Briefings in Functional Genomics最新文献_第3页

A comprehensive review of deep learning-based variant calling methods. 基于深度学习的变体调用方法综述。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-07-19 DOI: 10.1093/bfgp/elae003

Ren Junjun, Zhang Zhengqian, Wu Ying, Wang Jialiang, Liu Yongzhuang

引用次数: 0

Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease. 炎症性肠病中长非编码RNA基因的系统分析和表征。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-07-19 DOI: 10.1093/bfgp/elad044

Rania Velissari, Mirolyuba Ilieva, James Dao, Henry E Miller, Jens Hedelund Madsen, Jan Gorodkin, Masanori Aikawa, Hideshi Ishii, Shizuka Uchida

{"title":"Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease.","authors":"Rania Velissari, Mirolyuba Ilieva, James Dao, Henry E Miller, Jens Hedelund Madsen, Jan Gorodkin, Masanori Aikawa, Hideshi Ishii, Shizuka Uchida","doi":"10.1093/bfgp/elad044","DOIUrl":"10.1093/bfgp/elad044","url":null,"abstract":"The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https://ibd-db.shinyapps.io/IBDB/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11260263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157627","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}

引用次数: 0

Competing endogenous RNAs in head and neck squamous cell carcinoma: a review. 头颈部鳞状细胞癌中竞争性内源性RNA的研究进展。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-07-19 DOI: 10.1093/bfgp/elad049

Avantika Agrawal, Vaibhav Vindal

{"title":"Competing endogenous RNAs in head and neck squamous cell carcinoma: a review.","authors":"Avantika Agrawal, Vaibhav Vindal","doi":"10.1093/bfgp/elad049","DOIUrl":"10.1093/bfgp/elad049","url":null,"abstract":"Our understanding of RNA biology has evolved with recent advances in research from it being a non-functional product to molecules of the genome with specific regulatory functions. Competitive endogenous RNA (ceRNA), which has gained prominence over time as an essential part of post-transcriptional regulatory mechanism, is one such example. The ceRNA biology hypothesis states that coding RNA and non-coding RNA co-regulate each other using microRNA (miRNA) response elements. The ceRNA components include long non-coding RNAs, pseudogene and circular RNAs that exert their effect by interacting with miRNA and regulate the expression level of its target genes. Emerging evidence has revealed that the dysregulation of the ceRNA network is attributed to the pathogenesis of various cancers, including the head and neck squamous cell carcinoma (HNSCC). This is the most prevalent cancer developed from the mucosal epithelium in the lip, oral cavity, larynx and pharynx. Although many efforts have been made to comprehend the cause and subsequent treatment of HNSCC, the morbidity and mortality rate remains high. Hence, there is an urgent need to understand the holistic progression of HNSCC, mediated by ceRNA, that can have immense relevance in identifying novel biomarkers with a defined therapeutic intervention. In this review, we have made an effort to highlight the ceRNA biology hypothesis with a focus on its involvement in the progression of HNSCC. For the identification of such ceRNAs, we have additionally highlighted a number of databases and tools.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523465","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}

引用次数: 0

An overview of key online resources for human genomics: a powerful and open toolbox for in silico research. 人类基因组学主要在线资源概览：用于硅学研究的强大而开放的工具箱。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-07-12 DOI: 10.1093/bfgp/elae029

Diego A Forero, Diego A Bonilla, Yeimy González-Giraldo, George P Patrinos

引用次数: 0

Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases. 基于公共数据库转录组数据的中华绒螯蟹遗传变异挖掘。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-07-10 DOI: 10.1093/bfgp/elae030

Yuanfeng Xu, Fan Yu, Wenrong Feng, Jia Wei, Shengyan Su, Jianlin Li, Guoan Hua, Wenjing Li, Yongkai Tang

