Comparative and Functional Genomics最新文献

{"title":"Genome-Wide Analyses of MADS-Box Genes Reveal Their Involvement in Seed Development and Oil Accumulation of Tea-Oil Tree (Camellia oleifera)","authors":"Xianzhi Zhang,&nbsp;Wenliang He,&nbsp;Xinyi Wang,&nbsp;Yongliang Duan,&nbsp;Yongjuan Li,&nbsp;Yi Wang,&nbsp;Qingbin Jiang,&nbsp;Boyong Liao,&nbsp;Sheng Zhou,&nbsp;Yongquan Li","doi":"10.1155/2024/3375173","DOIUrl":"10.1155/2024/3375173","url":null,"abstract":"<p>The seeds of <i>Camellia oleifera</i> produce high amount of oil, which can be broadly used in the fields of food, industry, and medicine. However, the molecular regulation mechanisms of seed development and oil accumulation in <i>C. oleifera</i> are unclear. In this study, evolutionary and expression analyses of the MADS-box gene family were performed across the <i>C. oleifera</i> genome for the first time. A total of 86 MADS-box genes (<i>ColMADS</i>) were identified, including 60 M-type and 26 MIKC members. More gene duplication events occurred in M-type subfamily (6) than that in MIKC subfamily (2), and <i>SEP-like</i> genes were lost from the MIKC^C clade. Furthermore, 8, 15, and 17 differentially expressed <i>ColMADS</i> genes (DEGs) were detected between three developmental stages of seed (S1/S2, S2/S3, and S1/S3), respectively. Among these DEGs, the <i>STK-like ColMADS12</i> and <i>TT16-like ColMADS17</i> were highly expressed during the seed formation (S1 and S2), agreeing with their predicted functions to positively regulate the seed organogenesis and oil accumulation. While <i>ColMADS57</i> and <i>ColMADS07</i> showed increasing expression level with the seed maturation (S2 and S3), conforming to their potential roles in promoting the seed ripening. In all, these results revealed a critical role of MADS-box genes in the <i>C. oleifera</i> seed development and oil accumulation, which will contribute to the future molecular breeding of <i>C. oleifera</i>.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11300058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893369","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}

{"title":"MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing","authors":"Federico Gabrielli,&nbsp;Filomena Tiziana Papa,&nbsp;Fabio Di Pietro,&nbsp;Andreu Paytuví-Gallart,&nbsp;Daniel Julian,&nbsp;Walter Sanseverino,&nbsp;Cinzia Alfonsi","doi":"10.1155/2024/8859058","DOIUrl":"https://doi.org/10.1155/2024/8859058","url":null,"abstract":"<p><b>Objective:</b> The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy.</p><p><b>Methods:</b> Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed.</p><p><b>Results:</b> MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )–specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2.</p><p><b>Conclusion:</b> MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/8859058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141315483","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}

{"title":"Pancreatitis as a Main Consequence of APOC2-Related Hypertriglyceridemia: The Role of Nonsense and Frameshift Variants","authors":"Bahareh Rabbani,&nbsp;Mohadeseh Aghli Moghadam,&nbsp;Shiva Esmaeili,&nbsp;Amirhassan Rabbani,&nbsp;Bahman Akbari,&nbsp;Nejat Mahdieh","doi":"10.1155/2024/6653857","DOIUrl":"10.1155/2024/6653857","url":null,"abstract":"<div>\u0000 <p><i>APOC2-</i>related hypertriglyceridemia occurs due to biallelic variants of this gene. Here, genotype-phenotype architecture of all pathogenic <i>APOC2</i> variants is investigated among heterozygous and homozygous individuals. Clinical heterogeneity of various types of the variants is also described, and pancreatitis in more than half of homozygotes carrying chain-termination variants is highlighted as well. For this study, patients were selected who had a plasma triglyceride level above 250 mg/dL. The coding and intronic regions of the <i>APOC2</i> gene were amplified using the Sanger sequencing to investigate the presence of variants. The genotypes, lipid profiles, and detailed clinical features were documented for all <i>APOC2</i>-related patients and heterozygous individuals. Pathogenicity of the variants was predicted and categorized using available bioinformatics tools such as MutationTaster and PolyPhen-2 and ACMG criteria. MetaDome and Phyre2 were applied for structural and functional in silico analyses. 40% (12 out of 30) of <i>APOC2</i> variants were chain-termination (nonsense and frameshift) variants. These types of variants were determined in 60.53% of patients. 55% of these patients showed pancreatitis followed by lipemia retinalis (29%), abdominal pain (24%), hepatosplenomegaly (24%), and xanthomas (18%). The mean age of onset was about 22 years old. In at least 50% of 38 homozygous individuals, the TG level was more than 2000 mg/dL. More than 25% of heterozygous individuals showed at least one symptom. Pancreatitis and a severe form of HTG were found in 5 and 2% of heterozygous individuals, respectively. The main clinical features of <i>APOC2</i>-related hypertriglyceridemia include pancreatitis, lipemia retinalis, abdominal pain, hepatosplenomegaly, and xanthomas. Nonsense and frameshift homozygous variants usually lead to a severe form of hypertriglyceridemia. Pancreatitis is one of the main consequences of these types of mutations; thus, it is important to consider this point when evaluating asymptomatic individuals. Heterozygous individuals may become symptomatic due to the role of unknown modifying agent including environmental genetic factors.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/6653857","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141188205","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}

