Genes & genomics最新文献

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Striate palmoplantar keratoderma: a novel DSG1 mutation, combined with an LDLR mutation. 流纹掌跖角化症:一种新型 DSG1 基因突变,并伴有 LDLR 基因突变。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-11-06 DOI: 10.1007/s13258-024-01587-7
Li He, Guannan Zhu
{"title":"Striate palmoplantar keratoderma: a novel DSG1 mutation, combined with an LDLR mutation.","authors":"Li He, Guannan Zhu","doi":"10.1007/s13258-024-01587-7","DOIUrl":"https://doi.org/10.1007/s13258-024-01587-7","url":null,"abstract":"<p><strong>Background: </strong>Palmoplantar keratoderma (PPK) is a heterogeneous group of disorders characterized by abnormal thickening of the skin on the palms and soles. Striate palmoplantar keratoderma (SPPK) is commonly caused by heterozygous mutations in the desmoglein-1 (DSG1) gene.</p><p><strong>Objective: </strong>This study aimed to report a case of a 36-year-old Chinese female patient with SPPK caused by a novel DSG1 gene mutation, along with her family history, and explore its potential relationship with other genetic variants.</p><p><strong>Methods: </strong>Whole-exome sequencing was performed on the patient and their family members to identify the pathogenic mutation, which was validated by Sanger sequencing. Histological and electron microscopy analyses were conducted to examine the pathological characteristics of skin tissue.of skin tissue.</p><p><strong>Results: </strong>A frameshift mutation, c.1285del, in exon 10 of the DSG1 gene was identified, leading to a loss of protein function and resulting in SPPK. This mutation was also detected in two other family members with similar phenotypes. Additionally, a classical splicing variant, c.313+2dup, in the low-density lipoprotein receptor (LDLR) gene associated with hypercholesterolemia was identified in the patient; however, no direct association with SPPK was observed.</p><p><strong>Conclusion: </strong>This study was the first to report a novel mutation in the DSG1 gene associated with SPPK and suggested a potential role of the LDLR gene variant in SPPK patients, providing new insights for further research into the genetic mechanisms underlying SPPK.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582776","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}
引用次数: 0
Analysis of key pathways and genes in nodal structure on rat skin surface using gene ontology and KEGG pathway. 利用基因本体论和 KEGG 通路分析大鼠皮肤表面结节结构的关键通路和基因。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-11-06 DOI: 10.1007/s13258-024-01582-y
Joonyoung Shin, A Yeong Park, Suk Ju, Hyorin Lee, Hyung Won Kang, Dongwoon Han, Sungchul Kim
{"title":"Analysis of key pathways and genes in nodal structure on rat skin surface using gene ontology and KEGG pathway.","authors":"Joonyoung Shin, A Yeong Park, Suk Ju, Hyorin Lee, Hyung Won Kang, Dongwoon Han, Sungchul Kim","doi":"10.1007/s13258-024-01582-y","DOIUrl":"https://doi.org/10.1007/s13258-024-01582-y","url":null,"abstract":"<p><strong>Background: </strong>We have previously reported anatomical, histological, and gene expression characteristics of the nodal structure of rat skin surface and suggested its potential as an acupuncture point. However, the specific characteristics of the interactions among the genes expressed in this structure remain unclear.</p><p><strong>Objective: </strong>We aimed to determine gene expression changes by analyzing interaction networks of genes up-regulated in nodal structures and to explore relationships with acupuncture points.</p><p><strong>Methods: </strong>We investigated the relationship between the nodal structures and acupuncture points by analyzing the interactions of up-regulated genes, their Gene Ontology biological functions, and the characteristics of Kyoto Encyclopedia of Genes and Genomes pathways. RNA-seq and STRING analysis provided comprehensive information on these gene groups.</p><p><strong>Results: </strong>Interactions between up-regulated genes in nodal structures were classified into three groups. The first group, which includes Wnt7b, Wnt3, and Wnt16, showed significant interactions in pathways such as Wnt signaling, Alzheimer's disease, and regulation of stem cell pluripotency. The second group, composed of Fos, Dusp1, Pla2g4e, Pla2g4f, and Fgfr3, demonstrated a notable association with the MAPK signaling pathway. Lastly, the third group, consisting of Adcy1, Pla2g4e, Pla2g4f, and Dusp1 exhibited effective interactions with the inflammatory mediator regulation of TRP channels and serotonergic synapse.</p><p><strong>Conclusion: </strong>Continued research on nodal structures where these genes are expressed is needed to improve our understanding of skin anatomy and physiology as well as their potential clinical utility as acupuncture points.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582751","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}
