Biochemical Genetics最新文献

{"title":"Spectrum of Genetic Mutations Among Iranian Patients with Gangliosidosis.","authors":"Sheyda Khalilian, Mohadeseh Fathi, Mona Alizadeh, Fatemeh Larki Darabi, Shadab Salehpour, Saeed Anvari, Mohammad Miryounesi, Soudeh Ghafouri-Fard","doi":"10.1007/s10528-025-11090-7","DOIUrl":"https://doi.org/10.1007/s10528-025-11090-7","url":null,"abstract":"<p><p>Gangliosidosis is a hereditary metabolic disorder inherited in an autosomal recessive manner. This disorder is marked by the accumulation of gangliosides in the central nervous system, leading to considerable and progressive neurological deficits. In the current study, we described the clinical findings and genetic variations observed in 12 patients manifesting symptoms of gangliosidosis disorders. The results of molecular investigations revealed the presence of different variants in the HEXA (three cases), HEXB (four cases) and GLB1 genes (five cases) in the patients. Notably, the c.833C > T (p.A278V) variant in the HEXB was detected in two unrelated cases. Four novel variants were also detected, including two likely pathogenic variants in the HEXB gene, namely c.1083-2del and c.1616_1622dup (p.Ile541Metfs*14). A single case had three variants in the GLB1 gene, including two novel variants (c.545C > T and c.631G > C); and a previously reported pathogenic variant (c.601C > T). The current study broadens the spectrum of genetic variations in Iranian patients with different types of gangliosidosis. This information is also important for the process of genetic counseling in the affected families.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762497","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}

{"title":"Correction: CircRNA‑PTPRA Knockdown Inhibits Atherosclerosis Progression by Repressing ox‑LDL‑Induced Endothelial Cell Injury via Sponging of miR‑671‑5p.","authors":"Xueting Luo, Xiaoli Zhou","doi":"10.1007/s10528-025-11089-0","DOIUrl":"https://doi.org/10.1007/s10528-025-11089-0","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717708","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}

{"title":"LncRNA ABHD11-AS1 Elevates CALM2 to Promote Metastasis of Thyroid Cancer Through Sponging miR-876-5p.","authors":"Juan Lv, Fukun Chen, Ling Lv, Lu Zhang, Huangren Zou, Yanlin Liu, Yuke Bai, Ruotong Fang, Tiantian Qin, Zhiyong Deng","doi":"10.1007/s10528-025-11072-9","DOIUrl":"https://doi.org/10.1007/s10528-025-11072-9","url":null,"abstract":"<p><p>In the past decade, the treatment of thyroid cancer (TC) has been brought to a new era, but tumor metastasis still is an intractable difficulty in clinical. LncRNA ABHD11-AS1 has been confirmed to be involved in TC progression. However, its specific mechanism remains unknown. Tissues from TC patients and TC cells served as mainly experimental subjects in this study. The migration of TC cells was assessed using the scratch assay, and the ability of cell invasion was evaluated by transwell assay. RT-qPCR and western blot were conducted to determine the levels of related genes and proteins. The dual-luciferase reporter assay was used to validate the relationships among ABHD11-AS1, miR-876-5p and CALM2. ABHD11-AS1 and CALM2 are elevated in TC cancer samples and cells, while the expression of miR-876-5p is reduced. Subsequently, the ability of TC cells to migrate, invade and EMT was inhibited by both ABHD11-AS1 knockdown or miR-876-5p overexpression. Moreover, the suppression of malignant characteristics in TC cells resulting from ABHD11-AS knockdown was counteracted by the inhibition of miR-876-5p or the upregulation of CALM2. On the mechanism, ABHD11-AS1 elevated CALM2 and promoted the malignant development of TC cells by acting as a miR-876-5p sponge. ABHD11-AS1 mediated the miR-876-5p/CALM2 axis to drive the metastasis of thyroid cancer.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673117","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}