{"title":"Genetic variation mining of the Chinese mitten crab (Eriocheir sinensis) based on transcriptome data from public databases.","authors":"Yuanfeng Xu, Fan Yu, Wenrong Feng, Jia Wei, Shengyan Su, Jianlin Li, Guoan Hua, Wenjing Li, Yongkai Tang","doi":"10.1093/bfgp/elae030","DOIUrl":"https://doi.org/10.1093/bfgp/elae030","url":null,"abstract":"At present, public databases house an extensive repository of transcriptome data, with the volume continuing to grow at an accelerated pace. Utilizing these data effectively is a shared interest within the scientific community. In this study, we introduced a novel strategy that harnesses SNPs and InDels identified from transcriptome data, combined with sample metadata from databases, to effectively screen for molecular markers correlated with traits. We utilized 228 transcriptome datasets of Eriocheir sinensis from the NCBI database and employed the Genome Analysis Toolkit software to identify 96 388 SNPs and 20 645 InDels. Employing the genome-wide association study analysis, in conjunction with the gender information from databases, we identified 3456 sex-biased SNPs and 639 sex-biased InDels. The KOG and KEGG annotations of the sex-biased SNPs and InDels revealed that these genes were primarily involved in the metabolic processes of E. sinensis. Combined with SnpEff annotation and PCR experimental validation, a highly sex-biased SNP located in the Kelch domain containing 4 (Klhdc4) gene, CHR67-6415071, was found to alter the splicing sites of Klhdc4, generating two splice variants, Klhdc4_a and Klhdc4_b. Additionally, Klhdc4 exhibited robust expression across the ovaries, testes, and accessory glands. The sex-biased SNPs and InDels identified in this study are conducive to the development of unisexual cultivation methods for E. sinensis, and the alternative splicing event caused by the sex-biased SNP in Klhdc4 may serve as a potential mechanism for sex regulation in E. sinensis. The analysis strategy employed in this study represents a new direction for the rational exploitation and utilization of transcriptome data in public databases.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141565172","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}

引用次数: 0

Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia. FLT3突变型急性髓性白血病中基因组变异与DNA甲基化之间的相互关系

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-06-30 DOI: 10.1093/bfgp/elae028

Bac Dao, Van Ngu Trinh, Huy V Nguyen, Hoa L Nguyen, Thuc Duy Le, Phuc Loi Luu

{"title":"Crosstalk between genomic variants and DNA methylation in FLT3 mutant acute myeloid leukemia.","authors":"Bac Dao, Van Ngu Trinh, Huy V Nguyen, Hoa L Nguyen, Thuc Duy Le, Phuc Loi Luu","doi":"10.1093/bfgp/elae028","DOIUrl":"https://doi.org/10.1093/bfgp/elae028","url":null,"abstract":"Acute myeloid leukemia (AML) is a type of blood cancer with diverse genetic variations and DNA methylation alterations. By studying the interaction of gene mutations, expression, and DNA methylation, we aimed to gain valuable insights into the processes that lead to block differentiation in AML. We analyzed TCGA-LAML data (173 samples) with RNA sequencing and DNA methylation arrays, comparing FLT3 mutant (48) and wild-type (125) cases. We conducted differential gene expression analysis using cBioPortal, identified DNA methylation differences with ChAMP tool, and correlated them with gene expression changes. Gene set enrichment analysis (g:Profiler) revealed significant biological processes and pathways. ShinyGo and GeneCards were used to find potential transcription factors and their binding sites among significant genes. We found significant differentially expressed genes (DEGs) negatively correlated with their most significant methylation probes (Pearson correlation coefficient of -0.49, P-value <0.001) between FLT3 mutant and wild-type groups. Moreover, our exploration of 450 k CpG sites uncovered a global hypo-methylated status in 168 DEGs. Notably, these methylation changes were enriched in the promoter regions of Homebox superfamily gene, which are crucial in transcriptional-regulating pathways in blood cancer. Furthermore, in FLT3 mutant AML patient samples, we observed overexpress of WT1, a transcription factor known to bind homeobox gene family. This finding suggests a potential mechanism by which WT1 recruits TET2 to demethylate specific genomic regions. Integrating gene expression and DNA methylation analyses shed light on the impact of FLT3 mutations on cancer cell development and differentiation, supporting a two-hit model in AML. This research advances understanding of AML and fosters targeted therapeutic strategy development.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472885","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}

引用次数: 0

Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework. 利用混合深度学习框架鉴定双链 RNA 及其对昆虫的沉默效率。