引用次数: 0
Enhanced adaptive permutation test with negative binomial distribution in genome-wide omics datasets. 在全基因组 omics 数据集中使用负二项分布的增强型自适应 permutation 检验。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-11-06 DOI: 10.1007/s13258-024-01584-w
Iksoo Huh, Taesung Park
{"title":"Enhanced adaptive permutation test with negative binomial distribution in genome-wide omics datasets.","authors":"Iksoo Huh, Taesung Park","doi":"10.1007/s13258-024-01584-w","DOIUrl":"https://doi.org/10.1007/s13258-024-01584-w","url":null,"abstract":"<p><strong>Background: </strong>The permutation test has been widely used to provide the p-values of statistical tests when the standard test statistics do not follow parametric null distributions. However, the permutation test may require huge numbers of iterations, especially when the detection of very small p-values is required for multiple testing adjustments in the analysis of datasets with a large number of features.</p><p><strong>Objective: </strong>To overcome this computational burden, we suggest a novel enhanced adaptive permutation test that estimates p-values using the negative binomial (NB) distribution. By the method, the number of permutations are differently determined for individual features according to their potential significance.</p><p><strong>Methods: </strong>In detail, the permutation procedure stops, when test statistics from the permuted dataset exceed the observed statistics from the original dataset by a predefined number of times. We showed that this procedure reduced the number of permutations especially when there were many insignificant features. For significant features, we enhanced the reduction with Stouffer's method after splitting datasets.</p><p><strong>Results: </strong>From the simulation study, we found that the enhanced adaptive permutation test dramatically reduced the number of permutations while keeping the precision of the permutation p-value within a small range, when compared to the ordinary permutation test. In real data analysis, we applied the enhanced adaptive permutation test to a genome-wide single nucleotide polymorphism (SNP) dataset of 327,872 features.</p><p><strong>Conclusion: </strong>We found the analysis with the enhanced adaptive permutation took a feasible time for genome-wide omics datasets, and successfully identified features of highly significant p-values with reasonable confidence intervals.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582769","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}
引用次数: 0
Bacterial profile-based body fluid identification using a machine learning approach. 利用机器学习方法进行基于细菌特征的体液识别。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-11-06 DOI: 10.1007/s13258-024-01594-8
Sungmin Kim, Han Chul Lee, Jeong Eun Sim, Su Jeong Park, Hye Hyun Oh
{"title":"Bacterial profile-based body fluid identification using a machine learning approach.","authors":"Sungmin Kim, Han Chul Lee, Jeong Eun Sim, Su Jeong Park, Hye Hyun Oh","doi":"10.1007/s13258-024-01594-8","DOIUrl":"https://doi.org/10.1007/s13258-024-01594-8","url":null,"abstract":"<p><strong>Background: </strong>Identifying the origins of biological traces is critical for the reconstruction of crime scenes in forensic investigations. Traditional methods for body fluid identification rely on chemical, enzymatic, immunological, and spectroscopic techniques, which can be sample-consuming and depend on simple color-change reactions. However, these methods have limitations when residual samples are insufficient after DNA extraction.</p><p><strong>Objective: </strong>This study aimed to develop a method for body fluid identification by leveraging bacterial DNA profiling to overcome the limitations of the conventional approaches.</p><p><strong>Methods: </strong>Bacterial profiles were determined by sequencing the hypervariable region of the 16 S rRNA gene, using DNA metabarcoding of evidence collected from criminal cases. Amplicon sequence variants (ASVs) were analyzed to identify significant microbial patterns in different body fluid samples.</p><p><strong>Results: </strong>The bacterial profile-based method demonstrated high discriminatory power with a machine learning model trained using the naïve Bayes algorithm, achieving an accuracy of over 98% in classifying samples into one of four body fluid types: blood, saliva, vaginal secretion, and mixture traces of vaginal secretions and semen.</p><p><strong>Conclusion: </strong>Bacterial profiling enhances the accuracy and robustness of body fluid identification in forensic analysis, providing a valuable alternative to traditional methods by utilizing DNA and microbial community data despite the uncontrollable conditions. This approach offers significant improvements in the classification accuracy and practical applicability in forensic investigations.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582765","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}