{"title":"The Role of Coagulation-Related Genes in Glioblastoma: A Comprehensive Analysis of the Tumor Microenvironment, Prognosis, and Treatment.","authors":"Jingyi Yang, Lei Shen, Yuankun Cai, Ji Wu, Keyu Chen, Dongyuan Xu, Yu Lei, Songshan Chai, Nanxiang Xiong","doi":"10.1007/s10528-025-11086-3","DOIUrl":"https://doi.org/10.1007/s10528-025-11086-3","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The influence of coagulation on glioma biology has not been comprehensively elucidated. This study explores the role of coagulation-related genes (CRGs) in glioblastoma (GBM) from the perspectives of the tumor microenvironment (TME), differences in coagulation function among GBM patients, treatment, and prognosis. Somatic mutation analysis was performed on single nucleotide polymorphism (SNP) and copy number variation data from GBM patients in the TCGA cohort. Publicly available single-cell RNA sequencing data were used to analyze the role of coagulation in the GBM TME and its underlying biological mechanisms. Unsupervised clustering of GBM patients from the CGGA693 cohort was conducted, and coagulation function for each patient was assessed using ssGSEA scoring. Prognosis was assessed with Kaplan-Meier survival analysis, and immune infiltration was analyzed through ESTIMATE. A risk signature based on five CRGs (CFI, GNG12, MMP2, LEFTY2, and SERPINC1) was constructed and validated using LASSO regression and random survival forest analyses to predict responses to immunotherapy and identify potential sensitive drugs. Finally, the roles of LEFTY2 and SERPINC1 in GBM progression was verified by immunohistochemistry, cell counting kit-8 (CCK8) assay and wound healing assay, and the anti-GBM effect of the drug PLX4720 was verified by CCK8 assay, wound healing assay, and colony formation assay. Somatic mutation analysis revealed SNP events of CRG mutations in 117 out of 461 GBM cases (25.38%). Single-cell analysis of the GBM TME revealed significant activation of the coagulation pathway in endothelial cells, with intercellular communication mediated via the SPP1-integrin pathway (p &lt; 0.01). Clustering analysis and ssGSEA identified two coagulation-related subtypes in GBM: coagulation-activated and coagulation-inhibited subtypes. Patients in the coagulation-activated subtype exhibited shorter overall survival and poorer prognosis compared to those in the coagulation-inhibited subtype (p = 0.0085). Immune infiltration analysis showed lower tumor purity and higher levels of immune-suppressive cells in the coagulation-activated subtype (p &lt; 0.001). The CRG-based risk signature accurately predicted prognosis (p &lt; 0.0001) and responses to immunotherapy in the IMvigor210 cohort (p = 0.0062). Based on the risk model, PLX4720 was identified as a potential sensitive drug (p &lt; 0.001), and drug validation experiments demonstrated that PLX4720 inhibited the proliferation and migration of glioma cells (p &lt; 0.0001). In vitro experiments demonstrated that LEFTY2 and SERPINC1 were significantly overexpressed in GBM compared to normal brain tissue, and knockdown of LEFTY2 and SERPINC1 inhibited glioma cell proliferation and migration (p &lt; 0.05). The CRG-based risk signature model effectively predicts the prognosis of GBM patients and aids in assessing the efficacy of ICI therapy and chemotherapy. Furthermore, the genes LEFTY2, SERPINC1 and the drug PLX4720 offer po","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668557","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}

{"title":"Genome-Wide Identification, Characterization, and Expression Analysis of the BTB domain-Containing Protein Gene Family in Poplar.","authors":"Ruotong Jing, Xuan Liu, Ruili Li, Liang Du","doi":"10.1007/s10528-025-11083-6","DOIUrl":"https://doi.org/10.1007/s10528-025-11083-6","url":null,"abstract":"<p><p>In recent years, the BTB (Bric-a-brac/Tramtrack/Broad complex) gene family in plants has garnered widespread attention for its regulatory roles in plant growth and development. However, knowledge regarding BTBs in poplar trees remains limited. Here, we identified 94 BTB gene family members across the genome of Populus alba L. Through phylogenetic analysis, these members were classified into seven subfamilies and 16 branches, followed by comprehensive bioinformatics and biological analyses. Structural analysis revealed that poplar BTB gene family exhibits both high conservation and diversity, with distinct gene structures and protein features. Expression pattern analysis demonstrated differential expression of poplar BTB genes across various tissues, hormone treatments, and under drought stress, suggesting their potential roles in poplar growth and development and drought response. This study provides a vital foundation and reference for unraveling the BTB-involved regulatory mechanisms underlying poplar growth and development and drought response.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668723","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}