IF 2.5 3区生物学

Briefings in Functional Genomics Pub Date : 2024-06-23 DOI: 10.1093/bfgp/elae027

Han Cheng, Liping Xu, Cangzhi Jia

{"title":"Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework.","authors":"Han Cheng, Liping Xu, Cangzhi Jia","doi":"10.1093/bfgp/elae027","DOIUrl":"https://doi.org/10.1093/bfgp/elae027","url":null,"abstract":"RNA interference (RNAi) technology is widely used in the biological prevention and control of terrestrial insects. One of the main factors with the application of RNAi in insects is the difference in RNAi efficiency, which may vary not only in different insects, but also in different genes of the same insect, and even in different double-stranded RNAs (dsRNAs) of the same gene. This work focuses on the last question and establishes a bioinformatics software that can help researchers screen for the most efficient dsRNA targeting target genes. Among insects, the red flour beetle (Tribolium castaneum) is known to be one of the most sensitive to RNAi. From iBeetle-Base, we extracted 12 027 efficient dsRNA sequences with a lethality rate of ≥20% or with experimentation-induced phenotypic changes and processed these data to correspond to specific silence efficiency. Based on the first complied novel benchmark dataset, we specifically designed a deep neural network to identify and characterize efficient dsRNA for RNAi in insects. The dna2vec word embedding model was trained to extract distributed feature representations, and three powerful modules, namely convolutional neural network, bidirectional long short-term memory network, and self-attention mechanism, were integrated to form our predictor model to characterize the extracted dsRNAs and their silencing efficiencies for T. castaneum. Our model dsRNAPredictor showed reliable performance in multiple independent tests based on different species, including both T. castaneum and Aedes aegypti. This indicates that dsRNAPredictor can facilitate prescreening for designing high-efficiency dsRNA targeting target genes of insects in advance.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443790","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}

引用次数: 0

Long-read RNA sequencing can probe organelle genome pervasive transcription. 长读 RNA 测序可探测细胞器基因组的普遍转录。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-06-17 DOI: 10.1093/bfgp/elae026

Matheus Sanita Lima, Douglas Silva Domingues, Alexandre Rossi Paschoal, David Roy Smith

{"title":"Long-read RNA sequencing can probe organelle genome pervasive transcription.","authors":"Matheus Sanita Lima, Douglas Silva Domingues, Alexandre Rossi Paschoal, David Roy Smith","doi":"10.1093/bfgp/elae026","DOIUrl":"https://doi.org/10.1093/bfgp/elae026","url":null,"abstract":"40 years ago, organelle genomes were assumed to be streamlined and, perhaps, unexciting remnants of their prokaryotic past. However, the field of organelle genomics has exposed an unparallel diversity in genome architecture (i.e. genome size, structure, and content). The transcription of these eccentric genomes can be just as elaborate - organelle genomes are pervasively transcribed into a plethora of RNA types. However, while organelle protein-coding genes are known to produce polycistronic transcripts that undergo heavy posttranscriptional processing, the nature of organelle noncoding transcriptomes is still poorly resolved. Here, we review how wet-lab experiments and second-generation sequencing data (i.e. short reads) have been useful to determine certain types of organelle RNAs, particularly noncoding RNAs. We then explain how third-generation (long-read) RNA-Seq data represent the new frontier in organelle transcriptomics. We show that public repositories (e.g. NCBI SRA) already contain enough data for inter-phyla comparative studies and argue that organelle biologists can benefit from such data. We discuss the prospects of using publicly available sequencing data for organelle-focused studies and examine the challenges of such an approach. We highlight that the lack of a comprehensive database dedicated to organelle genomics/transcriptomics is a major impediment to the development of a field with implications in basic and applied science.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332590","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}

引用次数: 0

Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer. 整合单细胞测序数据以揭示癌症中铁凋亡机制的进展。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-06-14 DOI: 10.1093/bfgp/elae025

