首页 > 最新文献

Journal of Applied Genetics最新文献

英文 中文
What, how, and why? - anti-EHEC phages and their application potential in medicine and food industry. 是什么、如何以及为什么?- 抗 EHEC 噬菌体及其在医药和食品工业中的应用潜力。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-11-11 DOI: 10.1007/s13353-024-00918-4
Agnieszka Necel, Aleksandra Dydecka, Gracja Topka-Bielecka, Wojciech Wesołowski, Natalia Lewandowska, Sylwia Bloch, Bożena Nejman-Faleńczyk

Enterohemorrhagic Escherichia coli (EHEC) are pathogens that, only in the United States, cause more than 250,000 foodborne infections a year. Since antibiotics or other antidiarrheal agents may increase the hemolytic-uremic syndrome (HUS) development risk, currently only supportive therapy, including hydration, is used. Therefore, many methods to fight EHEC bacteria focus on their use in food processing to prevent human infection. One of the proposed anti-EHEC agents is bacteriophages, known for their bactericidal effect, host specificity, and lack of cross-resistance with antibiotics. In this review article, we provide an overview of the characteristics like source of isolation, morphology, kinetics of life cycle, and treatment potential of over 130 bacteriophages able to infect EHEC strains. Based on the reviewed literature, we conclude that bacteriophages may play a highly significant role in regulating EHEC propagation. In addition, we also point out the phage features that should be taken into account not only when using bacteriophages but also when examining their properties. This may contribute to accelerating the pace of work on the preventive use of bacteriophages, which is extremely needed in the modern world of the food industry, but also stimulate interest in phages and accelerate regulatory work that would enable the use of bacteriophages also in medicine, to fight the drug-resistant strains.

肠出血性大肠杆菌(EHEC)是一种病原体,仅在美国,每年造成的食源性感染就超过 25 万例。由于抗生素或其他止泻药可能会增加患溶血性尿毒症(HUS)的风险,因此目前只采用包括补水在内的支持疗法。因此,许多抗 EHEC 细菌的方法都侧重于在食品加工中使用它们,以防止人类感染。噬菌体是拟议的抗 EHEC 制剂之一,因其杀菌作用、宿主特异性和与抗生素无交叉耐药性而闻名。在这篇综述文章中,我们概述了 130 多种能感染 EHEC 菌株的噬菌体的特征,如分离来源、形态、生命周期动力学和治疗潜力。根据所查阅的文献,我们得出结论:噬菌体可能在调节 EHEC 繁殖方面发挥着非常重要的作用。此外,我们还指出了不仅在使用噬菌体时,而且在研究其特性时都应考虑到的噬菌体特征。这可能有助于加快预防性使用噬菌体的工作进度,而这正是现代食品工业所急需的,同时也能激发人们对噬菌体的兴趣,加快监管工作,从而使噬菌体也能用于医学领域,与耐药菌株作斗争。
{"title":"What, how, and why? - anti-EHEC phages and their application potential in medicine and food industry.","authors":"Agnieszka Necel, Aleksandra Dydecka, Gracja Topka-Bielecka, Wojciech Wesołowski, Natalia Lewandowska, Sylwia Bloch, Bożena Nejman-Faleńczyk","doi":"10.1007/s13353-024-00918-4","DOIUrl":"10.1007/s13353-024-00918-4","url":null,"abstract":"<p><p>Enterohemorrhagic Escherichia coli (EHEC) are pathogens that, only in the United States, cause more than 250,000 foodborne infections a year. Since antibiotics or other antidiarrheal agents may increase the hemolytic-uremic syndrome (HUS) development risk, currently only supportive therapy, including hydration, is used. Therefore, many methods to fight EHEC bacteria focus on their use in food processing to prevent human infection. One of the proposed anti-EHEC agents is bacteriophages, known for their bactericidal effect, host specificity, and lack of cross-resistance with antibiotics. In this review article, we provide an overview of the characteristics like source of isolation, morphology, kinetics of life cycle, and treatment potential of over 130 bacteriophages able to infect EHEC strains. Based on the reviewed literature, we conclude that bacteriophages may play a highly significant role in regulating EHEC propagation. In addition, we also point out the phage features that should be taken into account not only when using bacteriophages but also when examining their properties. This may contribute to accelerating the pace of work on the preventive use of bacteriophages, which is extremely needed in the modern world of the food industry, but also stimulate interest in phages and accelerate regulatory work that would enable the use of bacteriophages also in medicine, to fight the drug-resistant strains.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"219-240"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142620735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Analysis of nutritional composition in opaque2- and crtRB1-based single- and double-biofortified super sweet corn. 基于不透明2和crtRB1的单一和双重生物强化超级甜玉米的营养成分分析。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-05-11 DOI: 10.1007/s13353-024-00873-0
Bhavna Singh, Vignesh Muthusamy, Smriti Shrivastava, Gulab Chand, Nisrita Gain, Vinay Bhatt, Rajkumar U Zunjare, Firoz Hossain

