Biochemical Genetics最新文献

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Clinico-Morphological and Genetic Features of Colorectal Cancer in Multiple Primary Cancers Cases. 结直肠癌多原发病例的临床形态学和遗传学特征。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-02-16 DOI: 10.1007/s10528-026-11328-y
Natalya N Timoshkina, Dmitry Yu Gvaldin, Dema Alset, Inna A Novikova, Oleg I Kit
{"title":"Clinico-Morphological and Genetic Features of Colorectal Cancer in Multiple Primary Cancers Cases.","authors":"Natalya N Timoshkina, Dmitry Yu Gvaldin, Dema Alset, Inna A Novikova, Oleg I Kit","doi":"10.1007/s10528-026-11328-y","DOIUrl":"10.1007/s10528-026-11328-y","url":null,"abstract":"","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6046-6060"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146199875","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
Complete Genome Sequencing of Streptomyces sp. Qhu-M197 Isolated from Alpine Meadows in the Qinghai-Tibetan Plateau Uncovers Biosynthetic Gene Clusters Encoding Bioactive Natural Products. 青藏高原高寒草甸链霉菌qku - m197全基因组测序揭示了编码生物活性天然产物的生物合成基因簇
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-01-08 DOI: 10.1007/s10528-025-11313-x
Xin Xiang, Jiakai Fan, Xingyu Liu, Guangzhi Li, Chenghang Sun, Benyin Zhang
{"title":"Complete Genome Sequencing of Streptomyces sp. Qhu-M197 Isolated from Alpine Meadows in the Qinghai-Tibetan Plateau Uncovers Biosynthetic Gene Clusters Encoding Bioactive Natural Products.","authors":"Xin Xiang, Jiakai Fan, Xingyu Liu, Guangzhi Li, Chenghang Sun, Benyin Zhang","doi":"10.1007/s10528-025-11313-x","DOIUrl":"10.1007/s10528-025-11313-x","url":null,"abstract":"<p><p>Streptomyces spp. is a crucial source for the drug discovery and development, especially those from extreme environments. The complete genome was sequenced to uncover the biosynthetic potential of the strain Qhu-M197 producing mithramycin isolated from the alpine meadow of the Qinghai-Tibetan Plateau. The results revealed that the genome consists of one linear chromosome and two plasmids with the size of 9.12 megabases (Mb) and the guanine-cytosine (G + C) content of 71.52%. The phylogenetic analyses of 16S rRNA gene and genome of strain Qhu-M197 suggested the strain belonged to Streptomyces genus, and the closest phylogenetic relationship between the strain Qhu-M197 and S. phaeoluteigriseus DSM 41896<sup>T</sup>. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between Qhu-M197 and S. phaeoluteigriseus DSM 41896<sup>T</sup> are 97.47% and 84.1%, respectively, indicating that they likely belong to the same species. However, comparative genomic analysis with closely related species reveals that Qhu-M197 may represent a novel strain of S. phaeoluteigriseus, highlighting its potential distinction at the strain level. The biosynthetic gene clusters (BGCs) analyzed by antiSMASH v7.0 revealed that Qhu-M197 had 33 BGCs encoding secondary metabolites. Interestingly, about 64% BGCs show less than 50% similarity to those annotated, which provides new opportunities for the discovery of novel natural products.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5752-5771"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145931400","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
Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.). 全基因组关联研究揭示番茄(Solanum lycopersicum L.)农艺性状控制新位点。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-02-07 DOI: 10.1007/s10528-026-11329-x
Jagesh Kumar Tiwari, Nagendra Rai, Manish Kumar Singh, Rajat Singh, Tushar Kant, Suresh Reddy Yerasu, Achuit Kumar Singh, Rajesh Kumar
