Genes & genomics最新文献

{"title":"Advances in cancer genomics and precision oncology.","authors":"Yonjong Heo, Woo-Jin Kim, Yong-Joon Cho, Jae-Won Jung, Nam-Soo Kim, Ik-Young Choi","doi":"10.1007/s13258-024-01614-7","DOIUrl":"10.1007/s13258-024-01614-7","url":null,"abstract":"<p><strong>Background: </strong>Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division. Utilization of next-generation sequencing in cancer gene panels has enabled the identification of actionable gene alterations in cancer patients to guide personalized precision medicine.</p><p><strong>Objective: </strong>The aim is to provide information that can identify actionable gene alterations, enabling personalized precision medicine for cancer patients.</p><p><strong>Results & discussion: </strong>Equipped with next-generation sequencing techniques, international collaboration programs on cancer genomics have identified numerous mutations, gene fusions, microsatellite variations, copy number variations, and epigenetics changes that promote the transformation of normal cells into tumors. Cancer classification has traditionally been based on cell type or tissue-of-origin and the morphological characteristics of the cancer. However, interactive genomic analyses have currently reclassified cancers based on systemic molecular-based taxonomy. Although all cancer-causing genes and mechanisms have yet to be completely understood or identified, personalized or precision medicine is now currently possible for some forms of cancer. Unlike the \"one-size-fits-all\" approach of traditional medicine, precision medicine allows for customized or personalized treatment based on genomic information.</p><p><strong>Conclusion: </strong>Despite the availability of numerous cancer gene panels, technological innovation in genomics and expansion of knowledge on the cancer genome will allow precision oncology to manage even more types of cancers.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"399-416"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative analysis of genetic variability and functional traits in lung adenocarcinoma epithelial cells via single-cell RNA sequencing, GWAS, bayesian deconvolution, and machine learning.","authors":"Chenggen Gao, Jintao Wu, Fangyan Zhong, Xianxin Yang, Hanwen Liu, Junming Lai, Jing Cai, Weimin Mao, Huijuan Xu","doi":"10.1007/s13258-025-01621-2","DOIUrl":"10.1007/s13258-025-01621-2","url":null,"abstract":"<p><strong>Background: </strong>Lung adenocarcinoma remains a leading cause of cancer-related mortality worldwide, characterized by high genetic and cellular heterogeneity, especially within the tumor microenvironment.</p><p><strong>Objective: </strong>This study integrates single-cell RNA sequencing (scRNA-seq) with genome-wide association studies (GWAS) using Bayesian deconvolution and machine learning techniques to unravel the genetic and functional complexity of lung adenocarcinoma epithelial cells.</p><p><strong>Methods: </strong>We performed scRNA-seq and GWAS analysis to identify critical cell populations affected by genetic variations. Bayesian deconvolution and machine learning techniques were applied to investigate tumor progression, prognosis, and immune-epithelial cell interactions, particularly focusing on immune checkpoint markers such as PD-L1 and CTLA-4.</p><p><strong>Results: </strong>Our analysis highlights the importance of genes like SLC2A1, which regulates glucose metabolism and correlates with tumor invasiveness and poor prognosis. Immune-epithelial interactions suggest a suppressive tumor microenvironment, potentially hindering immune responses. Additionally, machine learning models identify core prognostic genes such as F12, GOLM1, and S100P, which are significantly associated with patient survival.</p><p><strong>Conclusions: </strong>This comprehensive approach provides novel insights into lung adenocarcinoma biology, emphasizing the role of genetic and immune factors in tumor progression. The findings support the development of personalized therapeutic strategies targeting both tumor cells and the immune microenvironment.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"435-468"},"PeriodicalIF":1.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12000210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo).","authors":"Md Jahid Hasan Jone, Md Nure Adil Siddique, Manosh Kumar Biswas, Mohammad Rashed Hossain","doi":"10.1007/s13258-025-01617-y","DOIUrl":"10.1007/s13258-025-01617-y","url":null,"abstract":"<p><strong>Background: </strong>TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done.</p><p><strong>Objective: </strong>The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions.</p><p><strong>Methods: </strong>The chromosomal location, gene structure, conserved motifs, protein domains, structural homology, cis-regulating elements, transcript expression patterns, and potential protein-protein interactions were analyzed using various databases and webtools.</p><p><strong>Results: </strong>A total of 29 putative TCP genes are identified in melon. These genes were classified into two classes: Class-I (13 genes) and Class-II (16 genes). The results revealed that the putative CmTCP genes are distributed across nine of the twelve melon chromosomes and exhibit diverse expression patterns in different tissues which mostly indicates their potential role in floral organ development, lateral branching, growth and development. Phylogenetic analysis suggests that some CmTCP genes may have similar functions to their homologs in other plant species, while others may have undergone functional diversification.