Genomics and Informatics最新文献

Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers 胃癌患者的肠道元基因组分析显示，Akkermansia、Gammaproteobacteria 和 Veillonella 微生物群是潜在的非侵入性生物标记物

Genomics and Informatics Pub Date : 2024-05-21 DOI: 10.1186/s44342-024-00001-8

Anju R. Nath, Jeyakumar Natarajan

引用次数: 0

Cell line-specific features of 3D chromatin organization in hepatocellular carcinoma. 肝细胞癌中三维染色质组织的细胞系特异性特征

Genomics and Informatics Pub Date : 2023-06-01 Epub Date: 2023-06-30 DOI: 10.5808/gi.23015

Yeonwoo Kim, Hyeokjun Yang, Daeyoup Lee

{"title":"Cell line-specific features of 3D chromatin organization in hepatocellular carcinoma.","authors":"Yeonwoo Kim, Hyeokjun Yang, Daeyoup Lee","doi":"10.5808/gi.23015","DOIUrl":"10.5808/gi.23015","url":null,"abstract":"Liver cancer, particularly hepatocellular carcinoma (HCC), poses a significant global threat to human lives. To advance the development of innovative diagnostic and treatment approaches, it is essential to examine the hidden features of HCC, particularly its 3D genome architecture, which is not well understood. In this study, we investigated the 3D genome organization of four HCC cell lines-Hep3B, Huh1, Huh7, and SNU449-using in situ Hi-C and assay for transposase-accessible chromatin sequencing. Our findings revealed that HCC cell lines had more long-range interactions, both intra-and interchromosomal, compared to human mammary epithelial cells (HMECs). Unexpectedly, HCC cell lines displayed cell line-specific compartmental modifications at the megabase (Mb) scale, which could potentially be leveraged in determining HCC subtypes. At the sub-Mb scale, we observed decreases in intra-TAD (topologically associated domain) interactions and chromatin loops in HCC cell lines compared to HMECs. Lastly, we discovered a correlation between gene expression and the 3D chromatin architecture of SLC8A1, which encodes a sodium-calcium antiporter whose modulation is known to induce apoptosis by comparison between HCC cell lines and HMECs. Our findings suggest that HCC cell lines have a distinct 3D genome organization that is different from those of normal and other cancer cells based on the analysis of compartments, TADs, and chromatin loops. Overall, we take this as evidence that genome organization plays a crucial role in cancer phenotype determination. Further exploration of epigenetics in HCC will help us to better understand specific gene regulation mechanisms and uncover novel targets for cancer treatment.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e19"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10259040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

COVID-19 progression towards ARDS: a genome wide study reveals host factors underlying critical COVID-19. COVID-19 向 ARDS 的发展：一项全基因组研究揭示了关键 COVID-19 的宿主因素。

Genomics and Informatics Pub Date : 2023-06-01 Epub Date: 2023-06-30 DOI: 10.5808/gi.22080

Shama Mujawar, Gayatri Patil, Srushti Suthar, Tanuja Shendkar, Vaishnavi Gangadhar

