Comparative and Functional Genomics最新文献

{"title":"Recurrent Inflammatory Myofibroblastic Tumor of Larynx Harboring a Novel THBS1::ALK Fusion","authors":"Namra Ajmal,&nbsp;Stacey M. Gargano,&nbsp;Ujwala Gosavi,&nbsp;Madalina Tuluc","doi":"10.1155/2024/4937501","DOIUrl":"https://doi.org/10.1155/2024/4937501","url":null,"abstract":"<p>Inflammatory myofibroblastic tumor (IMT) is a rare soft tissue tumor primarily occurring in the abdominopelvic region of young patients, and it is characterized by spindle-shaped myofibroblasts, or fibroblasts surrounded by inflammatory infiltrate. Herein, we report a case of a 24-year-old male with a firm submucosal mass in the anterior right vocal fold diagnosed as an IMT that recurred 14 months later. The tumor demonstrated a novel THBS1::ALK fusion containing Exons 1–7 of the thrombospondin 1 (<i>THBS1</i>) gene fused to Exon 19 of the anaplastic lymphoma kinase (<i>ALK</i>) gene via next-generation sequencing with the NextSeq sequencer. The fusion of <i>THBS1</i> to <i>ALK</i> potentially results in increased expression and constitutive activation of the ALK kinase domain. These findings not only broaden the repertoire of known <i>ALK</i> fusion partners implicated in tumorigenesis but also provide a novel avenue for investigating the etiology of recurrent IMT by considering this fusion event as a causal factor. To our knowledge, this is the second case of IMT of the larynx with this novel mutation reported in the literature and the first such case with a detailed description of this specific fusion and clinical recurrence.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/4937501","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141980362","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":"SKF96365 Inhibits Tumor Proliferation by Inducing Apoptosis and Autophagy in Human Esophageal Squamous Cell Carcinoma","authors":"Jiaxin Zhang,&nbsp;Huiqiong Han,&nbsp;Yihan Liu,&nbsp;Jiayao Xu,&nbsp;Daidi Zhang,&nbsp;Wenjia Wang,&nbsp;Yaping Gao,&nbsp;Zhengrui Li,&nbsp;Yanru Qin","doi":"10.1155/2024/4501154","DOIUrl":"https://doi.org/10.1155/2024/4501154","url":null,"abstract":"<p>Calcium channel blockers are emerging as a new generation of attractive anticancer drugs. SKF96365, originally thought to be a store-operated calcium entry (SOCE) inhibitor, is now often used as a TRPC channel blocker and is widely used in medical diagnostics. SKF96365 has shown antitumor effects on a variety of cancer cell lines. The objective of this study was to investigate the anticancer effect of SKF96365 on esophageal cancer in vivo and in vitro. Cell Counting Kit-8 (CCK-8) and colony formation were used to test the proliferation inhibition of SKF96365 on cell lines. Western blot and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining were used to detect cell apoptosis rates. In addition, we demonstrated the antitumor effect of SKF96365 in vivo in xenografted mice. As a result, SKF96365 significantly inhibited the proliferation of K510, K30, and EC9706 in vitro. SKF96365 induces apoptosis in three cell lines through the poly(adenosine diphosphate–ribose) polymerase (PARP), caspase-9, and BCL-2 pathways in a dose-dependent and time-dependent manner. Moreover, SKF96365 treatment also induced apoptosis and inhibited tumor growth in nude mice. The calcium channel TRPC1 was significantly downregulated by SKF96365. Autophagy was also induced during the treatment of SKF96365. In summary, SKF96365 induces apoptosis (PARP, caspase-9, and BCL-2) and autophagy (LC3-A/B) by inhibiting TRPC1 in esophageal cancer cells, thereby inhibiting tumor growth.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/4501154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141980335","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":"Discovery of a Novel Shared Variant Among RTEL1 Gene and RTEL1-TNFRSF6B lncRNA at Chromosome 20q13.33 in Familial Progressive Myoclonus Epilepsy","authors":"Sima Chaudhari,&nbsp;Lavanya Prakash Acharya,&nbsp;Dushyanth Babu Jasti,&nbsp;Akshay Pramod Ware,&nbsp;Sankar Prasad Gorthi,&nbsp;Kapaettu Satyamoorthy","doi":"10.1155/2024/7518528","DOIUrl":"https://doi.org/10.1155/2024/7518528","url":null,"abstract":"<p><b>Background:</b> Progressive myoclonus epilepsy (PME) is a neurodegenerative disorder marked by recurrent seizures and progressive myoclonus. To date, based on the phenotypes and causal genes, more than 40 subtypes of PMEs have been identified, and more remain to be characterized. Our study is aimed at identifying the aberrant gene(s) possibly associated with PMEs in two siblings born to asymptomatic parents, in the absence of known genetic mutations.