{"title":"Identification and Validation of Immune Implication of R-Spondin 1 and an R-Spondin 1-Related Prognostic Signature in Esophagus Cancer","authors":"Yuansheng Lin,&nbsp;Xinqi Lou,&nbsp;Shengjun Li,&nbsp;Wei Cai,&nbsp;Tuanjie Che","doi":"10.1155/2024/7974277","DOIUrl":"10.1155/2024/7974277","url":null,"abstract":"<div>\u0000 <p>R-spondin 1 (RSPO1), which encodes a secretory-activating protein, is a promising therapeutic target for various tumors. The aim of this study was to establish a robust RSPO1-related signature specific to esophageal cancer (ESCA). Our comprehensive study involved meticulous analysis of RSPO1 expression in ESCA tissues and validation across ESCA cell lines and clinical samples using The Cancer Genome Atlas (TCGA) and GTEx databases. Using TCGA-ESCA dataset, we employed single-sample gene set enrichment analysis (ssGSEA) to elucidate the complex interaction between RSPO1 expression and the abundance of 22 specific immune cell types infiltrating ESCA. The biological significance of RSPO1 was further elucidated using KEGG, GO, and GSEA, demonstrating its relevance to pivotal tumor and immune pathways. This study culminated in the construction of prognostic nomograms enriched by calibration curves, facilitating the projection of individual survival probabilities at intervals of one, three, and five years. A substantial decrease in RSPO1 expression was observed within ESCA tissues and cell lines compared to their normal esophageal counterparts, and a significant decrease in the proportion of activated dendritic cells was evident within ESCA, accompanied by an augmented presence of macrophages and naive B cells relative to normal tissue. GSEA and KEGG analyses showed that RSPO1 was associated with tumor and immune pathways. Additionally, an independent prognostic risk score based on the RSPO1-related gene signature was developed and validated for patients with ESCA. Finally, RT-qPCR and western blotting were performed to confirm RSPO1 expression in normal and ESCA cell lines and tissue samples. In summary, our investigation underscores the pivotal role of RSPO1 in orchestrating tumor immunity and proposes RSPO1 as a prospective target for immunotherapeutic interventions in ESCA. Furthermore, the intricate profile of the two RSPO1-related genes has emerged as a promising predictive biomarker with notable potential for application in ESCA.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/7974277","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141172340","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}