{"title":"COVID-19 progression towards ARDS: a genome wide study reveals host factors underlying critical COVID-19.","authors":"Shama Mujawar, Gayatri Patil, Srushti Suthar, Tanuja Shendkar, Vaishnavi Gangadhar","doi":"10.5808/gi.22080","DOIUrl":"10.5808/gi.22080","url":null,"abstract":"Coronavirus disease 2019 (COVID-19) is a viral infection produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus epidemic, which was declared a global pandemic in March 2020. The World Health Organization has recorded around 43.3 billion cases and 59.4 million casualties to date, posing a severe threat to global health. Severe COVID-19 indicates viral pneumonia caused by the SARS-CoV-2 infections, which can induce fatal consequences, including acute respiratory distress syndrome (ARDS). The purpose of this research is to better understand the COVID-19 and ARDS pathways, as well as to find targeted single nucleotide polymorphism. To accomplish this, we retrieved over 100 patients' samples from the Sequence Read Archive, National Center for Biotechnology Information. These sequences were processed through the Galaxy server next generation sequencing pipeline for variant analysis and then visualized in the Integrative Genomics Viewer, and performed statistical analysis using t-tests and Bonferroni correction, where six major genes were identified as DNAH7, CLUAP1, PPA2, PAPSS1, TLR4, and IFITM3. Furthermore, a complete understanding of the genomes of COVID-19-related ARDS will aid in the early identification and treatment of target proteins. Finally, the discovery of novel therapeutics based on discovered proteins can assist to slow the progression of ARDS and lower fatality rates.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e16"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10227226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insight from sirtuins interactome: topological prominence and multifaceted roles of SIRT1 in modulating immunity, aging and cancer. 来自SIRT1相互作用组的见解:SIRT1在调节免疫、衰老和癌症中的拓扑突出和多方面作用。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23003

Nur Diyana Zulkifli, Nurulisa Zulkifle

{"title":"Insight from sirtuins interactome: topological prominence and multifaceted roles of SIRT1 in modulating immunity, aging and cancer.","authors":"Nur Diyana Zulkifli, Nurulisa Zulkifle","doi":"10.5808/gi.23003","DOIUrl":"https://doi.org/10.5808/gi.23003","url":null,"abstract":"The mammalian sirtuin family, consisting of SIRT1-SIRT7, plays a vital role in various biological processes, including cancer, diabetes, neurodegeneration, cardiovascular disease, cellular metabolism, and cellular homeostasis maintenance. Due to their involvement in these biological processes, modulating sirtuin activity seems promising to impact immune- and aging-related diseases, as well as cancer pathways. However, more understanding is required regarding the safety and efficacy of sirtuin-targeted therapies due to the complex regulatory mechanisms that govern their activity, particularly in the context of multiple targets. In this study, the interaction landscape of the sirtuin family was analyzed using a systems biology approach. A sirtuin protein-protein interaction network was built using the Cytoscape platform and analyzed using the NetworkAnalyzer and stringApp plugins. The result revealed the sirtuin family's association with numerous proteins that play diverse roles, suggesting a complex interplay between sirtuins and other proteins. Based on network topological and functional analysis, SIRT1 was identified as the most prominent among sirtuin family members, demonstrating that 25 of its protein partners are involved in cancer, 22 in innate immune response, and 29 in aging, with some being linked to a combination of two or more pathways. This study lays the foundation for the development of novel therapies that can target sirtuins with precision and efficacy. By illustrating the various interactions among the proteins in the sirtuin family, we have revealed the multifaceted roles of SIRT1 and provided a framework for their possible roles to be precisely understood, manipulated, and translated into therapeutics in the future.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e23"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10576645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bioinformatic analyses reveal the prognostic significance and potential role of ankyrin 3 (ANK3) in kidney renal clear cell carcinoma. 生物信息学分析揭示了锚蛋白3 (ANK3)在肾透明细胞癌中的预后意义和潜在作用。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23013

Keerakarn Somsuan, Siripat Aluksanasuwan

{"title":"Bioinformatic analyses reveal the prognostic significance and potential role of ankyrin 3 (ANK3) in kidney renal clear cell carcinoma.","authors":"Keerakarn Somsuan, Siripat Aluksanasuwan","doi":"10.5808/gi.23013","DOIUrl":"https://doi.org/10.5808/gi.23013","url":null,"abstract":"Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OSkirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e22"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10231152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Assessing the impact of recombination on the estimation of isolation-with-migration models using genomic data: a simulation study. 利用基因组数据评估重组对迁移隔离模型估计的影响:一项模拟研究。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23016

