Gene最新文献

{"title":"Autocrine small extracellular vesicles induce tubular phenotypic transformation in diabetic nephropathy via miR-21-5p.","authors":"Mengting Zhang, Yukang Lu, Lanfeng Wang, Yiping Mao, Xinyi Hu, Zhiping Chen","doi":"10.1016/j.gene.2024.149156","DOIUrl":"10.1016/j.gene.2024.149156","url":null,"abstract":"<p><strong>Background: </strong>Diabetic nephropathy (DN) is one of the most common and serious microvascular complications associated with diabetes. DN is the leading contributor to the majority of cases of end-stage renal disease (ESRD). Small extracellular vesicles (sEVs) can transport various genetic materials to recipient cells. The objective of this study was to explore how sEVs released from HK-2 cells when stimulated by high glucose levels influence renal tubular phenotypic transformation through miR-21-5p.</p><p><strong>Methods: </strong>Both human and cell studies were utilized to explore the crosstalk between proximal renal tubules in DN. sEVs from plasma and cells were isolated using ultracentrifugation, and the differential expression of miR-21-5p in plasma sEVs from DN patients versus healthy controls was quantified using Quantitative Real-time PCR (RT-qPCR). A DN model was constructed by stimulating HK-2 cells with glucose. The expression of epithelial-mesenchymal transition (EMT) proteins in each cell group was analyzed by Western Blot (WB), while miR-21-5p levels in both cells and their sEVs were quantified using RT-qPCR. A stable transfected HK-2 cell line was constructed. The CCK8 assay, scratch assay, and WB were employed to detect EMT proteins, aiming to explore how autocrine sEVs affect tubular phenotypic transformation in diabetic nephropathy (DN).</p><p><strong>Results: </strong>The expression of miR-21-5p in plasma sEVs was significantly elevated in the DN group compared to the healthy control group. High glucose (HG) stimulation of HK-2 cells resulted in higher miR-21-5p expression in both cells and their sEVs, leading to enhanced proliferation, migration, and EMT capacities in these cells. Co-incubation of HK-2 cells with HG-sEVs significantly enhanced the proliferation, migration, and EMT capabilities of the recipient cells, but miR-21-5p knockdown reversed these effects.</p><p><strong>Conclusion: </strong>These results indicate that high glucose stimulates HK-2 cells to secrete sEVs, which promote DN proliferation, migration, and EMT through miR-21-5p, thereby offering new insights into the treatment of DN.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149156"},"PeriodicalIF":2.6,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142800273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of GWAS models and GS reveals the genetic architecture of ear shank in maize.","authors":"Jiale Jiang, Jiaojiao Ren, Yukang Zeng, Xiaoming Xu, Shaohang Lin, Zehui Fan, Yao Meng, Yirui Ma, Xin Li, Penghao Wu","doi":"10.1016/j.gene.2024.149140","DOIUrl":"10.1016/j.gene.2024.149140","url":null,"abstract":"<p><p>Maize is one of the most important crops for human food, animal feed, and industrial raw materials. Ear shank length (ESL) and ear shank node number (ESNN) are crucial selection criteria in maize breeding, impacting grain yield and dehydration rate during mechanical harvesting. To unravel the genetic basis of ESL and ESNN in maize, an association panel consisting of 379 multi-parent doubled-haploid (DH) lines was developed for genome-wide association studies (GWAS) and genomic selection (GS). The heritabilities of ESL and ESNN were 0.68 and 0.55, respectively, which were controlled by genetic factors and genotype-environment interaction factors. Using five different models for GWAS, 11 significant single nucleotide polymorphisms (SNPs) located on chromosomes 1, 2, and 4 were identified for ESL, with the phenotypic variation explained (PVE) value of each single SNP ranging from 4.91% to 21.35%, and 11 significant SNPs located on chromosomes 1, 2, 4, and 5 were identified for ESNN, with the PVE value of each SNP ranging from 1.22% to 18.42%. Genetic regions in bins 1.06, 2.06, and 2.08 were significantly enriched in SNPs associated with ear shank-related traits. The GS prediction accuracy using all markers by the five-fold cross-validation method for ESL and ESNN was 0.39 and 0.37, respectively, which was significantly improved by using only 500-1000 significant SNPs with the lowest P-values. The optimal training population size (TPS) and marker density (MD) for ear shank-related traits were 50%-60% and 3000, respectively. Our results provide new insights into the GS of ear shank-related traits.