{"title":"Single-Cell RNA Sequencing Identifies Crucial Genes Influencing the Polarization of Tumor-Associated Macrophages in Liver Cancer","authors":"Kedong Xu,&nbsp;Mingyi Dong,&nbsp;Zhengqiang Wu,&nbsp;Linfei Luo,&nbsp;Fei Xie,&nbsp;Fan Li,&nbsp;Hongyan Huang,&nbsp;Fenfen Wang,&nbsp;Xiaofeng Xiong,&nbsp;Zhili Wen","doi":"10.1155/2024/7263358","DOIUrl":"10.1155/2024/7263358","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. In the context of hepatocellular carcinoma (HCC), tumor-associated macrophages (TAMs) are pivotal for the immunosuppressive nature of the tumor microenvironment (TME). This investigation delves into the functional transformations of TAMs within the TME by leveraging single-cell transcriptomics to pinpoint critical genes influencing TAM subset polarization. <i>Methods</i>. We procured single-cell and bulk transcriptomic data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), implementing quality assurance, dimensional reduction, clustering, and annotation on the single-cell sequencing data. To examine cellular interactions, CellChat was utilized, while single-cell regulatory network inference and clustering (SCENIC) was applied to deduce transcription factors (TFs) and their associated targets. Through gene enrichment, survival, and immune infiltration correlation analyses, we sought to pinpoint and validate influential genes. A TAM model under HCC conditions was then established to confirm the expression levels of these key genes. <i>Results</i>. Our analysis encompassed 74,742 cells and 23,110 genes. Through postdimensional reduction and clustering, we identified seven distinct cell types and nine TAM subtypes. Analysis via CellChat highlighted a predominance of M2-phenotype-inclined TAM subsets within the tumor’s core. SCENIC pinpointed the transcription factor PRDM1 and its target genes as pivotal in this region. Further analysis indicated these genes’ involvement in macrophage polarization. Employing trajectory analysis, survival analysis, and immune infiltration correlation, we scrutinized and validated genes likely directing M2 polarization. Experimental validation confirmed PRDM1’s heightened expression in TAMs conditioned by HCC. <i>Conclusions</i>. Our findings suggest the PRDM1 gene is a key regulator of M2 macrophage polarization, contributing to the immunosuppressive TME in HCC.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/7263358","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141151726","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}

{"title":"A DIRIGENT Gene GmDIR26 Regulates Pod Dehiscence in Soybean","authors":"Zheng Wang,&nbsp;Xiaofang Zhang,&nbsp;Rui Hou,&nbsp;Huiying Zhang,&nbsp;Xu Guo,&nbsp;Xiaofei Ma,&nbsp;Aiqin Xu,&nbsp;Hong Zhu,&nbsp;Shuai Li","doi":"10.1155/2024/2439396","DOIUrl":"10.1155/2024/2439396","url":null,"abstract":"<div>\u0000 <p>Pod dehiscence brings much loss for modern agricultural production, and multiple pod dehiscence components have been identified in many plant species. However, the pod dehiscence regulation factors in soybean are limited. In this study, we investigate the function of <i>GmDIR26</i>, a close homologues gene of pod dehiscence genes <i>GmPdh1</i>, <i>PvPdh1</i>, and <i>CaPdh1</i>, in the regulation of pod dehiscence in soybean. The secondary and tertiary structure analysis reveals that GmDIR26 protein has a similar structure with GmPdh1, PvPdh1, and CaPdh1 proteins. Synteny analysis of soybean and chickpea genomes shows that the genomic region surrounding <i>GmDIR26</i> and <i>CaPdh1</i> might be evolved from the same ancestor, and these two genes might have similar function. <i>GmDIR26</i> shows an increased expression pattern during pod development and reaches a peak at beginning seed stage. Meanwhile, <i>GmDIR26</i> exhibits high expression levels in dorsal suture and pod wall, but low expression pattern in ventral suture. In addition, <i>GmDIR26</i> shows higher expression levels in pod dehiscence genotype than that in pod indehiscence accessions. Overexpression of <i>GmDIR26</i> in soybean increases pod dehiscence in transgenic plants, of which the lignin layer in inner sclerenchyma pods is thicker and looser. The expression levels of several pod dehiscence genes are altered. Our study provides important information for further modification of pod dehiscence resistance soybean and characterization of soybean pod dehiscence regulation network.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/2439396","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837853","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}

{"title":"A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species","authors":"Rongxuan Hu,&nbsp;Haifeng Huang,&nbsp;Ying Zhou,&nbsp;Yanshan Liu,&nbsp;Yaning Ren,&nbsp;Yuanfen Liao,&nbsp;Cunyin Yuan,&nbsp;Xiaohong Gu,&nbsp;Yubao Cui","doi":"10.1155/2024/3779688","DOIUrl":"10.1155/2024/3779688","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of <i>Dermatophagoides farinae</i>, a common allergenic mite species. <i>Methods</i>. We achieved a chromosome-level assembly of <i>D. farinae</i>’s genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. <i>Results</i>. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. <i>Conclusion</i>. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing <i>D. farinae</i> allergy research and treatment strategies.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/3779688","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140665227","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}