Sweet corn has emerged as a favorite food item worldwide owing to its kernel sweetness. However, traditional sweet corn cultivars are poor in provitamin-A (proA) and essential amino acids, viz., lysine and tryptophan. So far, no sweet corn hybrid with high nutritional qualities has been commercialized elsewhere. Here, we analyzed accumulation of provitamin-A (proA), lysine, and tryptophan in a set of mutant versions of (i) crtRB1-, (ii) o2-, and (iii) crtRB1 + o2-based sweet corn inbreds and hybrids with (iv) traditional sweet corn (wild-type: O2 + CrtRB1). The crtRB1- and crtRB1 + o2-based genotypes possessed significantly higher proA (17.31 ppm) over traditional sweet corn (2.83 ppm), while o2- and crtRB1 + o2-based genotypes possessed significantly higher lysine (0.345%) and tryptophan (0.080%) over traditional sweet corn (lysine 0.169%, tryptophan 0.036%). Late sowing favored high kernel lysine, proA, and green cob yield among hybrids. Sweetness (17.87%) among the improved inbreds and hybrids was comparable to the original sweetcorn genotypes (17.84%). Among the four genotypic classes, crtRB1 + o2-based improved genotypes showed stronger association among traits over genotypes with o2 and crtRB1 genes alone. Significant association was observed among (i) proA and BC (r = 0.99), (ii) proA and BCX (r = 0.93), (iii) lysine and tryptophan (r = 0.99), and (iv) green cob yield with fodder yield (r = 0.73) in sweet corn hybrids. The study demonstrated that combining crtRB1 and o2 genes did not pose any negative impact on nutritional, yield, and agronomic performance. Sweet corn with crtRB1 + o2 assumes significance for alleviating malnutrition through sustainable and cost-effective approach.