</p><p><b>Methods:</b> Clinical assessments and molecular analyses, such as the repeat expansion test for <i>CSTB</i>; SCA1, 2, 3, 6, and 7; whole exome sequencing (WES); and mitochondrial genome sequencing coupled with computational analysis, were performed.</p><p><b>Results:</b> A family-based segregation analysis of WES data was performed to identify novel genes associated with PMEs. The potassium channel, <i>KCNH8</i> [c.298T&gt;C; (p.Tyr100His)], a DNA repair gene, regulator of telomere elongation helicase 1 (<i>RTEL1</i>) [c.691G&gt;T; (p.Asp231Tyr)] and long noncoding RNA, <i>RTEL1-TNFRSF6B</i> [chr20:62298898_G&gt;T; NR_037882.1, hg19] were among the candidate genes that were found to be associated with PMEs. These homozygous variations in siblings belong to genes with a loss-of-function intolerant (pLI) score of ≤ 0.86, expected to be detrimental by multiple computational analyses, and were heterozygous in parents. Additionally, computational analysis and the expression of <i>RTEL1</i> and <i>RTEL1-TNFRSF6B</i> revealed that <i>RTEL1-TNFRSF6B</i> may modulate <i>RTEL1</i> via hsa-miR-3529-3p. In the patient with the severe phenotype, a further deleterious mutation in <i>SLC22A17</i> was identified. No de novo variants specific to these probands were identified in the mitochondrial genome.</p><p><b>Conclusions:</b> Our study is the first to report variants in <i>KCNH8</i>, <i>RTEL1</i>, and <i>RTEL1-TNFRSF6B</i> among PME cases. These genes when characterized fully may shed light on pathogenicity and have the potential to be used in the diagnosis of PME.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1155/2024/7518528","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967843","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":"Priestia flexa as a Novel Urinary Tract Pathogen in Daloa, Côte d’Ivoire: Insights From Genomic Sequencing","authors":"Dého Aristide Gbégbé,&nbsp;Okran Beyosse Christophe Kacou,&nbsp;N’goran Parfait N’zi,&nbsp;Djédoux Maxime Angaman","doi":"10.1155/2024/6239250","DOIUrl":"10.1155/2024/6239250","url":null,"abstract":"<p>Bacterial strains coded 21LM367, 21LM07, and 21LM1136 were isolated from the urine of patients with urinary tract infections (UTIs) at the Centre Hospitalier Régional de Daloa in Côte d’Ivoire. Based on average nucleotide identity (ANI) analysis, DNA-DNA digital hybridisation (dDDH), and other comparative genomic methods, strains 21LM07, 21LM367, and 21LM1136 were determined to be <i>Priestia flexa</i>. The size of the assembled complete genomes ranged from 8,624,538 to 4,007,501 bp. The average GC content was 37.76%, 46.33%, and 43.03% for strains 21LM07, 21LM367, and 21LM1136, respectively. The total number of coding regions (CDS) in each genome was 4172, 8497, and 6795, respectively, for strains 21LM07, 21LM367, and 21LM1136. Genomic prediction analysis revealed that a total of 4241, 8583, and 6881 genes were annotated in the 21LM07, 21LM367, and 21LM1136 genomes, respectively. No virulence or resistance genes were predicted in the genomes of strains 21LM07 and 21LM1136. On the other hand, two genes conferring resistance to beta-lactam and tetracyclines as well as nine virulence genes were predicted in the genome of 21LM367. In addition, 438, 350, and 153 mobile genetic elements (MGEs) were predicted in the genomes of strains 21LM367, 21LM1136, and 21LM07, respectively. Strain 21LM07 was characterised by the absence of plasmids in its genome. Two plasmids were predicted in the genomes of isolates 21LM367 and 21LM1136; however, rep7a and IncI2 were predicted to contain the tet(K) resistance gene. No typical multilocus sequences could be characterised in the genomes of the different strains.</p>","PeriodicalId":55239,"journal":{"name":"Comparative and Functional Genomics","volume":"2024 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916629","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":"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}