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149140"},"PeriodicalIF":2.6,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyphenol oxidase gene editing changed the flavonoid composition and browning process of litchi (Litchi chinensis Sonn.) callus","authors":"Shujun Wang,&nbsp;Fang Li,&nbsp;Guo Wang,&nbsp;Huanling Li,&nbsp;Xiaoxu Li,&nbsp;Xueren Cao,&nbsp;Jiabao Wang","doi":"10.1016/j.gene.2024.149130","DOIUrl":"10.1016/j.gene.2024.149130","url":null,"abstract":"<div><div>Postharvest pericarp browning, caused primarily by the enzymatic oxidation of phenols, reduces the shelf life and market value of litchi fruit and is considered a major limitation for the development of the litchi industry. Previous studies have shown that polyphenol oxidase (PPO) is a key enzyme and that flavonoids are important substrates for enzymatic browning; however, direct evidence is still lacking. This study investigated the differences in the browning process among the wild type (WT) and four PPO gene-edited litchi calli to verify the function of PPO in the browning of litchi tissues. Compared to the WT callus, the proliferation rate, relative expression of litchi PPO gene (<em>LcPPO</em>), PPO activity and color changes significantly decreased or slowed down in all gene-edited calli, indicating that the latter exhibited a slower browning process. Using a liquid chromatography tandem mass spectrometry approach (LC-MS/MS), 83 metabolites of flavonoids were identified, of which 58 were differentially accumulated metabolites (DAMs). Venn analysis revealed 12 common DAMs across different genotypic contrasts that were mostly enriched in the flavonoid biosynthesis pathway. It was presumed that the decrease of <em>LcPPO</em> expression in gene-edited calli led to the reduced PPO activity, then reduced the (−)-epicatechin oxidation. The accumulation of (−)-epicatechin caused the common upregulation of procyanidin B2 and upstream substances such as dihydrokaempferol, taxifolin, naringenin chalcone, 7,4′-dihydroxyflavone, and rutin in their biosynthesis pathways. The results provide novel evidence that (−)-epicatechin acts as the primary direct substrate in the enzymatic browning reaction mediated by PPO.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149130"},"PeriodicalIF":2.6,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"N6-methyladenosine in inflammatory diseases: Important actors and regulatory targets","authors":"Zewen Li ,&nbsp;Yongfeng Lao ,&nbsp;Rui Yan ,&nbsp;Fuhan Li ,&nbsp;Xin Guan ,&nbsp;Zhilong Dong","doi":"10.1016/j.gene.2024.149125","DOIUrl":"10.1016/j.gene.2024.149125","url":null,"abstract":"<div><div>N6-methyladenosine (m6A) is one of the most prevalent epigenetic modifications in eukaryotic cells. It regulates RNA function and stability by modifying RNA methylation through writers, erasers, and readers. As a result, m6A plays a critical role in a wide range of biological processes. Inflammation is a common and fundamental pathological process. Numerous studies have investigated the role of m6A modifications in inflammatory diseases. This review highlights the mechanisms by which m6A contributes to inflammation, focusing on pathogen-induced infectious diseases, autoimmune disorders, allergic conditions, and metabolic disorder-related inflammatory diseases.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149125"},"PeriodicalIF":2.6,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142754875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MiR-433 inhibits cell invasion of glioblastoma via direct targeting TRPM8 based on bioinformatic analysis and experimental validation","authors":"Jianping Zeng ,&nbsp;Shoufang Tong ,&nbsp;Jing Liu ,&nbsp;Shuai Liu ,&nbsp;Rajneesh Mungur ,&nbsp;Shangshi Chen","doi":"10.1016/j.gene.2024.149121","DOIUrl":"10.1016/j.gene.2024.149121","url":null,"abstract":"<div><div>Understanding the essential role of miRNA in regulating cell invasion in glioblastoma opens up new avenues for targeted therapeutic interventions in the future. By screening out eligible miRNA expression data sets from the GEO database, the WGCNA package based on the R language is further used to construct a co-expression network model of the chip data set, to identify modules related to disease states and perform pivotal miRNA screening on the related modules. The target relationship between miRNA and TRPM8 was verified by bioinformatics and luciferase gene report, and the effect of miRNA overexpression on TRPM8 protein level was analyzed by Western blot. The result of miR-433 overexpression on the invasion ability of glioblastoma cells in vitro was examined by scratch test and Transwell invasion test. The results of this study indicate that the selected target miR-433 has a strong binding relationship with TRPM8 and can effectively regulate its expression. Furthermore, overexpression of miR-433 was found to inhibit the invasion ability of glioblastoma cells by targeting TRPM8. These data demonstrate that miR-433 can target TRPM8 to inhibit glioblastoma cell invasion.