甜玉米因其籽粒甜美而成为全世界最受欢迎的食品。然而,传统的甜玉米品种缺乏维生素 A(proA)和必需氨基酸,即赖氨酸和色氨酸。迄今为止,其他地方还没有高营养品质的甜玉米杂交种实现商业化。在这里,我们分析了一组突变型(i)crtRB1-、(ii)o2-、(iii)crtRB1 + o2 甜玉米近交系和杂交种与(iv)传统甜玉米(野生型:O2 + CrtRB1)中维生素 A(proA)、赖氨酸和色氨酸的积累情况。与传统甜玉米(2.83 ppm)相比,基于 crtRB1- 和 crtRB1 + o2 的基因型具有显著较高的 proA(17.31 ppm);与传统甜玉米(赖氨酸 0.169%,色氨酸 0.036%)相比,基于 o2- 和 crtRB1 + o2 的基因型具有显著较高的赖氨酸(0.345%)和色氨酸(0.080%)。晚播有利于提高杂交种的籽粒赖氨酸、proA 和青棒产量。改良近交系和杂交种的甜度(17.87%)与原始甜玉米基因型(17.84%)相当。在四个基因型类别中,基于 crtRB1 + o2 基因的改良基因型与仅有 o2 和 crtRB1 基因的基因型相比,在性状之间表现出更强的关联性。在甜玉米杂交种中,(i) proA 和 BC(r = 0.99)、(ii) proA 和 BCX(r = 0.93)、(iii) 赖氨酸和色氨酸(r = 0.99)以及 (iv) 青棒产量和饲料产量(r = 0.73)之间存在显著关联。研究表明,crtRB1 和 o2 基因的结合不会对营养、产量和农艺性能产生任何负面影响。含有 crtRB1 + o2 基因的甜玉米对于通过可持续和具有成本效益的方法缓解营养不良问题具有重要意义。
{"title":"Analysis of nutritional composition in opaque2- and crtRB1-based single- and double-biofortified super sweet corn.","authors":"Bhavna Singh, Vignesh Muthusamy, Smriti Shrivastava, Gulab Chand, Nisrita Gain, Vinay Bhatt, Rajkumar U Zunjare, Firoz Hossain","doi":"10.1007/s13353-024-00873-0","DOIUrl":"10.1007/s13353-024-00873-0","url":null,"abstract":"<p><p>Sweet corn has emerged as a favorite food item worldwide owing to its kernel sweetness. However, traditional sweet corn cultivars are poor in provitamin-A (proA) and essential amino acids, viz., lysine and tryptophan. So far, no sweet corn hybrid with high nutritional qualities has been commercialized elsewhere. Here, we analyzed accumulation of provitamin-A (proA), lysine, and tryptophan in a set of mutant versions of (i) crtRB1-, (ii) o2-, and (iii) crtRB1 + o2-based sweet corn inbreds and hybrids with (iv) traditional sweet corn (wild-type: O2 + CrtRB1). The crtRB1- and crtRB1 + o2-based genotypes possessed significantly higher proA (17.31 ppm) over traditional sweet corn (2.83 ppm), while o2- and crtRB1 + o2-based genotypes possessed significantly higher lysine (0.345%) and tryptophan (0.080%) over traditional sweet corn (lysine 0.169%, tryptophan 0.036%). Late sowing favored high kernel lysine, proA, and green cob yield among hybrids. Sweetness (17.87%) among the improved inbreds and hybrids was comparable to the original sweetcorn genotypes (17.84%). Among the four genotypic classes, crtRB1 + o2-based improved genotypes showed stronger association among traits over genotypes with o2 and crtRB1 genes alone. Significant association was observed among (i) proA and BC (r = 0.99), (ii) proA and BCX (r = 0.93), (iii) lysine and tryptophan (r = 0.99), and (iv) green cob yield with fodder yield (r = 0.73) in sweet corn hybrids. The study demonstrated that combining crtRB1 and o2 genes did not pose any negative impact on nutritional, yield, and agronomic performance. Sweet corn with crtRB1 + o2 assumes significance for alleviating malnutrition through sustainable and cost-effective approach.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"1-14"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Assessing cytotoxicity and endoplasmic reticulum stress in human blood-brain barrier cells due to silver and copper oxide nanoparticles. 评估纳米银和纳米氧化铜对人血脑屏障细胞的细胞毒性和内质网应激反应。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-02-09 DOI: 10.1007/s13353-024-00833-8
Luiza Chojnacka-Puchta, Dorota Sawicka, Lidia Zapor, Katarzyna Miranowicz-Dzierzawska

In recent years, it has been generally accepted that metal-based nanoparticles (NPs) may induce stress in the endoplasmic reticulum (ER), a key organelle where protein folding occurs. We examined ER stress in immortalized human cerebral microvascular cells (hCMEC/D3) after exposure to silver-NPs (Ag-NPs)- and copper oxide-NPs (CuO-NPs) induced toxicity at < 10 nm and < 40 nm or < 50 nm diameters, respectively. In cytotoxicity assessments, cells were exposed to different CuO-NPs (5-400 µg/mL) or Ag-NPs (1-10 µg/mL) concentration ranges for 24 h and 72 h, and tetrazole salt reduction assays (EZ4U) were performed. Also, Ag-NP or CuO-NP effects on cell proliferation, apoptosis (caspase 3/7 assays), and ER stress and cell morphology were evaluated. In ER stress assessments, RNA-like endoplasmic reticulum kinase (PERK), activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1a), and others stress factor mRNA levels were determined after 24 h treatment using Real-Time PCR. Increased stress sensors (IRE1a, PERK, and ATF6) mRNA levels were observed after exposure to Ag-NPs (< 10 and < 40 nm) or CuO-NPs (< 50 nm). We investigated the expression of tight junction (TJ) proteins (barrier junctions) and showed that both types of NP reduced of OCLN gene expression. Morphological changes were observed after Ag-NP or CuO-NP exposure using holotomographic microscopy. Our data suggest that Ag- and CuO-NPs should undergo future in vitro and in vivo toxicology studies, especially for downstream biomedical application and occupational risk assessments.