引用次数: 0
Impact of potential biomarkers, SNRPE, COX7C, and RPS27, on idiopathic Parkinson's disease. 潜在生物标志物 SNRPE、COX7C 和 RPS27 对特发性帕金森病的影响。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-28 DOI: 10.1007/s13258-024-01591-x
Jaehwan Cheon, Haejin Jung, Byung Yong Kang, Mikyung Kim
{"title":"Impact of potential biomarkers, SNRPE, COX7C, and RPS27, on idiopathic Parkinson's disease.","authors":"Jaehwan Cheon, Haejin Jung, Byung Yong Kang, Mikyung Kim","doi":"10.1007/s13258-024-01591-x","DOIUrl":"https://doi.org/10.1007/s13258-024-01591-x","url":null,"abstract":"<p><strong>Background: </strong>Parkinson's disease (PD) is a progressive neuro-degenerative disorder most common in older adults which is associated with impairments in movement and other body functions. Most PD cases are classified as idiopathic PD (IPD), meaning that the etiology remains unidentified.</p><p><strong>Objective: </strong>To identify key genes and molecular mechanisms to identify biomarkers applicable to IPD.</p><p><strong>Methods: </strong>We applied a bioinformatics approach using a gene expression in whole blood dataset to pinpoint differentially expressed genes (DEGs) and pathways involved in IPD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs were subsequently performed. A protein-protein interaction (PPI) network was then constructed to select hub genes that may influence IPD. We further investigated the levels of differentially methylated regions (DMRs) and differentially expressed microRNA (DEMs) of whole blood of patients with IPD to validate hub genes. Additionally, we examined the hub gene expression patterns in the substantia nigra (STN) using single-cell RNA sequencing datasets.</p><p><strong>Results: </strong>In total, we identified 124 DEGs in the blood samples of patients with IPD, with GO and KEGG analyses highlighting their significant enrichment. Analysis of PPI networks revealed three major clusters and hub genes: small nuclear ribonucleoprotein polypeptide E (SNRPE), cytochrome C oxidase subunit 7 C (COX7C), and ribosomal protein S27 (RPS27). DMRs and DEMs analyses revealed hub gene regulation via epigenetic and RNA interference. In particular, SNRPE and RPS27 showed identically regulated gene expression in the STN.</p><p><strong>Conclusion: </strong>This study suggests that SNRPE, COX7C, and RPS27 in whole-blood samples derived from patients may be useful biomarkers for IPD.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521723","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}
引用次数: 0
A novel frameshift TBX4 variant in a family with ischio-coxo-podo-patellar syndrome and variable severity. 一个患有等位-狐狸-脚趾-髌骨综合征且病情轻重不一的家族中出现了一种新型框架移位 TBX4 变异。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-28 DOI: 10.1007/s13258-024-01589-5
Giada Moresco, Ornella Rondinone, Alessia Mauri, Rita Gorgoglione, Daniela Maria Grazia Graziani, Michal Dziuback, Monica Rosa Miozzo, Silvia Maria Sirchia, Luca Pietrogrande, Angela Peron, Laura Fontana
{"title":"A novel frameshift TBX4 variant in a family with ischio-coxo-podo-patellar syndrome and variable severity.","authors":"Giada Moresco, Ornella Rondinone, Alessia Mauri, Rita Gorgoglione, Daniela Maria Grazia Graziani, Michal Dziuback, Monica Rosa Miozzo, Silvia Maria Sirchia, Luca Pietrogrande, Angela Peron, Laura Fontana","doi":"10.1007/s13258-024-01589-5","DOIUrl":"https://doi.org/10.1007/s13258-024-01589-5","url":null,"abstract":"<p><strong>Background: </strong>Congenital anomalies of the knee are a spectrum of rare disorders with wide clinical and genetic variability, which are mainly due to the complex processes underlying knee development. Despite progresses in understanding pathomechanisms and associated genes, many patients remain undiagnosed.</p><p><strong>Objective: </strong>To uncover the genetic bases of a congenital patellar dislocation affecting multiple family members with variable severity.</p><p><strong>Methods: </strong>We performed ES in the proband and his father, both showing bilateral patellar dislocation, his sister with a milder similar condition, and his unaffected mother. Sanger sequencing was then performed in the proband's brother and paternal aunt, both affected as well.