{"title":"Screening Therapeutic Core Genes in Sepsis Using Network Pharmacology and Single-Cell RNA Sequencing.","authors":"Guihong Chen, Wen Zhang, Chenglin Wang, Yingchun Hu, Shaolan Li","doi":"10.1007/s10528-025-11075-6","DOIUrl":"https://doi.org/10.1007/s10528-025-11075-6","url":null,"abstract":"<p><p>Sepsis, a life-threatening condition characterized by a systemic inflammatory response, leads to organ dysfunction and high mortality rates. Honeysuckle, a traditional herbal remedy, has shown promise in attenuating organ damage and inhibiting pro-inflammatory factors in sepsis. However, the underlying molecular mechanisms remain unclear. We employed a multi-omics approach to elucidate honeysuckle's potential therapeutic effects in sepsis. RNA sequencing was performed on blood samples from 22 sepsis patients and 10 healthy controls to identify differentially expressed genes. Network pharmacology was utilized to predict effective ingredients and therapeutic targets of honeysuckle in sepsis. Meta-analysis compared gene expression between sepsis survivors and non-survivors. Single-cell RNA sequencing was employed to localize target gene expression at the cellular level. We identified 1328 differentially expressed genes in sepsis, with 221 upregulated and 1107 downregulated. Network analysis revealed 15 genes linked to 12 honeysuckle components. Four genes-DPP4, CD40LG, BCL2, and TP53-emerged as core therapeutic targets, showing decreased expression in non-survivors but upregulation in survivors. Single-cell analysis demonstrated that these genes were primarily expressed in T cells and other immune cells, suggesting their role in regulating immune response and inflammation. This study uses single-cell RNA sequencing and network analysis to identify DPP4, CD40LG, BCL2, and TP53 as key regulatory targets in sepsis, providing insights into disease mechanisms and potential therapeutic interventions. Network pharmacology analysis suggests possible interactions with honeysuckle compounds, though experimental validation is needed.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143668545","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}

{"title":"Truncated Variants in FAM20A and WDR72 Genes Underlie Autosomal Recessive Amelogenesis Imperfecta in Four Pakistani Families.","authors":"Sadaqat Ullah, Sher Alam Khan, Samin Jan, Salah Ud Din, Nazif Muhammad, Zia Ur Rehman, Abid Jan, Muhammad Tariq, Noor Muhammad, Abdul Ghani, Naveed Wasif, Saadullah Khan","doi":"10.1007/s10528-025-11087-2","DOIUrl":"https://doi.org/10.1007/s10528-025-11087-2","url":null,"abstract":"<p><p>Amelogenesis Imperfecta (AI) is a set of hereditary diseases affecting enamel development, leading to various types of enamel defects, potentially impacting oral health unassociated with other generalized defects. AI manifests in syndromic and non-syndromic forms and can be inherited through autosomal recessive, autosomal dominant, or X-linked inheritance patterns. Genetic studies have identified sequence variants in a number of genes (≥ 70) linked to both syndromic and non-syndromic AI, highlighting the genetic diversity underlying the condition. The current study involved clinical evaluation and exome sequencing, aimed at identifying the causative variants in four unrelated consanguineous Pakistani families presenting AI phenotypes. The exome sequencing results revealed a novel homozygous frameshift variant FAM20A: NM_017565.4, c.188dupA; p.(Asp63Glufs*17) in families A, B, and C while a nonsense homozygous variant WDR72: NM_182758.4, c.2686C > T; p. (Arg896*) in family D. The segregation of both variants was confirmed by Sanger sequencing. Bioinformatics analysis predicted the pathogenicity of these genetic variants. These alterations suggest functional consequences, potentially impairing the FAM20A and WDR72 proteins and causing dental anomalies. This investigation significantly broadens our understanding of FAM20A and WDR72's involvement in AI. Furthermore, this study highlights the genetic heterogeneity of AI (involving FAM20A and WDR72 in this study) within the Pakistani population.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661829","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}

{"title":"Evaluation of D-Dimer, P-Selectin, and miR-17-5p Expression in ICU and Non-ICU COVID-19 Patients: A Cross-sectional Study.","authors":"Vida Shirani Asl, Mohsen Moghaddami, Sahar Abbasi, Niloofar Sohrabi, Parisa Tandel, Gholamhossein Tamaddon","doi":"10.1007/s10528-025-11062-x","DOIUrl":"https://doi.org/10.1007/s10528-025-11062-x","url":null,"abstract":"<p><p>COVID-19, caused by SARS-CoV-2 infection, frequently induces thrombotic complications in affected individuals. P-selectin, a pivotal platelet marker, plays a central role in platelet-leukocyte aggregation, contributing to hemostasis and thrombosis. Additionally, D-dimer serves as an indicator of coagulation system activity, while miR-17-5p exhibits antiviral properties in respiratory infections. This study aimed to evaluate and compare the expression levels of D-dimer, P-selectin, and miR-17-5p in COVID-19 patients hospitalized in intensive care units (ICUs) and those in non-ICU wards. This cross-sectional study included 50 COVID-19 patients, divided into ICU and non-ICU groups. P-selectin expression was assessed using Flow cytometry, D-dimer levels were measured via chemiluminescence, and miR-17-5p expression was analyzed using quantitative real-time polymerase chain reaction (qRT-PCR). Our analysis revealed no significant difference in P-selectin expression levels between ICU and non-ICU patients (p = 0.1068). However, the expression levels of D-dimer and miR-17-5p were significantly elevated in ICU patients compared to non-ICU patients, with corresponding p-values of 0.032 and 0.0176, respectively. The heightened expression of D-dimer and miR-17-5p in ICU patients suggests their potential utility as predictive biomarkers for assessing the hemostatic status of COVID-19 patients.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655590","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}