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149121"},"PeriodicalIF":2.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of hypoxia on survival, apoptosis, and the transcriptome of the Chinese yellow pond turtle (Mauremys mutica)","authors":"Lingjing Wei ,&nbsp;Congyan Yu ,&nbsp;Shan Xiao ,&nbsp;Kang Liu ,&nbsp;Yudian Lu ,&nbsp;Baojiang Gan ,&nbsp;Peng Zhu ,&nbsp;Sheng Zhang","doi":"10.1016/j.gene.2024.149120","DOIUrl":"10.1016/j.gene.2024.149120","url":null,"abstract":"<div><div><em>Mauremys mutica</em> is a widely cultured pond turtle in China that can hold its breath underwater for up to 7 h. However, the adaptive mechanism of this hypoxia-resistant phenotype remains unknown. In the present study, no <em>M. mutica</em> died until 6 h of hypoxic stress. Inflammation was observed in the lungs of dead individuals along with a lung cell apoptosis rate of 12.3% in the death group, which was about six times that of the survival group. Transcriptome sequencing produced 379,659,748 clean reads, and 38,981 genes were obtained. A total of 1566, 1555 and 756 differentially expressed genes (DEGs) were detected between the survival group and the death group, the survival group and the control group, and the death group and the control group, respectively. And the DEGs were enriched in the inflammation, apoptosis, sugar transport, antioxidant<em>,</em> fructose, and mannose metabolism, arginine and proline metabolism, glycosaminoglycan biosynthesis, P53, and MAPK signaling pathways. This study offers new insight into the molecular mechanisms occurring in the lungs of <em>M. mutica</em> during acute hypoxia, which may facilitate genetic selection for hypoxia-resistant lines in<!--> <em>M. mutica</em>.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149120"},"PeriodicalIF":2.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142715726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Unveiled Novel regulator of Adeno-associated virus production in HEK293 cells.","authors":"Junyu Yan, Ziqian Li, Yue Shu, Hui Chen, Tianxingzi Wang, Xin Li, Yuhang Zhang, LiLi Li, Yuntao Zhang","doi":"10.1016/j.gene.2024.149122","DOIUrl":"10.1016/j.gene.2024.149122","url":null,"abstract":"<p><p>The field of gene therapy using Adeno-associated viral (AAV) vector delivery is rapidly advancing in the biotherapeutics industry. Despite its successes, AAV manufacturing remains a challenge due to limited production yields. The triple plasmid transfection of HEK293 cells represents the most extensively utilized system for AAV production. The regulatory factors and mechanisms underlying viral production in HEK293 cells are largely unknown. In this study, we isolated high-titer AAV production clones from a parental HEK293 population using a single limiting dilution step, and subsequently elucidating their underlying molecular mechanisms through whole transcriptome analysis. LncRNA TCONS_00160397 was upregulated in clones and shown to promoted HEK293 cells proliferation and improved the titer of AAV production. Mechanistically, results from proteomics and metabolomics indicated that TCONS_00160397 regulated the ABC transporters pathway. These findings furnish a rich repository of knowledge and actionable targets for the rational optimization of HEK293-based producer lines, thereby paving the way for tangible improvements in AAV vector output and expediting the broad implementation of gene therapies.</p>","PeriodicalId":12499,"journal":{"name":"Gene","volume":" ","pages":"149122"},"PeriodicalIF":2.6,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142709758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-coding RNAs mediating the regulation of genes and signaling pathways in aortic valve calcification","authors":"Silpa Sivan,&nbsp;Gayathri Vijayakumar,&nbsp;Indulekha CL Pillai","doi":"10.1016/j.gene.2024.149117","DOIUrl":"10.1016/j.gene.2024.149117","url":null,"abstract":"","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149117"},"PeriodicalIF":2.