Zhaolan Du, Yi Shi, Jianjun Tan

{"title":"Advances in integrating single-cell sequencing data to unravel the mechanism of ferroptosis in cancer.","authors":"Zhaolan Du, Yi Shi, Jianjun Tan","doi":"10.1093/bfgp/elae025","DOIUrl":"https://doi.org/10.1093/bfgp/elae025","url":null,"abstract":"Ferroptosis, a commonly observed type of programmed cell death caused by abnormal metabolic and biochemical mechanisms, is frequently triggered by cellular stress. The occurrence of ferroptosis is predominantly linked to pathophysiological conditions due to the substantial impact of various metabolic pathways, including fatty acid metabolism and iron regulation, on cellular reactions to lipid peroxidation and ferroptosis. This mode of cell death serves as a fundamental factor in the development of numerous diseases, thereby presenting a range of therapeutic targets. Single-cell sequencing technology provides insights into the cellular and molecular characteristics of individual cells, as opposed to bulk sequencing, which provides data in a more generalized manner. Single-cell sequencing has found extensive application in the field of cancer research. This paper reviews the progress made in ferroptosis-associated cancer research using single-cell sequencing, including ferroptosis-associated pathways, immune checkpoints, biomarkers, and the identification of cell clusters associated with ferroptosis in tumors. In general, the utilization of single-cell sequencing technology has the potential to contribute significantly to the investigation of the mechanistic regulatory pathways linked to ferroptosis. Moreover, it can shed light on the intricate connection between ferroptosis and cancer. This technology holds great promise in advancing tumor-wide diagnosis, targeted therapy, and prognosis prediction.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319002","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}

引用次数: 0

AMLdb: a comprehensive multi-omics platform to identify biomarkers and drug targets for acute myeloid leukemia. AMLdb：鉴定急性髓性白血病生物标志物和药物靶点的综合性多组学平台。

IF 4 3区生物学

Briefings in Functional Genomics Pub Date : 2024-06-12 DOI: 10.1093/bfgp/elae024

Keerthana Vinod Kumar, Ambuj Kumar, Kavita Kundal, Avik Sengupta, Kunjulakshmi R, Subashani Singh, Bhanu Teja Korra, Simran Sharma, Vandana Suresh, Mayilaadumveettil Nishana, Rahul Kumar

{"title":"AMLdb: a comprehensive multi-omics platform to identify biomarkers and drug targets for acute myeloid leukemia.","authors":"Keerthana Vinod Kumar, Ambuj Kumar, Kavita Kundal, Avik Sengupta, Kunjulakshmi R, Subashani Singh, Bhanu Teja Korra, Simran Sharma, Vandana Suresh, Mayilaadumveettil Nishana, Rahul Kumar","doi":"10.1093/bfgp/elae024","DOIUrl":"https://doi.org/10.1093/bfgp/elae024","url":null,"abstract":"Acute myeloid leukemia (AML) is one of the leading leukemic malignancies in adults. The heterogeneity of the disease makes the diagnosis and treatment extremely difficult. With the advent of next-generation sequencing (NGS) technologies, exploration at the molecular level for the identification of biomarkers and drug targets has been the focus for the researchers to come up with novel therapies for better prognosis and survival outcomes of AML patients. However, the huge amount of data from NGS platforms requires a comprehensive AML platform to streamline literature mining efforts and save time. To facilitate this, we developed AMLdb, an interactive multi-omics platform that allows users to query, visualize, retrieve, and analyse AML related multi-omics data. AMLdb contains 86 datasets for gene expression profiles, 15 datasets for methylation profiles, CRISPR-Cas9 knockout screens of 26 AML cell lines, sensitivity of 26 AML cell lines to 288 drugs, mutations in 41 unique genes in 23 AML cell lines, and information on 41 experimentally validated biomarkers. In this study, we have reported five genes, i.e. CBFB, ENO1, IMPDH2, SEPHS2, and MYH9 identified via our analysis using AMLdb. ENO1 is uniquely identified gene which requires further investigation as a novel potential target while other reported genes have been previously confirmed as targets through experimental studies. Top of form we believe that these findings utilizing AMLdb can make it an invaluable resource to accelerate the development of effective therapies for AML and assisting the research community in advancing their understanding of AML pathogenesis. AMLdb is freely available at https://project.iith.ac.in/cgntlab/amldb.","PeriodicalId":55323,"journal":{"name":"Briefings in Functional Genomics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307484","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}

引用次数: 0