{"title":"Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.).","authors":"Jagesh Kumar Tiwari, Nagendra Rai, Manish Kumar Singh, Rajat Singh, Tushar Kant, Suresh Reddy Yerasu, Achuit Kumar Singh, Rajesh Kumar","doi":"10.1007/s10528-026-11329-x","DOIUrl":"10.1007/s10528-026-11329-x","url":null,"abstract":"<p><p>The genetic basis of agronomic traits is critical for enhancing yield, quality, and disease resistance in tomato. In this study, genome-wide association study (GWAS) was performed on a diverse panel of 72 tomato accessions to identify genomic regions linked to 18 agronomic, processing, and disease resistance traits. Phenotypic data were collected over two growing seasons, and genotyping was conducted using genotyping-by-sequencing (GBS) on the Illumina platform. A total of 78,828 high-quality single nucleotide polymorphisms (SNPs) were identified, primarily located in intergenic (54.66%), upstream (15.46%), downstream (14.35%), intronic (10.73%), and exonic (2.90%) regions. After stringent filtering, 7751 SNPs were retained for GWAS, leading to the identification of 47 significant quantitative trait loci (QTLs) associated with 13 traits. Fruit length exhibited the highest number of QTLs (23), while chromosomes 1 and 4 contained the most QTLs (9 each). Several candidate genes were identified for key traits, including F-box protein CPR1-like and transcription factor bHLH162-like for fruit weight, F-box protein At5g49610 for fruit length, transcription factor TGA9 for fruit diameter, F-box protein CPR1-like and Beta-D-xylosidase 2 for fruit yield, Cinnamoyl-CoA reductase-like SNL6 and UDP-glucosyltransferase, as well as stress-induced protein KIN2-like and serine/threonine-protein kinase BLUS1 for ToLCV resistance. Population structure and phylogenetic analyses indicated variation among ancestral populations (K = 3). These findings provide valuable genomic resources and identify candidate genes for key traits, supporting genomics-driven breeding in tomato.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5972-5995"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146130880","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
Genetic Variability and Diversity Analysis for Nutritional and Anti-nutritional Traits in Pearl Millet [Pennisetum glaucum (L.) R.Br]. 珍珠粟(Pennisetum glaucum, L.)营养和抗营养性状的遗传变异及多样性分析R.Br]。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-02-18 DOI: 10.1007/s10528-026-11335-z
Tripti Singhal, S P Singh, Sunaina Yadav, Naveen Aavula, Chandan Kapoor, Nirupma Singh, C Tara Satyavathi
{"title":"Genetic Variability and Diversity Analysis for Nutritional and Anti-nutritional Traits in Pearl Millet [Pennisetum glaucum (L.) R.Br].","authors":"Tripti Singhal, S P Singh, Sunaina Yadav, Naveen Aavula, Chandan Kapoor, Nirupma Singh, C Tara Satyavathi","doi":"10.1007/s10528-026-11335-z","DOIUrl":"10.1007/s10528-026-11335-z","url":null,"abstract":"<p><p>Addressing micronutrient malnutrition requires targeted biofortification of staple crops such as pearl millet [Pennisetum glaucum (L.) R.Br.], which is widely consumed in arid and semi-arid regions. This study assessed 47 advanced breeding lines developed at ICAR-IARI, New Delhi, to evaluate genetic variability, heritability, and diversity for nutritional (iron, zinc, protein, starch, oil, amylose) and anti-nutritional (phytate and phenol) traits. Substantial variation was observed for grain iron (33.9-121.4 mg/kg), zinc (27.4-90.0 mg/kg), and protein (7.99-15.56%). High genotypic and phenotypic coefficients of variation, coupled with high heritability and genetic advance for iron, zinc, and protein, indicated the predominance of additive gene action, suggesting that simple phenotypic selection can be effectively employed for trait improvement. Correlation analysis revealed strong positive associations between iron, zinc, and protein, enabling simultaneous enhancement of these key traits. Multivariate analyses (PCA and hierarchical clustering) identified three distinct genetic clusters, with one group (Cluster II) exhibiting superior iron and zinc profiles. The presence of broad genetic diversity and favourable trait combinations underscore the potential of these genotypes as donors in breeding programs aimed at developing nutrient-dense pearl millet varieties/ hybrids. This work contributes critical insights toward the genetic enhancement of pearl millet to alleviate hidden hunger and improve dietary quality in vulnerable populations.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6093-6109"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146218222","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