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OsPUKI, a PfkB protein, regulates seed germination in rice by influencing ABA synthesis","authors":"Yi Bao ,&nbsp;Zongfei Zhang ,&nbsp;Ni Peng,&nbsp;Ziting Qiu,&nbsp;Xin Yan,&nbsp;Jiexiu Ouyang,&nbsp;Shaobo Li,&nbsp;Xin Wang","doi":"10.1016/j.gene.2024.149118","DOIUrl":"10.1016/j.gene.2024.149118","url":null,"abstract":"<div><div>Rice seed germination is a crucial phase in rice growth and development, but its molecular mechanism has not been fully elucidated. In this study, we investigated the function of rice pfkB family gene <em>OsPUKI</em> in seed germination. Compared with WT (ZH11), <em>ospuki</em> mutants showed delayed seed germination and shorter shoot length. QRT-PCR results showed that <em>OsPUKI</em> was highly expressed in leaves and developing seeds of 21-day after pollination, and was highly expressed at the early stage of seed germination. GC-MS analysis demonstrated that content of abscisic acid (ABA) in <em>ospuki-3</em> was higher than that in WT. QRT-PCR analysis revealed that <em>ospuki</em> mutants had higher transcription levels of ABA synthesis-related genes <em>OsNCED2</em>, <em>OsNCED3</em>, <em>OsNCED4</em>, and <em>OsZEP1</em>. Furthermore, it was shown that <em>ospuki</em> mutants were more sensitive to fluridone (Flu) during seed germination and seedling growth than WT according to exogenous Flu treatment experiments. In short, our findings suggest that <em>OsPUKI</em> may positively regulates rice seed germination by influencing ABA synthesis.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149118"},"PeriodicalIF":2.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism Analysis of Increased Erucic Acid Content in Brassica napus L. Seeds Resulting Low Nighttime Temperature","authors":"Chao Mi ,&nbsp;Yanning Zhao ,&nbsp;Liangbin Lin ,&nbsp;Jinxiong Wang","doi":"10.1016/j.gene.2024.149119","DOIUrl":"10.1016/j.gene.2024.149119","url":null,"abstract":"<div><div><em>Brassica napus</em> L. (<em>B. napus</em> L.), a crop of <em>Brassica</em> in the family Cruciferae, is a major sources of edible vegetable oil and one of the four most widely grown. Oil accumulation is determined by genetic and environmental factors, including temperature, light, humidity, edatope, latitude, and altitude. Temperature also plays a crucial part in the maturation stage. A highly temperature-sensitive line (STSL, DH0729DH0815) and weakly temperature-sensitive line (WTSL, DH0729) were used to express <em>LOC106368911</em> and its effect on the erucic acid content of seeds under low nighttime temperatures. Condition of 20/18 °C (±0.5 °C, daytime/nighttime temperature, CK) and 20/13 °C (low nighttime temperature, LNT) were used in tests. Under LNT, the erucic acid content in STSL seeds increased significantly, whereas the WTSL change was not significant. The relative expression of <em>LOC106368911</em> was significantly increased in STSL at 27, 35 and 43 days after flowering (DAF), whereas the change in WTSL was not significant. The CDS sequence of the <em>LOC106368911</em> was cloned. Compared to the protein sequence encoded by the reference gene, STSL changed the 96th amino acid sequence from I (leucine) to L (isoleucine). However, there was no difference in the secondary and tertiary structures. Based on this, we cloned the <em>LOC106368911</em> promoter sequence and found that the mutation of C to T at position −790 in WTSL caused the loss of LTR (<em>cis</em>-acting element involved in low-temperature responsiveness, −791 to −786) element function in response to low temperature and increased erucic acid content. The <em>LOC106368911</em> promoter had 2 LTR elements in STSL (−791 to −786 and −588 to −583). A GUS reporter vector was constructed to study the transient expression in tobacco leaf transformations. <em>GUS</em> gene expression at 13 ℃ after 2 h was significantly higher than that at 18 ℃. Base and number differences in the LTR element were found in the <em>LOC106368911</em> promoter sequence of STSL and WTSL. Base mutations occurred in the LTR element in WTSL, which resulted in decrease or loss of erucic acid content in response to low nighttime temperatures.</div></div>","PeriodicalId":12499,"journal":{"name":"Gene","volume":"936 ","pages":"Article 149119"},"PeriodicalIF":2.6,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}