</p><p><strong>Results: </strong>ES and Sanger sequencing identified the presence of the novel heterozygous frameshift mutation c.735delT in the TBX4 gene in all affected family members. TBX4 is associated with autosomal dominant ischio-coxo-podo-patellar syndrome with/without pulmonary arterial hypertension (ICPPS, #147891), reaching a diagnosis in the family. Intrafamilial clinical heterogeneity suggests that other factors might be involved, such as additional variants in TBX4 or in other modifier genes. Interestingly, we identified three additional variants in the TBX4 gene in the proband only, whose phenotype is more severe. Despite being classified as benign, one of these variants is predicted to disrupt a splicing protein binding site, and may therefore affect TBX4 alternative splicing, accounting for the more severe phenotype of the proband.</p><p><strong>Conclusion: </strong>We expand and further delineate the genotypic and phenotypic spectrum of ICPPS. Further studies are necessary to shed light on the potential effect of this variant and on the variable phenotypic expressivity of TBX4-related phenotypes.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521713","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}
引用次数: 0
A novel CLRN2 variant: expanding the mutation spectrum and its critical role in isolated hearing impairment. 新型 CLRN2 变异:扩大突变谱及其在孤立性听力障碍中的关键作用。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-24 DOI: 10.1007/s13258-024-01590-y
Farooq Ahmad, Arif Mahmood, Ibrahim Abdullah Almazni, Afnan Mohammed Shakoori, Fatemah Alhakami, Qamre Alam, Muhammad Ismail, Muhammad Umair
{"title":"A novel CLRN2 variant: expanding the mutation spectrum and its critical role in isolated hearing impairment.","authors":"Farooq Ahmad, Arif Mahmood, Ibrahim Abdullah Almazni, Afnan Mohammed Shakoori, Fatemah Alhakami, Qamre Alam, Muhammad Ismail, Muhammad Umair","doi":"10.1007/s13258-024-01590-y","DOIUrl":"https://doi.org/10.1007/s13258-024-01590-y","url":null,"abstract":"<p><strong>Background: </strong>Biallelic variants in the CLRN2 gene have been reported to cause autosomal recessive profound hearing impairment in humans. CLRN2 belongs to the clarin gene family that encodes a tetraspan protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina.</p><p><strong>Methods: </strong>Here, we present a consanguineous family suffering from autosomal recessive non-syndromic profound hearing impairment (HI). We employed state of the art Whole exome sequencing (WES), Sanger sequencing followed by routine bioinformatics filtration steps and homology modeling to elucidate the effect of mutation at the protein level.</p><p><strong>Results: </strong>ES followed by Sanger sequencing revealed a novel homozygous nonsense variant in the CLRN2 gene [c.414 C > A; p.Cys138*]. Furthermore, insilico protein modeling of the wildtype and mutated version of the CLRN2 protein revealed large-scale changes that predict to compromise the routine normal function of the protein.</p><p><strong>Conclusion: </strong>Our finding further extends the mutations spectrum of CLRN2 gene and confirms its important role in hearing homeostasis and with developmental disorder in humans.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498909","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}
引用次数: 0
Retrotransposons and DNA transposons: insights into evolutionary genomics. 逆转录转座子和 DNA 转座子:对进化基因组学的启示。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-24 DOI: 10.1007/s13258-024-01583-x
Seyoung Mun, Kyudong Han
{"title":"Retrotransposons and DNA transposons: insights into evolutionary genomics.","authors":"Seyoung Mun, Kyudong Han","doi":"10.1007/s13258-024-01583-x","DOIUrl":"https://doi.org/10.1007/s13258-024-01583-x","url":null,"abstract":"","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142498910","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}
引用次数: 0
Transcriptome analysis of tilapia streptococcus agalactiae in response to baicalin. 罗非鱼链球菌对黄芩苷反应的转录组分析。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-22 DOI: 10.1007/s13258-024-01541-7
Qing-Qin Huang, Shao-Long Liu, Ji-Hui Huang, Fei Wang, Zi-Chen Zhao, Heng-Wei Deng, Chuan Lin, Wei-Liang Guo, Zhi-Hong Zhong, Jian-Long Li, Dong-Dong Zhang, Shi-Feng Wang, Yong-Can Zhou