</p><p><strong>Conclusion: </strong>This study paves the way for future investigations into the specific roles of individual CmTCP genes in melon and for elucidating the mechanisms by which TCP proteins regulate leaf elongation, floral development, and lateral branching.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"367-382"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CKAP4 is a potential therapeutic target to overcome resistance to EGFR-TKIs in lung adenocarcinoma.","authors":"Seongeun Song, Sangmyung Rhee","doi":"10.1007/s13258-024-01606-7","DOIUrl":"10.1007/s13258-024-01606-7","url":null,"abstract":"<p><strong>Background: </strong>Epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) are standard treatments for non-small cell lung cancer (NSCLC) patients with EGFR mutations; however, drug resistance limits their efficacy. Cytoskeleton-associated protein 4 (CKAP4) has been linked to cancer progression, but its role in EGFR-TKI resistance remains unclear.</p><p><strong>Objective: </strong>This study investigates the clinical relevance of CKAP4 as a therapeutic target to overcome EGFR-TKI resistance in lung adenocarcinoma (LUAD) patients.</p><p><strong>Methods: </strong>GEO datasets were analyzed to identify 24 differentially expressed genes associated with EGFR-TKI resistance, with CKAP4 selected via functional annotation and scoring using the VarElect tool. The prognostic significance of CKAP4 was evaluated using public databases, and its upregulation was confirmed in osimertinib-tolerant H1975 cells through quantitative reverse transcription-polymerase chain reaction.</p><p><strong>Results: </strong>Integrated bioinformatics analysis identified CKAP4 as strongly associated with EGFR-TKI resistance. Elevated CKAP4 expression was particularly linked to poorer clinical outcomes in LUAD patients. Notably, osimertinib-tolerant cells exhibited high CKAP4 expression, correlating positively with increased half-maximal inhibitory concentrations of EGFR-TKIs. LUAD patients with upregulated CKAP4 showed significantly reduced overall and relapse-free survival.</p><p><strong>Conclusion: </strong>This study underscores the prognostic value of CKAP4 in EGFR-mutated LUAD and highlights its potential as a therapeutic target to counter EGFR-TKI resistance.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"331-340"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of wild soybean (Glycine soja) under salt stress and identification of salt-responsive genes.","authors":"Man Bo Lee, Taekyeom Kim, Dae Yeon Kim, Su Kyoung Lee, Jae Yoon Kim","doi":"10.1007/s13258-024-01599-3","DOIUrl":"10.1007/s13258-024-01599-3","url":null,"abstract":"<p><strong>Background: </strong>Soil salinity has been a serious threat to agricultural production worldwide, including soybeans. Glycine soja, the wild ancestor of cultivated soybeans, harbors high genetic diversity and possesses attractive rare alleles.</p><p><strong>Objective: </strong>We conducted a transcriptome analysis of G. soja subjected to salt stress to profile the transcriptomes and identify salt-responsive genes.</p><p><strong>Methods: </strong>G. soja was subjected to salt stress at 0, 24, and 48 h. RNA was sequenced using the Illumina NovaSeq 6000 platform. Transcriptome sequencing was used to identify differentially expressed genes (DEGs) and differential alternative splicing genes (DASGs) and to analyze alterations in salt-responsive genes.</p><p><strong>Results: </strong>A total of 249 and 1890 DEGs were identified at 24 and 48 h under salt stress, respectively. Among the DEGs, 45 and 252 transcription factors, including bHLH, MYB, and WRKY, were identified at 24 and 48 h, respectively. Additionally, 602 and 1850 DASGs were identified at 24 and 48 h, respectively. For DASGs, significant GO term enrichments included 'mRNA processing', 'Chromatin organization', 'Nucleus', and 'Transcription cofactor activity' at 48 h. The KEGG pathways, 'Spliceosome' and the 'mRNA surveillance pathway', were significantly enriched in DASGs at 48 h. Salt-responsive genes were identified in DEGs and/or DASGs, specifically GsJ3, GsACA12, GsACA13, GsHSFA2-like, and GsHSF30-like.</p><p><strong>Conclusion: </strong>Through the analysis of DEGs, DASGs, and transcription factor predictions, we identified key factors involved in the salt stress response and tolerance of G. soja, which could contribute to salt-tolerant soybean cultivar through genetic engineering strategies.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"351-365"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of SNPs associated with fatty acid contents in mutant soybean lines by a genome-wide association study.","authors":"Jeong Woo Lee, Jung Min Kim, Dae June Kim, Ji Su Seo, Bo-Keun Ha, Soon-Jae Kwon","doi":"10.1007/s13258-024-01608-5","DOIUrl":"10.1007/s13258-024-01608-5","url":null,"abstract":"<p><strong>Background: </strong>Vegetable oils are primarily composed of unsaturated fatty acids. Soybean [Glycine max (L.) Merr.] oil, accounting for 28% of the global production of vegetable oil, contains mainly two saturated fatty acids (palmitic acid and stearic acid) and three unsaturated fatty acids (oleic acid, linoleic acid, and linolenic acid) in seeds.