Voltage-Gated Sodium Channel NaV1.2: Structural Perspective of the Genetic Variability. 电压门控钠通道NaV1.2:遗传变异的结构视角。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-02-03 DOI: 10.1007/s10528-026-11327-z
Tomás Oliveira-Madureira, Bárbara Leal, Luísa Azevedo
{"title":"Voltage-Gated Sodium Channel Na<sub>V</sub>1.2: Structural Perspective of the Genetic Variability.","authors":"Tomás Oliveira-Madureira, Bárbara Leal, Luísa Azevedo","doi":"10.1007/s10528-026-11327-z","DOIUrl":"10.1007/s10528-026-11327-z","url":null,"abstract":"<p><p>The SCN2A gene encodes the alpha subunit of a voltage-gated sodium channel which is necessary for creating and propagating action potentials in neurons. Impairment of the Na<sub>v</sub>1.2 function is associated with neurodevelopmental disorders such as Developmental and Epileptic Encephalopathy, Self-limited Neonatal/Infantile Seizures, and Autism Spectrum Disorder. In this study, we used orthologous sequence comparisons, as well as disease associated variants to analyze their location in the structure of Na<sub>v</sub>1.2, with the aim of understanding the impact of genetic variants in the structure of this protein at an evolutionary and clinical level. Our analyses reveal different spatial distribution of interspecific variation where different residues locate preferentially in the first cytoplasmic linker, while disease-associated variants tend to cluster in the voltage-sensing segments of the protein domains. Altogether, these discoveries point to structurally important segments in the Na<sub>v</sub>1.2 structure that have been conserved through evolution due to their role in maintaining the function of the channel.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5959-5971"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13388790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146111674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microsatellite Markers Display High Diversity in Bean Anthracnose Pathogen Colletotrichum lindemuthianum in Kashmir. 克什米尔地区豆炭疽病病原菌lindemuthium微卫星标记多样性研究
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-01-24 DOI: 10.1007/s10528-026-11322-4
Tabia Fayaz, Aasiya Nabi, Naziya Nabi, Irtifa Lateef, Raja Junaid, Qadrul Nisa, Sehla Khursheed, Adfar Bashir, Zainab Rashid, H Itoo, Rafiq A Shah, Saba Banday, Sajad M Zargar, Imran Khan, M D Shah, Bilal A Padder
{"title":"Microsatellite Markers Display High Diversity in Bean Anthracnose Pathogen Colletotrichum lindemuthianum in Kashmir.","authors":"Tabia Fayaz, Aasiya Nabi, Naziya Nabi, Irtifa Lateef, Raja Junaid, Qadrul Nisa, Sehla Khursheed, Adfar Bashir, Zainab Rashid, H Itoo, Rafiq A Shah, Saba Banday, Sajad M Zargar, Imran Khan, M D Shah, Bilal A Padder","doi":"10.1007/s10528-026-11322-4","DOIUrl":"10.1007/s10528-026-11322-4","url":null,"abstract":"<p><p>Common bean (Phaseolus vulgaris) anthracnose, caused by Colletotrichum lindemuthianum affects and decreases its yield substantially. Fifty Simple Sequence Repeat (SSR) markers were used to analyze the genetic and genotypic variation among 36 C. lindemuthianum isolates. Among the 50 SSRs, 24 were polymorphic and amplified 66 alleles. Most of the SSRs had polymorphic information content (PIC) values > 0.30, indicating their strong discriminative competence. Distance based dendrogram analysis and population structure analysis divided 36 C. lindemuthianum isolates into three clusters. Analysis of molecular variance at spatiotemporal levels showed high genetic variation among the populations. The six C. lindemuthianum subpopulations had high Shannon-Wiener indices. The multilocus genotype and genetic diversity indices show that C. lindemuthianum populations in Kashmir are diverse. The three geographic subpopulations of C. lindemuthianum rejected the null hypothesis of linkage equilibrium (p = 0.001). Before this study, all PCR based genetic diversity studies on C. lindemuthianum relied on dominant markers. This study is the first to identify 24 robust SSRs, which can be utilized to elucidate the population structure of the common bean anthracnose pathogen.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5887-5902"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146040149","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