近年来,人们普遍认为金属基纳米粒子(NPs)可能会诱导内质网(ER)产生应激,而内质网是蛋白质折叠的关键细胞器。我们研究了永生的人脑微血管细胞(hCMEC/D3)在暴露于银纳米粒子(Ag-NPs)和氧化铜纳米粒子(CuO-NPs)诱导的毒性后的ER应激反应。
{"title":"Assessing cytotoxicity and endoplasmic reticulum stress in human blood-brain barrier cells due to silver and copper oxide nanoparticles.","authors":"Luiza Chojnacka-Puchta, Dorota Sawicka, Lidia Zapor, Katarzyna Miranowicz-Dzierzawska","doi":"10.1007/s13353-024-00833-8","DOIUrl":"10.1007/s13353-024-00833-8","url":null,"abstract":"<p><p>In recent years, it has been generally accepted that metal-based nanoparticles (NPs) may induce stress in the endoplasmic reticulum (ER), a key organelle where protein folding occurs. We examined ER stress in immortalized human cerebral microvascular cells (hCMEC/D3) after exposure to silver-NPs (Ag-NPs)- and copper oxide-NPs (CuO-NPs) induced toxicity at < 10 nm and < 40 nm or < 50 nm diameters, respectively. In cytotoxicity assessments, cells were exposed to different CuO-NPs (5-400 µg/mL) or Ag-NPs (1-10 µg/mL) concentration ranges for 24 h and 72 h, and tetrazole salt reduction assays (EZ4U) were performed. Also, Ag-NP or CuO-NP effects on cell proliferation, apoptosis (caspase 3/7 assays), and ER stress and cell morphology were evaluated. In ER stress assessments, RNA-like endoplasmic reticulum kinase (PERK), activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1a), and others stress factor mRNA levels were determined after 24 h treatment using Real-Time PCR. Increased stress sensors (IRE1a, PERK, and ATF6) mRNA levels were observed after exposure to Ag-NPs (< 10 and < 40 nm) or CuO-NPs (< 50 nm). We investigated the expression of tight junction (TJ) proteins (barrier junctions) and showed that both types of NP reduced of OCLN gene expression. Morphological changes were observed after Ag-NP or CuO-NP exposure using holotomographic microscopy. Our data suggest that Ag- and CuO-NPs should undergo future in vitro and in vivo toxicology studies, especially for downstream biomedical application and occupational risk assessments.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"87-103"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139706775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Genomic Profiling Reveals Immune-Related Gene Differences in Lung Cancer Patients Stratified by PD1/PDL1 Expression: Implications for Immunotherapy Efficacy. 基因组剖析揭示了肺癌患者按 PD1/PDL1 表达分层的免疫相关基因差异:免疫疗法疗效的意义。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-02-16 DOI: 10.1007/s13353-024-00841-8
Zhifeng Ye, Ting Huang, Keke Hu, HeRan Zhou, Ling Huang, Lu Wang

Lung cancer remains a leading cause of global cancer-related mortality, and the exploration of innovative therapeutic approaches, such as PD1/PDL1 immunotherapy, is critical. This study leverages comprehensive data from the Cancer Genome Atlas (TCGA) to investigate the differential expression of PD1/PDL1 in lung cancer patients and explores its implications. Clinical data, RNA expression, somatic mutations, and copy number variations of 1017 lung cancer patients were obtained from TCGA. Patients were categorized into high (HE) and low (LE) PD1/PDL1 expression groups based on mRNA levels. Analyses included differential gene expression, functional enrichment, protein-protein interaction networks, and mutational landscape exploration. The study identified 391 differentially expressed genes, with CD4 and PTPRC among the upregulated genes in the HE group. Although overall survival did not significantly differ between HE and LE groups, enrichment analysis revealed a strong association with immunoregulatory signaling pathways, emphasizing the relevance of PD1/PDL1 in immune response modulation. Notably, TP53 mutations were significantly correlated with high PD1/PDL1 expression. This study provides a comprehensive analysis of PD1/PDL1 expression in lung cancer, uncovering potential biomarkers and highlighting the intricate interplay between PD1/PDL1 and the immune response. The identified upregulated genes, including CD4 and PTPRC, warrant further investigation for their roles in the context of lung cancer and immunotherapy. The study underscores the importance of considering molecular heterogeneity in shaping personalized treatment strategies for lung cancer patients. Limitations, such as the retrospective nature of TCGA data, should be acknowledged.