</p><p><strong>Objective: </strong>The five fatty acids determine soybean oil quality. We aimed to identify genetic relationship between genomics and fatty acid contents in soybean mutant pool.</p><p><strong>Methods: </strong>This study used a mutant diversity pool (MDP) comprising 192 soybean lines. A genome-wide association study (GWAS) was conducted with the diverse fatty acid contents in MDP and 17,631 filtered SNPs from genotyping-by-sequencing (GBS).</p><p><strong>Results: </strong>The GWAS revealed nine significant SNPs within intragenic regions that were associated with fatty acid composition. These SNPs corresponded to six genes (Glyma.03g042500, Glyma.07g069200, Glyma.13g150200, Glyma.14g223100, Glyma.15g084700, and Glyma.15g274000), of which three (Glyma.03g042500, Glyma.13g150200, and Glyma.15g274000) were predicted to be candidate genes influencing oleic acid, linoleic acid, and linolenic acid contents. Analyses of SNP allelic effects revealed the largest and smallest significant differences in fatty acid contents were 5.53% (linolenic acid) and 0.4% (stearic acid), respectively.</p><p><strong>Conclusion: </strong>The present study detected significant phenotypic variations and genetic associations underlying the fatty acid composition of soybean seeds in MDP lines. The mutant seeds differed from the original cultivars in terms of fatty acids composition, with the allelic effects of significant SNPs influencing the fatty acid content in seeds. These findings may be useful for enhancing breeding strategies to optimize soybean oil quality for various uses.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"307-320"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142876942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative bioinformatics approaches reveal key hub genes in cyanobacteria: insights from Synechocystis sp. PCC 6803 and Geminocystis sp. NIES-3708 under abiotic stress conditions.","authors":"Abbas Karimi-Fard, Abbas Saidi, Masoud Tohidfar, Seyede N Emami","doi":"10.1007/s13258-025-01615-0","DOIUrl":"10.1007/s13258-025-01615-0","url":null,"abstract":"<p><strong>Background: </strong>Cyanobacteria, particularly Synechocystis sp. PCC 6803, serve as model organisms for studying acclimation strategies that enable adaptation to various environmental stresses. Understanding the molecular mechanisms underlying these adaptations provides insight into how cells adjust gene expression in response to challenging conditions.</p><p><strong>Objective: </strong>To analyze the transcriptome data of Synechocystis sp. PCC 6803 under light, salinity, and iron stress conditions and to identify hub genes potentially involved in stress response, specifically comparing the findings with Geminocystis sp. NIES-3708.</p><p><strong>Methods: </strong>A comprehensive bioinformatics approach was applied, integrating meta-analysis, weighted gene co-expression network analysis (WGCNA), and a Random Forest (RF) machine learning algorithm. These approaches underscore the robustness of our findings, allowing for a more nuanced understanding of gene interactions and their functional relevance in stress responses. This methodology was used to identify key hub genes in Synechocystis sp. PCC 6803 that may have conserved roles in Geminocystis sp. NIES-3708. A total of four potential hub genes, including slr1392, slr1484, sll1549, and sll1863, were identified. Among these, only sll1549 had a homolog (GM3708_2556) with 71% sequence similarity and 70% query coverage in Geminocystis sp. NIES-3708. The expression of GM3708_2556 was further evaluated under nitrate, salt, and combined salinity-nitrate stress conditions using RT-qPCR.</p><p><strong>Results: </strong>Transcript levels of GM3708_2556 increased significantly under salt stress (3.35-fold, p-value < 0.05) and combined salinity-nitrate stress (2.24-fold, p-value < 0.05) compared to control conditions, while no significant change was observed under nitrate stress alone. These results suggest that GM3708_2556 may play a crucial role in the organism's response to salt stress, with potential interactions in nitrate metabolism.</p><p><strong>Conclusion: </strong>This study highlights the gene GM3708_2556 as a significant factor in salt stress response, with implications for conserved functional roles across cyanobacterial species. Furthermore, the findings have potential relevance to biotechnology, particularly in engineering stress-resistant cyanobacterial strains for applications in sustainable agriculture and bioenergy production.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"383-397"},"PeriodicalIF":1.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential role of ARG1 c.57G > A variant in Argininemia.","authors":"Yixiao Li, Rujin Tian, Dong Wang, Haozheng Zhang, Yi Zhou, Chunli Ma, Han Zhang, Kaihui Zhang, Shu Liu","doi":"10.1007/s13258-024-01595-7","DOIUrl":"10.1007/s13258-024-01595-7","url":null,"abstract":"<p><strong>Background and objective: </strong>Argininemia (OMIM: 207800), as well as arginase deficiency, a disorder of the urea cycle caused by deficiency of arginase 1 (ARG1, NP_000036.2), is a scarce autosomal recessive genetic disease. The patients who suffered with argininemia often showed spastic paraplegia, epileptic seizures, severe mental retardation, and even the hyperammonemia. In neonatal screening, we found a healthy baby with mild elevated arginine levels. We have demonstrated the genetic etiology of the patient.