Association of IL1B Gene Polymorphisms (rs1143634 and rs16944) with Schizophrenia in Iranian Patients. IL1B基因多态性(rs1143634和rs16944)与伊朗精神分裂症患者的关系
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2025-10-13 DOI: 10.1007/s10528-025-11255-4
Shiva Mehrabi, Lily Mirtabatabaei, Siavash Shakerian, Flora Forouzesh, Maryam Razavi, Toktam-Sadat Tavabe-Ghavami, Mahsa Mohammadi-Lapevandani, Yeganeh Ghasemi, Fatemeh Alizadeh
{"title":"Association of IL1B Gene Polymorphisms (rs1143634 and rs16944) with Schizophrenia in Iranian Patients.","authors":"Shiva Mehrabi, Lily Mirtabatabaei, Siavash Shakerian, Flora Forouzesh, Maryam Razavi, Toktam-Sadat Tavabe-Ghavami, Mahsa Mohammadi-Lapevandani, Yeganeh Ghasemi, Fatemeh Alizadeh","doi":"10.1007/s10528-025-11255-4","DOIUrl":"10.1007/s10528-025-11255-4","url":null,"abstract":"<p><p>Schizophrenia (SCZ) is a deleterious neuropsychological disorder with a worldwide incidence of 1% and unknown etiology. Understanding the role of genetic variants in disease development would enable us to explain the disorder's molecular mechanism and find a more effective prognostic approach. Several studies in various European and East Asian populations have displayed the association of schizophrenia with functional polymorphisms such as rs16944 and rs1143634 that lie within inflammatory pathway genes. This study aimed to evaluate the association of Interleukin-1 beta (IL1B) variants (rs16944, rs1143634) with schizophrenia in the Iranian population for the first time. 565 individuals (240 cases and 325 controls) were recruited. Genotyping was conducted for IL1B single nucleotide polymorphisms (SNPs) (rs16944 and rs1143634) using polymerase chain reaction-Restriction fragment length polymorphism (PCR-RFLP). In addition, the haplotype analysis was conducted. All statistical analysis was performed using SPSS version 26. Regarding rs1143634 (C > T), T carrier genotypes (CT, TT) compared to CC homozygous genotypes showed a significantly more protective effect (p-value < 0.001). Similarly, concerning the co-dominant model, CT heterozygous genotypes in comparison with homozygous genotypes (CC, TT) illustrated a protective impact regarding schizophrenia (p-value < 0.001). Findings showed a significant difference between cases and healthy controls regarding the rs1143634 (C > T) allele frequency (p-value = 0.025), whereas it determined no considerable difference given rs16944 (p-value = 0.41). Furthermore, in the case of rs16944 (T > C), we found no significant association between case and control groups (p-value = 0.69). Haplotype analysis demonstrated that the C-C (rs1143634-rs16944) haplotype was significantly associated with the risk of schizophrenia (p-value = 0.013). The findings suggest that IL1B rs1143634 (C > T) is significantly associated with SCZ in the Iranian population.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6173-6184"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278655","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
FBXW7 Inhibited M2 Macrophage Polarization in Endometrial Cancer by Reducing CCL2 Secretion Through Ubiquitination of MYBL2 Subtitle: The Role of FBXW7 on M2 Macrophage Polarization in EC. FBXW7通过MYBL2泛素化减少CCL2分泌抑制子宫内膜癌中M2巨噬细胞极化
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-01-03 DOI: 10.1007/s10528-025-11309-7
Jing Wu, Xiaomei Zhang, Wei Xu, Xiaojuan Shen