肺癌仍然是全球癌症相关死亡的主要原因,因此探索创新治疗方法(如 PD1/PDL1 免疫疗法)至关重要。本研究利用癌症基因组图谱(TCGA)的综合数据研究肺癌患者中 PD1/PDL1 的差异表达并探讨其影响。研究人员从 TCGA 中获得了 1017 例肺癌患者的临床数据、RNA 表达、体细胞突变和拷贝数变异。根据 mRNA 水平将患者分为 PD1/PDL1 高表达组(HE)和低表达组(LE)。分析包括差异基因表达、功能富集、蛋白-蛋白相互作用网络和突变景观探索。研究发现了391个差异表达基因,其中CD4和PTPRC是HE组中上调的基因。虽然HE组和LE组的总生存率没有明显差异,但富集分析显示,HE组和LE组与免疫调节信号通路密切相关,强调了PD1/PDL1在免疫反应调节中的相关性。值得注意的是,TP53突变与PD1/PDL1的高表达显著相关。这项研究全面分析了肺癌中PD1/PDL1的表达,发现了潜在的生物标记物,并强调了PD1/PDL1与免疫反应之间错综复杂的相互作用。已发现的上调基因,包括 CD4 和 PTPRC,值得进一步研究它们在肺癌和免疫疗法中的作用。这项研究强调了在为肺癌患者制定个性化治疗策略时考虑分子异质性的重要性。应当承认研究的局限性,如TCGA数据的回顾性。
{"title":"Genomic Profiling Reveals Immune-Related Gene Differences in Lung Cancer Patients Stratified by PD1/PDL1 Expression: Implications for Immunotherapy Efficacy.","authors":"Zhifeng Ye, Ting Huang, Keke Hu, HeRan Zhou, Ling Huang, Lu Wang","doi":"10.1007/s13353-024-00841-8","DOIUrl":"10.1007/s13353-024-00841-8","url":null,"abstract":"<p><p>Lung cancer remains a leading cause of global cancer-related mortality, and the exploration of innovative therapeutic approaches, such as PD1/PDL1 immunotherapy, is critical. This study leverages comprehensive data from the Cancer Genome Atlas (TCGA) to investigate the differential expression of PD1/PDL1 in lung cancer patients and explores its implications. Clinical data, RNA expression, somatic mutations, and copy number variations of 1017 lung cancer patients were obtained from TCGA. Patients were categorized into high (HE) and low (LE) PD1/PDL1 expression groups based on mRNA levels. Analyses included differential gene expression, functional enrichment, protein-protein interaction networks, and mutational landscape exploration. The study identified 391 differentially expressed genes, with CD4 and PTPRC among the upregulated genes in the HE group. Although overall survival did not significantly differ between HE and LE groups, enrichment analysis revealed a strong association with immunoregulatory signaling pathways, emphasizing the relevance of PD1/PDL1 in immune response modulation. Notably, TP53 mutations were significantly correlated with high PD1/PDL1 expression. This study provides a comprehensive analysis of PD1/PDL1 expression in lung cancer, uncovering potential biomarkers and highlighting the intricate interplay between PD1/PDL1 and the immune response. The identified upregulated genes, including CD4 and PTPRC, warrant further investigation for their roles in the context of lung cancer and immunotherapy. The study underscores the importance of considering molecular heterogeneity in shaping personalized treatment strategies for lung cancer patients. Limitations, such as the retrospective nature of TCGA data, should be acknowledged.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"105-114"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Modulation of gene expression in immune-related organs by in ovo stimulation with probiotics and prophybiotics in broiler chickens. 肉鸡体内益生菌和预防性药物对免疫相关器官基因表达的调节作用
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-07-11 DOI: 10.1007/s13353-024-00891-y
Ramesha N Wishna-Kadawarage, Katarzyna Połtowicz, Rita M Hickey, Maria Siwek