</p><p><strong>Methods: </strong>The patient's clinical characteristic and family history were collected. The technologies including Next Generation Sequencing (NGS), Sanger sequencing, Bioinformatics Analysis, RNA extraction, cDNA obtained, Sanger sequencing, Minigene splicing assay, Real-time PCR, Single-molecule real-time (SMRT) sequencing were applied.</p><p><strong>Results: </strong>One homozygous variant, c.57G > A (p.Q19=), was identified in the proband, which was inherited from the parents. Through different detection methods, we found that the c.57G > A variant causes three different transcriptional versions: normal mRNA (mRNA from blood), mRNA with the exon2 deletion (73bp, mRNA from blood and minigene assay), and mRNA sequence from the SMRT sequencing (parts of exons and introns were detected, including exon 1-4, intron 1 and 4, and part of intron 2, 3, and 5). The expression of ARG1 mRNA and protein also decreased in the blood. The related genes of NMD (Nonsense-mediated mRNA decay), SMG1, UPF1, and UPF3b, were expressed higher than the controls in the blood, which hints the NMD could play a role in the mRNA decay regarding the cDNA with 73bp deletion by c.57G > A variant.</p><p><strong>Conclusions: </strong>The study is the first study considering a synonymous variant of the ARG1 gene influencing alternative splicing(AS). Otherwise, the variant c.57G > A is relatively frequent in the general population( MAF = 0.0146). Our discovery revealed the variant possesses partial pathogenic potential, which would contribute to the deeper understanding and gold model for the intricate relationship between genetic mutations, arginine metabolism, and physical function.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"197-205"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle.","authors":"Dongmei Zhu, Xingmin Geng, Fanyu Zeng, Shida Xu, Jieyu Peng","doi":"10.1007/s13258-024-01593-9","DOIUrl":"10.1007/s13258-024-01593-9","url":null,"abstract":"<p><strong>Background: </strong>The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle).</p><p><strong>Objective: </strong>To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle.</p><p><strong>Methods: </strong>In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR).</p><p><strong>Results: </strong>We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds.</p><p><strong>Conclusion: </strong>In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"171-182"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The diverse landscape of RNA modifications in cancer development and progression.","authors":"Hyung Seok Kim, Jung Woo Eun, Se Ha Jang, Ji Yun Kim, Jee-Yeong Jeong","doi":"10.1007/s13258-024-01601-y","DOIUrl":"10.1007/s13258-024-01601-y","url":null,"abstract":"<p><strong>Background: </strong>RNA modifications, a central aspect of epitranscriptomics, add a regulatory layer to gene expression by modifying RNA function without altering nucleotide sequences. These modifications play vital roles across RNA species, influencing RNA stability, translation, and interaction dynamics, and are regulated by specific enzymes that add, remove, and interpret these chemical marks.</p><p><strong>Objective: </strong>This review examines the role of aberrant RNA modifications in cancer progression, exploring their potential as diagnostic and prognostic biomarkers and as therapeutic targets. We focus on how altered RNA modification patterns impact oncogenes, tumor suppressor genes, and overall tumor behavior.</p><p><strong>Methods: </strong>We performed an in-depth analysis of recent studies and advances in RNA modification research, highlighting key types and functions of RNA modifications and their roles in cancer biology. Studies involving preclinical models targeting RNA-modifying enzymes were reviewed to assess therapeutic efficacy and potential clinical applications.</p><p><strong>Results: </strong>Aberrant RNA modifications were found to significantly influence cancer initiation, growth, and metastasis. Dysregulation of RNA-modifying enzymes led to altered gene expression profiles in oncogenes and tumor suppressors, correlating with tumor aggressiveness, patient outcomes, and response to immunotherapy. Notably, inhibitors of these enzymes demonstrated potential in preclinical models by reducing tumor growth and enhancing the efficacy of existing cancer treatments.</p><p><strong>Conclusions: </strong>RNA modifications present promising avenues for cancer diagnosis, prognosis, and therapy. Understanding the mechanisms of RNA modification dysregulation is essential for developing targeted treatments that improve patient outcomes. Further research will deepen insights into these pathways and support the clinical translation of RNA modification-targeted therapies.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":" ","pages":"135-155"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}