{"title":"Complete Genome Sequence Analysis of Bacillus subtilis MC4-2 Strain That against Tobacco Black Shank Disease","authors":"Chunlan Shi,&nbsp;Shuquan Zeng,&nbsp;Xi Gao,&nbsp;Mehboob Hussain,&nbsp;Mingchuan He,&nbsp;Xurong Niu,&nbsp;Congcong Wei,&nbsp;Rui Yang,&nbsp;Mingxian Lan,&nbsp;Yonghui Xie,&nbsp;Zhijiang Wang,&nbsp;Guoxing Wu,&nbsp;Ping Tang","doi":"10.1155/2024/8846747","DOIUrl":"10.1155/2024/8846747","url":null,"abstract":"<div>\u0000 <p>The MC4-2 bacterium strain was isolated and purified from the <i>Periplaneta americana</i> intestine as a biocontrol agent with good antagonistic effect against the pathogens of a soil-borne disease called tobacco black shank. The MC4-2 strain was found to have good broad-spectrum inhibition by plate stand-off test. Based on 16S rRNA and <i>gyrB</i> genes, ANI analysis, and other comparative genomics methods, it was determined that the MC4-2 strain was <i>Bacillus subtilis</i>. The complete genome sequence showed that the genome size was 4,076,630 bp, the average GC content was 43.78%, and the total number of CDSs was 4,207. Genomic prediction analysis revealed that a total of 145 genes were annotated by the CAZy, containing mainly GH and CE enzymes that break down carbohydrates such as glucose, chitin, starch, and alginate, and a large number of enzymes involved in glycosylation were present. A total of ten secondary metabolite clusters were predicted, six clusters of which were annotated as surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. The present investigation found the biological control mechanism of <i>B. subtilis</i> MC4-2, which provides a strong theoretical basis for the best use of this strain in biological control methods and provides a reference for the subsequent development of agents of this bacterium.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/8846747","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140300164","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}

{"title":"Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 3 Expression and Its Correlation with Prognosis and Growth of Serous Ovarian Cancer: Correlation of DYRK3 with Ovarian Cancer Survival","authors":"Jia Sun,&nbsp;Yingzi Zhang,&nbsp;Aijie Li,&nbsp;Hao Yu","doi":"10.1155/2024/6683202","DOIUrl":"10.1155/2024/6683202","url":null,"abstract":"<div>\u0000 <p><i>Background</i>. Epithelial ovarian cancer, primarily serous ovarian cancer (SOC), stands as a predominant cause of cancer-related mortality among women globally, emphasizing the urgent need for comprehensive research into its molecular underpinnings. Within this context, the dual-specificity tyrosine phosphorylation-regulated kinase 3 (DYRK3) has emerged as a potential key player with implications for prognosis and tumor progression. <i>Methods</i>. This study conducted a meticulous retrospective analysis of 254 SOC cases from our medical center to unravel the prognostic significance of DYRK3. Survival analyses underscored DYRK3 as an independent adverse prognostic factor in SOC, with a hazard ratio of 2.60 (95% CI 1.67-4.07, <i>P</i> &lt; 0.001). Experimental investigations involved DYRK3 knockdown in serous ovarian cancer cell lines (CAOV3 and OVCAR-3) through a shRNA strategy, revealing substantial decreases in cell growth and invasion capabilities. Bioinformatics analyses further hinted at DYRK3’s involvement in modulating the tumor immune microenvironment. In vivo experiments with DYRK3-knockdown cell lines validated these findings, demonstrating a notable restriction in the growth of ovarian cancer xenografts. <i>Results</i>. Our findings collectively illuminate DYRK3 as a pivotal tumor-promoting oncogene in SOC. Beyond its adverse prognostic implications, DYRK3 knockdown exhibited promising therapeutic potential by impeding cancer progression and potentially influencing the tumor immune microenvironment. <i>Conclusions</i>. This study establishes a compelling foundation for further research into DYRK3’s intricate role and therapeutic potential in ovarian cancer treatment. As we unravel the complexities surrounding DYRK3, our work not only contributes to the understanding of SOC pathogenesis but also unveils new prospects for targeted therapeutic interventions, holding promise for improved outcomes in ovarian cancer management.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/6683202","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140155485","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}

{"title":"Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes","authors":"Biigba Yakubu,&nbsp;Edwin Moses Appiah,&nbsp;Andrews Frimpong Adu","doi":"10.1155/2024/5536117","DOIUrl":"10.1155/2024/5536117","url":null,"abstract":"<div>\u0000 <p>The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). <i>Conclusion</i>. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium’s antibiotic resistance.</p>\u0000 </div>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/5536117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140026117","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}