{"title":"Transcriptome analysis of tilapia streptococcus agalactiae in response to baicalin.","authors":"Qing-Qin Huang, Shao-Long Liu, Ji-Hui Huang, Fei Wang, Zi-Chen Zhao, Heng-Wei Deng, Chuan Lin, Wei-Liang Guo, Zhi-Hong Zhong, Jian-Long Li, Dong-Dong Zhang, Shi-Feng Wang, Yong-Can Zhou","doi":"10.1007/s13258-024-01541-7","DOIUrl":"https://doi.org/10.1007/s13258-024-01541-7","url":null,"abstract":"<p><p>Streptococcus agalactiae (S. agalactiae) is a highly pathogenic bacterial pathogen in aquatic animals. Our previous study has demonstrated the significant inhibitory effect of baicalin on β-hemolytic/cytolytic activity, which is a key virulence factor of S. agalactiae. In this study, we aimed to elucidate the mechanism underlying baicalin's inhibition of S. agalactiae β-hemolytic/cytolytic activity by transcriptomic analysis. Bacteria were exposed to 39.06 µg/mL baicalin for 6 h, and their β-hemolytic/cytolytic activities were assessed using blood plates. Then, the differentially expressed genes (DEGs) were identified and characterized by RNA sequencing (RNA-Seq), and further confirmed using the qRT-PCR. A total of 10 DEGs with 7 significantly up-regulated and 3 significantly down-regulated, were found to be affected significantly under baicalin treatment. These DEGs were associated with 5 biological processes, 5 cellular components, and 3 molecular functions. They were primarily enriched in 3 pathways: lacD and lacC in galactose metabolism, lrgA and lrgB in the two-component system, and ribH/rib4 in riboflavin metabolism. These suggested that baicalin might inhibit the conversion of pyruvate to acetyl-CoA and malonyl-CoA, which are crucial precursors for β-hemolysin/cytolysin synthesis, and result in the accumulation of pyruvate, suppress the expressions of pyruvate cell membrane channel protein genes lrgA and lrgB. Baicalin could compensatory up-regulate the expressions of tryptophan/tyrosine ABC transporter family genes, ABC.X4.A, ABC.X4.P, and ABC.X4.S by inhibiting the expression of cyl A/B in cyl operons. Moreover, it hinders the conversion of D-glucose 1-phosphate to the dTDP-L-rhamnose pathway and leads to a deficiency of L-rhamnose, an important precursor for β-hemolysin/cytolysin synthesis.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463174","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}
引用次数: 0
Machine learning identification of NK cell immune characteristics in hepatocellular carcinoma based on single-cell sequencing and bulk RNA sequencing. 基于单细胞测序和大容量 RNA 测序的肝细胞癌 NK 细胞免疫特征的机器学习识别。
IF 1.6 4区 生物学
Genes & genomics Pub Date : 2024-10-21 DOI: 10.1007/s13258-024-01581-z
Fang Liu, Baohua Mei, Jianfeng Xu, Yong Zou, Gang Luo, Haiyu Liu
{"title":"Machine learning identification of NK cell immune characteristics in hepatocellular carcinoma based on single-cell sequencing and bulk RNA sequencing.","authors":"Fang Liu, Baohua Mei, Jianfeng Xu, Yong Zou, Gang Luo, Haiyu Liu","doi":"10.1007/s13258-024-01581-z","DOIUrl":"https://doi.org/10.1007/s13258-024-01581-z","url":null,"abstract":"<p><strong>Background: </strong>Hepatocellular carcinoma (HCC) is a highly malignant tumor; however, its immune microenvironment and mechanisms remain elusive. Single-cell sequencing allows for the exploration of immune characteristics within tumor at the cellular level. However, current knowledge regarding the roles of different immune cell populations in liver cancer progression is limited.</p><p><strong>Objective: </strong>The main objective of this study is to identify molecular markers with NK cell immune characteristics in hepatocellular carcinoma using various machine learning methods based on Single-Cell Sequencing and Bulk RNA Sequencing.</p><p><strong>Methods: </strong>We collected samples from eight normal liver tissues and eight HCC tumor tissues and performed single-cell RNA sequencing for immune cell clustering and expression profile analysis. Using various bioinformatic approaches, we investigated the immune phenotype associated with natural killer (NK) cells expressing high CD7 level. In addition, we verified the role of CD7 in the growth of HCC after NK cell and HCC cells cocultured by RT-qPCR, MTS and Flow cytometer experiments. Finally, we constructed a machine learning model to develop a prognostic prediction system for HCC based on NK cell-related genes.</p><p><strong>Results: </strong>Through single-cell typing, we found that the proportions of hepatocytes and NK cells were significantly elevated in the tumor samples. Moreover, we found that the expression of CD7 was high in HCC and correlated with prognosis. More importantly, Overexpression of CD7 in NK cells significantly inhibited the activity of MHCC97 cells and increased the number of apoptosis of HCC cells (p < 0.05). Furthermore, we observed that NK cells with high CD7 expression were associated with an activated immune phenotype.</p><p><strong>Conclusion: </strong>Our study found that CD7 is an important biomarker for assessing immune status and predicting survival of HCC patients; hence, it is a potential target for immune therapy against HCC.</p>","PeriodicalId":12675,"journal":{"name":"Genes & genomics","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463173","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}
引用次数: 0
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