene expression control, but the factors controlling IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified BUD13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in BUD13 was associated with increased IR, decreased mature Irf7 transcript and protein levels, and consequently a dampened type I interferon response, which compromised the ability of BUD13-deficient macrophages to withstand vesicular stomatitis virus (VSV) infection. Global analysis of BUD13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a BUD13-dependent manner. Deficiency of BUD13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, BUD13 facilitates the expression of genes at which IR occurs.

Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern.

BACKGROUND: Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. METHODS: A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. RESULTS: All SNPs conformed to Hardy-Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. CONCLUSION: SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exploration.

Association of BUD13 polymorphisms with metabolic syndrome in Chinese population: a case-control study.

BACKGROUND: BUD13 homolog (BUD13), one of submits of the retention and splicing complex, was identified in yeast as a splicing factor that affected nuclear pre-mRNA retention. While more and more studies demonstrated that BUD13 played a potential role in the pathogenesis of metabolic syndrome (MetS). This objective was to reassess whether novel locus of BUD13 were linked to MetS and individual complements in the northeast of China. METHODS: A total of 3850 individuals were recruited in this case-control study, including 1813 MetS cases and 2037 healthy controls. The diagnostic criteria was according to the International Diabetes Federation (IDF). Metabolic complements such as waist circumference (WC), triglyceride, high-density lipoprotein cholesterol (HDL-C), systolic and diastolic blood pressure (SBP and DBP), and fasting glucose were measured. We explored the association between two novel single nucleotide polymorphism (SNPs) of BUD13 (rs7118999 and rs10488698) and MetS and its complements. RESULTS: Using binary logistic regression analysis we found that there were no significant associations between SNPs and MetS in different heritance models (all P > 0.05). However, novel locus of BUD13 were linked to individual complements in MetS cases. Rs7118999 conferred to risk of WC (P = 0.016) and the carrier of TT might have higher susceptibility to MetS. While rs10488698 was associated with HDL-C (P = 0.001) and the carrier of TT was significantly associated with higher level of HDL-C. CONCLUSIONS: We concluded that novel mutations in BUD13 did not confer risk for MetS in our study population, but these mutations changed the level of metabolic complements.

Association study of BUD13-ZNF259 gene rs964184 polymorphism and hemorrhagic stroke risk.

We aimed to evaluate the association of rs964184 of BUD13-ZNF259 gene with the risk of hemorrhagic stroke (HS). A total of 138 HS cases and 587 controls were recruited for the association of rs964184 of BUD13-ZNF259 gene with the risk of HS. Tm shift PCR was used for genotyping. We were unable to find the association of rs964184 of BUD13-ZNF259 gene with the risk of HS (P>0.05). Significant difference was found in the TG level among the three genotypes (CC: 1.51±1.02; CG: 1.68±1.10; GG: 1.90±1.11, P=0.036). The TG level showed strong correlation with rs964184 genotypes (P=0.010, correlation=0.101). Significantly higher TC, HDL-C, and LDL-C levels were observed in the case group. And no difference was found in the TG, ApoA-I, ApoB. Our case-control study supported the significant association between rs964184 genotype and the blood TG concentration, although we were unable to find association between BUD13-ZNF259 rs964184 and the risk of HS in Han Chinese.

Association of the variants in the BUD13-ZNF259 genes and the risk of hyperlipidaemia.

The single nucleotide polymorphisms (SNPs) in the BUD13 homolog (BUD13) and zinc finger protein 259 (ZNF259) genes have been associated with one or more serum lipid traits in the European populations. However, little is known about such association in the Chinese populations. Our objectives were to determine the association of the BUD13/ZNF259 SNPs and their haplotypes with hypercholesterolaemia (HCH)/hypertriglyceridaemia (HTG) and to identify the possible gene-gene interactions among these SNPs. Genotyping of 6 SNPs was performed in 634 hyperlipidaemic and 547 normolipidaemic participants. The ZNF259 rs2075290, ZNF259 rs964184 and BUD13 rs10790162 SNPs were significantly associated with serum lipid levels in both HCH and non-HCH populations (P < 0.008-0.001). On single locus analysis, only BUD13 rs10790162 was associated with HCH (OR: 2.23, 95% CI: 1.05, 4.75, P = 0.015). The G-G-A-A-C-C haplotype, carrying rs964184-G-allele, was associated with increased risk of HCH (OR: 1.35, 95% CI: 1.10, 1.66, P = 0.005) and HTG (OR: 1.75, 95% CI: 1.39, 2.21, P = 0.000). The A-C-G-G-C-C and A-C-A-G-T-C haplotypes, carrying rs964184-C-allele, were associated with reduced risk of HCH (OR: 0.77, 95% CI: 0.61, 0.99, P = 0.039 and OR: 0.66, 95% CI: 0.47, 0.94, P = 0.021 respectively). On multifactor dimensionality reduction analyses, the two- to three-locus models showed a significant association with HCH and HTG (P < 0.01-0.001). The BUD13/ZNF259 SNPs, which were significant in the European populations, are also replicable in the Southern Chinese population. Moreover, inter-locus interactions may exist among these SNPs. However, further functional studies are required to clarify how these SNPs and genes actually affect the serum lipid levels.

Methylation of the DNA/RNA-binding protein Kin17 by METTL22 affects its association with chromatin.

Kin17 is a protein that was discovered through its immunoreactivity towards an antibody directed against prokaryotic RecA. Further study of Kin17 revealed a function in DNA replication and repair, as well as in pre-mRNA processing. Recently, it was found that Kin17 is methylated on lysine 135 by the newly discovered methyltransferase METTL22. To better understand the function of Kin17 and its regulation by methylation, we used multiple cell compartment protein affinity purification coupled with mass spectrometry (MCC-AP-MS) to identify novel interaction partners of Kin17 and to assess whether these interactions can take place on chromatin. Our results confirm that Kin17 interacts with METTL22 both in the soluble and chromatin fractions. We also show that many RNA-binding proteins, including the previously identified interactor BUD13 as well as spliceosomal and ribosomal subunits, associate with Kin17 in the soluble fraction. Interestingly, overexpression of METTL22 in HEK 293 cells displaces Kin17 from the chromatin to the cytoplasmic fraction, suggesting a role for methylation of lysine 135, a residue that lies within a winged helix domain of Kin17, in regulating association with chromatin. These results are discussed in view of the putative cellular function of Kin17. BIOLOGICAL SIGNIFICANCE: The results shown here broaden our understanding of METTL22, a member of a family of newly-discovered non-histone lysine methyltransferases and its substrate, Kin17, a DNA/RNA-binding protein with reported roles in DNA repair and replication and mRNA processing. An innovative method to study protein-protein interactions in multiple cell compartments is employed to outline the interaction network of both proteins. Functional experiments uncover a correlative role between Kin17 lysine methylation and its association with chromatin. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?