{"title":"Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema.","authors":"Asif S Tamboli, Jin-Suk Youn, Suhas K Kadam, Jae Hong Pak, Yeon-Sik Choo","doi":"10.1007/s10528-025-11082-7","DOIUrl":"https://doi.org/10.1007/s10528-025-11082-7","url":null,"abstract":"<p><p>Arisaema takesimense (Araceae) is a unique species found exclusively in Ulleung Island of Korea. This study presents the complete chloroplast (cp.) genome of A. takesimense, which comprises 174, 361 base pairs and exhibits a typical tetrad structure. The genome encodes 112 unique genes, including 78 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. In this study, a total of 49 long repeats and 139 simple sequence repeats (SSRs) were identified, predominantly located in intergenic spacer regions (IGS). Additionally, several hotspot regions, including trnS-G, accD-psaI, ndhF and rps15-ycf1, were identified, which are commonly shared among Araceae species. The analysis of these repeats revealed species-specific SSR types and hotspot regions that can be utilized for population genetic studies and species identification. A comparative genomic analysis of eleven Arisaema taxa revealed that the large single copy region (LSC) exhibits the most variability, with non-coding genes displaying more variation than coding genes. The borders between the LSC-IR-SSC regions in Arisaema taxa were generally well-preserved, and there were notable exceptions in the positions of LSC/IRa, LSC/IRb and SSC/IRb junctions for A. takesimense, A. ringens, and A. nepenthoides. A phylogenetic analysis based on the cp. genome revealed a close relationship between A. takesimense and A. bockii. The outcomes of this study substantially increase the genomic resources available for Araceae, serving as a valuable resource for species identification and evaluating intraspecific diversity within the Arisaema genus.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646765","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}

{"title":"Identification of DIO2 as a Molecular Therapeutic Target for Depression in Chronic Rhinosinusitis: A Comprehensive Bioinformatics and Experimental Study.","authors":"Hao Lv, Peiqiang Liu, Yunfei Wang, Jingyu Huang, Yulie Xie, Mengting Guan, Jianchao Cong, Yang Jiang, Yu Xu","doi":"10.1007/s10528-025-11085-4","DOIUrl":"https://doi.org/10.1007/s10528-025-11085-4","url":null,"abstract":"<p><p>Chronic rhinosinusitis (CRS) and depression are both common conditions with significant socioeconomic impact. The high co-occurrence of depression in CRS patients suggests a common pathophysiology, but the mechanisms are unclear. This study aimed to identify potential molecular links between the two conditions. We retrieved gene expression datasets for CRS and depression from the GEO database. Using differentially expressed genes (DEGs) analysis and weighted gene co-expression network analysis (WGCNA), we identified co-expression genes associated with CRS and depression. Enrichment analyses including GO, KEGG, and GSEA were performed to explore biological pathways. Machine learning algorithms including random forest and LASSO regression were engaged to screen for shared hub genes predictive of CRS and depression. Single-cell RNA sequencing (scRNA-seq) data were analyzed to delineate the expression profiles of the shared hub genes across different cell types. Animal experiments were employed to validate the role of core genes in CRS-related depression. We identified five shared hub genes: CHRDL1, DIO2, HSD17B6, PDE3A, and PLA2G5, with the TGF-β signaling, cytokine-cytokine interaction receptors, and cell adhesion as key biological pathways. DIO2, as identified by machine learning, is a promising diagnostic biomarker for CRS and depression. The scRNA-seq analysis showed that DIO2 is primarily expressed in neurons and astrocytes. Animal experiments showed that overexpression of DIO2 improved the depressive-like behaviors in CRS mice. This study sheds new light on the molecular basis of the comorbidity between CRS and depression. DIO2 is a potential diagnostic and therapeutic target for CRS patients with comorbid depression.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639354","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}