In ovo stimulation has been studied intensively as an alternative to antibiotic use in poultry production. We investigated the potential use of a probiotic in combination with a phytobiotic as a prophybiotic for in ovo stimulation and reported its beneficial effects on the gut microbiome of broiler chickens. The current study further investigates the gene expression in the immune-related organs of these chickens to understand the tissue-specific immunomodulatory effects of the treatments. The selected prophybiotic (Leuconostoc mesenteroides with garlic aqueous extract) and its probiotic component alone were injected into ROSS308 chicken eggs on the 12th day of incubation, and gene expression in cecal tonsils, spleen, and liver at 35 days of age was determined using qPCR method. The relative expression of each treatment was compared to the positive control, chickens injected with physiological saline in ovo. The results displayed a downregulation of pro- and anti-inflammatory cytokines in the cecal tonsils of the probiotic group and the liver of the prophybiotic group. The spleen displayed upregulated AVBD1 in both groups and upregulated IL1-β in the probiotic group. The probiotic group displayed increased expression of genes related to metabolism of energy (COX16), protein (mTOR), and lipids (CYP46A1) whereas the prophybiotic group displayed reduced expression of genes related to cholesterol synthesis (SREBP1) and glucose transportation (SLC2A2) in the liver. In conclusion, Leuconostoc mesenteroides differentially modulated gene expression in chickens when administered in ovo in combination with garlic aqueous extract. Further in ovo studies with different prophybiotic combinations are required to optimize the benefits in broiler chickens.

作为家禽生产中使用抗生素的一种替代方法,人们一直在对卵内刺激进行深入研究。我们研究了益生菌与植物生物制剂结合使用作为体内刺激的预防性生物制剂的可能性,并报告了其对肉鸡肠道微生物群的有益影响。目前的研究进一步调查了这些鸡免疫相关器官的基因表达,以了解治疗对特定组织的免疫调节作用。在 ROSS308 鸡孵化的第 12 天,将所选的预防性益生菌(大蒜水提取物的中肠白色念珠菌)和单独的益生菌成分注射到 ROSS308 鸡蛋中,并使用 qPCR 方法测定 35 日龄时盲肠扁桃体、脾脏和肝脏中的基因表达。将各处理的相对表达量与阳性对照(注射生理盐水)进行比较。结果显示,益生菌组的盲肠扁桃体和预防用药组的肝脏中的促炎和抗炎细胞因子下调。两组的脾脏均显示 AVBD1 上调,益生菌组显示 IL1-β 上调。益生菌组肝脏中与能量代谢(COX16)、蛋白质代谢(mTOR)和脂类代谢(CYP46A1)相关的基因表达增加,而预防菌组肝脏中与胆固醇合成(SREBP1)和葡萄糖运输(SLC2A2)相关的基因表达减少。总之,在卵内给药大蒜水提取物的情况下,白色念珠菌会对鸡体内的基因表达产生不同程度的调节作用。为了优化肉鸡的益处,还需要对不同的预防性药物组合进行进一步的体内研究。
{"title":"Modulation of gene expression in immune-related organs by in ovo stimulation with probiotics and prophybiotics in broiler chickens.","authors":"Ramesha N Wishna-Kadawarage, Katarzyna Połtowicz, Rita M Hickey, Maria Siwek","doi":"10.1007/s13353-024-00891-y","DOIUrl":"10.1007/s13353-024-00891-y","url":null,"abstract":"<p><p>In ovo stimulation has been studied intensively as an alternative to antibiotic use in poultry production. We investigated the potential use of a probiotic in combination with a phytobiotic as a prophybiotic for in ovo stimulation and reported its beneficial effects on the gut microbiome of broiler chickens. The current study further investigates the gene expression in the immune-related organs of these chickens to understand the tissue-specific immunomodulatory effects of the treatments. The selected prophybiotic (Leuconostoc mesenteroides with garlic aqueous extract) and its probiotic component alone were injected into ROSS308 chicken eggs on the 12th day of incubation, and gene expression in cecal tonsils, spleen, and liver at 35 days of age was determined using qPCR method. The relative expression of each treatment was compared to the positive control, chickens injected with physiological saline in ovo. The results displayed a downregulation of pro- and anti-inflammatory cytokines in the cecal tonsils of the probiotic group and the liver of the prophybiotic group. The spleen displayed upregulated AVBD1 in both groups and upregulated IL1-β in the probiotic group. The probiotic group displayed increased expression of genes related to metabolism of energy (COX16), protein (mTOR), and lipids (CYP46A1) whereas the prophybiotic group displayed reduced expression of genes related to cholesterol synthesis (SREBP1) and glucose transportation (SLC2A2) in the liver. In conclusion, Leuconostoc mesenteroides differentially modulated gene expression in chickens when administered in ovo in combination with garlic aqueous extract. Further in ovo studies with different prophybiotic combinations are required to optimize the benefits in broiler chickens.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"195-205"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141579731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
The analysis of transcriptomic signature of TNBC-searching for the potential RNA-based predictive biomarkers to determine the chemotherapy sensitivity. TNBC 转录组特征分析--寻找潜在的基于 RNA 的预测性生物标志物,以确定化疗敏感性。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-05-09 DOI: 10.1007/s13353-024-00876-x
Stanislaw Supplitt, Pawel Karpinski, Maria Sasiadek, Lukasz Laczmanski, Dorota Kujawa, Rafal Matkowski, Piotr Kasprzak, Mariola Abrahamowska, Adam Maciejczyk, Ewelina Iwaneczko, Izabela Laczmanska