{"title":"FBXW7 Inhibited M2 Macrophage Polarization in Endometrial Cancer by Reducing CCL2 Secretion Through Ubiquitination of MYBL2 Subtitle: The Role of FBXW7 on M2 Macrophage Polarization in EC.","authors":"Jing Wu, Xiaomei Zhang, Wei Xu, Xiaojuan Shen","doi":"10.1007/s10528-025-11309-7","DOIUrl":"10.1007/s10528-025-11309-7","url":null,"abstract":"<p><p>Impeding M2 macrophage polarization has been suggested to slow the progression of endometrial cancer (EC). F-box and WD repeat domain containing 7 (FBXW7) reportedly regulates the polarization and migration of macrophages in a multitude of cancers. Our pre-existing bioinformatics predictions showed a negative association between FBXW7 and M2-TAM infiltration in EC. This study aimed to investigate the role of FBXW7 in M2 macrophage polarization in EC by regulating the MYBL2/CCL2 axis. Cancer and adjacent cancerous tissues from patients with EC were collected to detect the differential expression of each factor. CCL2 levels in the cell culture medium were examined using enzyme-linked immunosorbent assay. Immunofluorescence staining was performed to determine the localization of FBXW7 and MYBL2 in EC cells. The number of M2 macrophages marker was determined by flow cytometry. The protein levels of FBXW7, MYBL2, CCL2, CD206, CD163, Arg1, and IL-10 were assessed using western blotting. The ubiquitination level of MYBL2 and the binding relationship between FBXW7 and MYBL2 were verified using co-immunoprecipitation. The effect of FBXW7/MYBL2/CCL2 axis on the malignant progression of EC in vivo was evaluated using tumor xenografts in nude mice. FBXW7 levels were decreased, whereas MYBL2 levels were increased in EC. Overexpression of FBXW7 downregulated CCL2 secretion in EC and inhibited M2 macrophage polarization. FBXW7 promoted the degradation of MYBL2 in a ubiquitination-dependent manner. FBXW7 knockdown inhibited CCL2 secretion by EC cells to restrain M2 macrophage polarization, which was countered by MYBL2 downregulation. In vivo functional assays demonstrated that FBXW7 overexpression significantly suppressed EC xenograft growth and enhanced tumor cell apoptosis. FBXW7 enhanced the ubiquitination and degradation of MYBL2 to reduce CCL2 secretion from EC, which inhibited macrophage polarization to the M2 type.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5731-5751"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145896130","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
ERBB2 as a Prognostic Biomarker in Prostate Cancer: Integration of Single-Cell Transcriptomics, Deep Learning, and Immunohistochemical Validation. ERBB2作为前列腺癌的预后生物标志物:单细胞转录组学、深度学习和免疫组织化学验证的整合。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-02-17 DOI: 10.1007/s10528-026-11333-1
Chen Wang, Li-Jing Zhu, Wei-Bo Mao, Ting Chen, Teng-Fei Gu, Sheng-Ping Hu, Yong-Tao Pan, Guo-Lin Yan, Yun-Peng Dong, Jie Li
{"title":"ERBB2 as a Prognostic Biomarker in Prostate Cancer: Integration of Single-Cell Transcriptomics, Deep Learning, and Immunohistochemical Validation.","authors":"Chen Wang, Li-Jing Zhu, Wei-Bo Mao, Ting Chen, Teng-Fei Gu, Sheng-Ping Hu, Yong-Tao Pan, Guo-Lin Yan, Yun-Peng Dong, Jie Li","doi":"10.1007/s10528-026-11333-1","DOIUrl":"10.1007/s10528-026-11333-1","url":null,"abstract":"<p><p>Biochemical recurrence (BCR) is a critical factor affecting the prognosis of prostate cancer (PCa) patients, while T cell exhaustion and metastatic prostate cancer (mPC)-related genes play significant roles in tumor progression. This study aims to identify key genes associated with BCR by integrating single-cell transcriptomics and deep learning techniques, and to validate their clinical significance. First, we identified highly expressed genes in CD8<sup>+</sup> T cell exhaustion clusters from single-cell RNA sequencing data (scRNA-seq) of PCa and intersected them with mPC-related genes. Based on these genes, significant prognostic factors were screened using Cox regression analysis, and a deep learning neural network model was constructed to predict the risk of biochemical recurrence in prostate cancer patients. The tumor-infiltrating lymphocyte (TILs) infiltration was predicted by stratifying patients into high- and low-risk groups. ERBB2 was identified as the most predictive gene through model analysis. Subsequently, ERBB2 expression was validated in an independent PCa cohort using immunohistochemistry (IHC), and its association with biochemical