Yujin Chung

{"title":"Assessing the impact of recombination on the estimation of isolation-with-migration models using genomic data: a simulation study.","authors":"Yujin Chung","doi":"10.5808/gi.23016","DOIUrl":"https://doi.org/10.5808/gi.23016","url":null,"abstract":"Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e27"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10576118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors. 核梭杆菌未鉴定蛋白的功能注释:毒力因子的鉴定。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.22065

Kanchan Rauthan, Saranya Joshi, Lokesh Kumar, Divya Goel, Sudhir Kumar

{"title":"Functional annotation of uncharacterized proteins from Fusobacterium nucleatum: identification of virulence factors.","authors":"Kanchan Rauthan, Saranya Joshi, Lokesh Kumar, Divya Goel, Sudhir Kumar","doi":"10.5808/gi.22065","DOIUrl":"https://doi.org/10.5808/gi.22065","url":null,"abstract":"Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as \"Uncharacterized.\" Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e21"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10593869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational approaches for molecular characterization and structure-based functional elucidation of a hypothetical protein from Mycobacterium tuberculosis. 一种假想的结核分枝杆菌蛋白的分子表征和基于结构的功能解析的计算方法。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23001

Abu Saim Mohammad Saikat

引用次数: 2

Comparison of digital PCR platforms using the molecular marker. 分子标记数字PCR平台的比较。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23008

Cherl-Joon Lee, Wonseok Shin, Minsik Song, Seung-Shick Shin, Yujun Park, Kornsorn Srikulnath, Dong Hee Kim, Kyudong Han

{"title":"Comparison of digital PCR platforms using the molecular marker.","authors":"Cherl-Joon Lee, Wonseok Shin, Minsik Song, Seung-Shick Shin, Yujun Park, Kornsorn Srikulnath, Dong Hee Kim, Kyudong Han","doi":"10.5808/gi.23008","DOIUrl":"https://doi.org/10.5808/gi.23008","url":null,"abstract":"Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e24"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10251734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome. 用生物信息学方法鉴定史蒂文斯-约翰逊综合征的致病变异。

Genomics and Informatics Pub Date : 2023-06-01 DOI: 10.5808/gi.23010

Muhammad Ma'ruf, Justitia Cahyani Fadli, Muhammad Reza Mahendra, Lalu Muhammad Irham, Nanik Sulistyani, Wirawan Adikusuma, Rockie Chong, Abdi Wira Septama

{"title":"A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome.","authors":"Muhammad Ma'ruf, Justitia Cahyani Fadli, Muhammad Reza Mahendra, Lalu Muhammad Irham, Nanik Sulistyani, Wirawan Adikusuma, Rockie Chong, Abdi Wira Septama","doi":"10.5808/gi.23010","DOIUrl":"https://doi.org/10.5808/gi.23010","url":null,"abstract":"Stevens-Johnson syndrome (SJS) produces a severe hypersensitivity reaction caused by Herpes simplex virus or mycoplasma infection, vaccination, systemic disease, or other agents. Several studies have investigated the genetic susceptibility involved in SJS. To provide further genetic insights into the pathogenesis of SJS, this study prioritized high-impact, SJS-associated pathogenic variants through integrating bioinformatic and population genetic data. First, we identified SJS-associated single nucleotide polymorphisms from the genome-wide association studies catalog, followed by genome annotation with HaploReg and variant validation with Ensembl. Subsequently, expression quantitative trait locus (eQTL) from GTEx identified human genetic variants with differential gene expression across human tissues. Our results indicate that two variants, namely rs2074494 and rs5010528, which are encoded by the HLA-C (human leukocyte antigen C) gene, were found to be differentially expressed in skin. The allele frequencies for rs2074494 and rs5010528 also appear to significantly differ across continents. We highlight the utility of these population-specific HLA-C genetic variants for genetic association studies, and aid in early prognosis and disease treatment of SJS.","PeriodicalId":36591,"journal":{"name":"Genomics and Informatics","volume":"21 2","pages":"e26"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10326529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10259044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0