Neoadjuvant chemotherapy is the foundation treatment for triple-negative breast cancer (TNBC) and frequently results in pathological complete response (pCR). However, there are large differences in clinical response and survival after neoadjuvant chemotherapy of TNBC patients. The aim was to identify genes whose expression significantly associates with the efficacy of neoadjuvant chemotherapy in patients with TNBC. Transcriptomes of 46 formalin-fixed paraffin-embedded (FFPE) tumor samples from TNBC patients were analyzed by RNA-seq by comparing 26 TNBCs with pCR versus 20 TNBCs with pathological partial remission (pPR). Subsequently, we narrowed down the list of genes to those that strongly correlated with drug sensitivity of 63 breast cancer cell lines based on Dependency Map Consortium data re-analysis. Furthermore, the list of genes was limited to those presenting specific expression in breast tumor cells as revealed in three large published single-cell RNA-seq breast cancer datasets. Finally, we analyzed which of the selected genes were significantly associated with overall survival (OS) in TNBC TCGA dataset. A total of 105 genes were significantly differentially expressed in comparison between pPR versus pCR. As revealed by PLSR analysis in breast cancer cell lines, out of 105 deregulated genes, 42 were associated with sensitivity to docetaxel, doxorubicin, paclitaxel, and/or cyclophosphamide. We found that 24 out of 42 sensitivity-associated genes displayed intermediate or strong expression in breast malignant cells using single-cell RNAseq re-analysis. Finally, 10 out of 24 genes were significantly associated with overall survival in TNBC TCGA dataset. Our RNA-seq-based findings suggest that there might be transcriptomic signature consisted of 24 genes specifically expressed in tumor malignant cells for predicting neoadjuvant response in FFPE samples from TNBC patients prior to treatment initiation. Additionally, nine out of 24 genes were potential survival predictors in TNBC. This group of 24 genes should be further investigated for its potential to be translated into a predictive test(s).