recurrence and clinicopathological features was evaluated through survival analysis and statistical methods. The deep learning model demonstrated excellent performance in predicting BCR, with ERBB2 identified as the most important predictive factor. IHC results revealed that patients with high ERBB2 expression had significantly shorter biochemical recurrence-free survival (bRFS) (P < 0.05). Moreover, high ERBB2 expression was significantly associated with higher prostate-specific antigen (PSA) levels, Node-Metastasis (NM) stage, and International Society of Urological Pathology (ISUP) grade (P < 0.05). This study, for the first time, integrates single-cell transcriptomics, deep learning, and IHC to reveal the critical role of ERBB2 in biochemical recurrence of PCa. High ERBB2 expression is not only a potential biomarker for poor prognosis in PCa patients but may also provide a novel target for personalized therapy.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"6077-6092"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146211758","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
Potential Targets in Nonalcoholic Steatohepatitis Based on Bioinformatics Analysis and Machine Learning Strategies. 基于生物信息学分析和机器学习策略的非酒精性脂肪性肝炎的潜在靶点。
IF 1.9 4区 生物学
Biochemical Genetics Pub Date : 2026-08-01 Epub Date: 2026-01-27 DOI: 10.1007/s10528-026-11321-5
Tiansu Lv, Lingling Zhu, Yuan Han, Zhe Cheng, Yutian Cao, Wenhui Zhang, Jiaxuan Huai, Wenlin Ma, Yixian He, Yiran Zhu, Qianhua Yan, Xiqiao Zhou
{"title":"Potential Targets in Nonalcoholic Steatohepatitis Based on Bioinformatics Analysis and Machine Learning Strategies.","authors":"Tiansu Lv, Lingling Zhu, Yuan Han, Zhe Cheng, Yutian Cao, Wenhui Zhang, Jiaxuan Huai, Wenlin Ma, Yixian He, Yiran Zhu, Qianhua Yan, Xiqiao Zhou","doi":"10.1007/s10528-026-11321-5","DOIUrl":"10.1007/s10528-026-11321-5","url":null,"abstract":"<p><p>NASH poses a significant threat to human health and is recognized as the leading contributor to HCC. In this study, we leveraged publicly accessible datasets to identify novel differentially expressed genes that may serve as potential targets in NASH or potentially NASH-induced HCC. The publicly available datasets were obtained from the GEO. Differential gene expression analysis and enrichment analysis was performed. Subsequently, WGCNA and PPI network were constructed. Lastly, machine learning was employed to identify key feature genes. Utilizing the integrated GEO database, we identified 446 genes exhibiting differential expression. Enrichment analysis indicated that these genes are predominantly associated with glucose and lipid metabolism and inflammatory processes. Through WGCNA, three modules were identified that demonstrated a significant correlation with NASH. Furthermore, core genes among the differentially expressed genes were extracted via protein and protein interaction analysis. Ultimately, machine learning techniques were employed, leading to the identification of three genes: FosB, Fos, and SOCS3. Notably, FosB exhibited consistent expression across various datasets, demonstrated strong predictive capabilities for NASH, and was associated with improved prognostic outcomes in hepatocellular carcinoma by data from TCGA. Additionally, in vitro immunohistochemistry experiments revealed significant reduction of FosB expression in NASH. Bioinformatics analyses conducted on various datasets, along with in vitro immunohistochemistry experiments, revealed significant downregulation of FosB in NASH. It indicates that FosB plays a critical role in the pathogenesis of NASH, and its expression is associated with the prognosis of patients with HCC. Further experimental studies are required to investigate the potential targeting of FosB in NASH and NASH-induced HCC.</p>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":" ","pages":"5903-5926"},"PeriodicalIF":1.9,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146049847","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}
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