新辅助化疗是治疗三阴性乳腺癌(TNBC)的基础疗法,通常可获得病理完全反应(pCR)。然而,TNBC 患者接受新辅助化疗后的临床反应和生存率存在很大差异。研究的目的是找出TNBC患者中表达与新辅助化疗疗效明显相关的基因。我们通过RNA-seq分析了46份福尔马林固定石蜡包埋(FFPE)的TNBC患者肿瘤样本的转录组,比较了26例pCR的TNBC和20例病理部分缓解(pPR)的TNBC。随后,我们根据依赖性图谱联盟(Dependency Map Consortium)的数据重新分析,将基因列表缩小到与 63 个乳腺癌细胞系的药物敏感性密切相关的基因。此外,我们还将基因列表限制在三个已发表的大型单细胞 RNA 序列乳腺癌数据集中显示的那些在乳腺肿瘤细胞中有特异性表达的基因。最后,我们分析了所选基因中哪些与 TNBC TCGA 数据集中的总生存期(OS)显著相关。在 pPR 与 pCR 的比较中,共有 105 个基因有明显的表达差异。乳腺癌细胞系的 PLSR 分析表明,在 105 个基因中,有 42 个与对多西他赛、多柔比星、紫杉醇和/或环磷酰胺的敏感性有关。通过单细胞 RNAseq 重新分析,我们发现 42 个敏感性相关基因中有 24 个在乳腺恶性细胞中显示中等或强表达。最后,在 TNBC TCGA 数据集中,24 个基因中有 10 个与总生存期显著相关。我们基于RNA-seq的研究结果表明,在TNBC患者开始治疗前的FFPE样本中,可能存在由24个在肿瘤恶性细胞中特异表达的基因组成的转录组特征,用于预测新辅助治疗反应。此外,24 个基因中有 9 个是 TNBC 潜在的生存预测因子。这组24个基因应进一步研究,以确定其转化为预测测试的潜力。
{"title":"The analysis of transcriptomic signature of TNBC-searching for the potential RNA-based predictive biomarkers to determine the chemotherapy sensitivity.","authors":"Stanislaw Supplitt, Pawel Karpinski, Maria Sasiadek, Lukasz Laczmanski, Dorota Kujawa, Rafal Matkowski, Piotr Kasprzak, Mariola Abrahamowska, Adam Maciejczyk, Ewelina Iwaneczko, Izabela Laczmanska","doi":"10.1007/s13353-024-00876-x","DOIUrl":"10.1007/s13353-024-00876-x","url":null,"abstract":"<p><p>Neoadjuvant chemotherapy is the foundation treatment for triple-negative breast cancer (TNBC) and frequently results in pathological complete response (pCR). However, there are large differences in clinical response and survival after neoadjuvant chemotherapy of TNBC patients. The aim was to identify genes whose expression significantly associates with the efficacy of neoadjuvant chemotherapy in patients with TNBC. Transcriptomes of 46 formalin-fixed paraffin-embedded (FFPE) tumor samples from TNBC patients were analyzed by RNA-seq by comparing 26 TNBCs with pCR versus 20 TNBCs with pathological partial remission (pPR). Subsequently, we narrowed down the list of genes to those that strongly correlated with drug sensitivity of 63 breast cancer cell lines based on Dependency Map Consortium data re-analysis. Furthermore, the list of genes was limited to those presenting specific expression in breast tumor cells as revealed in three large published single-cell RNA-seq breast cancer datasets. Finally, we analyzed which of the selected genes were significantly associated with overall survival (OS) in TNBC TCGA dataset. A total of 105 genes were significantly differentially expressed in comparison between pPR versus pCR. As revealed by PLSR analysis in breast cancer cell lines, out of 105 deregulated genes, 42 were associated with sensitivity to docetaxel, doxorubicin, paclitaxel, and/or cyclophosphamide. We found that 24 out of 42 sensitivity-associated genes displayed intermediate or strong expression in breast malignant cells using single-cell RNAseq re-analysis. Finally, 10 out of 24 genes were significantly associated with overall survival in TNBC TCGA dataset. Our RNA-seq-based findings suggest that there might be transcriptomic signature consisted of 24 genes specifically expressed in tumor malignant cells for predicting neoadjuvant response in FFPE samples from TNBC patients prior to treatment initiation. Additionally, nine out of 24 genes were potential survival predictors in TNBC. This group of 24 genes should be further investigated for its potential to be translated into a predictive test(s).</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"171-182"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Identification of genes involved in the tomato root response to Globodera rostochiensis parasitism under varied light conditions. 鉴定在不同光照条件下番茄根部对 Globodera rostochiensis 寄生反应的相关基因。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-08-14 DOI: 10.1007/s13353-024-00897-6
Mateusz Matuszkiewicz, Magdalena Święcicka, Marek D Koter, Marcin Filipecki

Understanding the intricate interplay between abiotic and biotic stresses is crucial for deciphering plant responses and developing resilient cultivars. Here, we investigate the combined effects of elevated light intensity and nematode infection on tomato seedlings. Chlorophyll fluorescence analysis revealed significant enhancements in PSII quantum yield and photochemical fluorescence quenching under high light conditions. qRT-PCR analysis of stress-related marker genes exhibited differential expression patterns in leaves and roots, indicating robust defense and antioxidant responses. Despite root protection from light, roots showed significant molecular changes, including downregulation of genes associated with oxidative stress and upregulation of genes involved in signaling pathways. Transcriptome analysis uncovered extensive gene expression alterations, with light exerting a dominant influence. Notably, light and nematode response synergistically induced more differentially expressed genes than individual stimuli. Functional categorization of differentially expressed genes upon double stimuli highlighted enrichment in metabolic pathways, biosynthesis of secondary metabolites, and amino acid metabolism, whereas the importance of specific pathogenesis-related pathways decreased. Overall, our study elucidates complex plant responses to combined stresses, emphasizing the importance of integrated approaches for developing stress-resilient crops in the face of changing environmental conditions.

了解非生物胁迫和生物胁迫之间错综复杂的相互作用,对于解读植物的反应和培育抗逆性强的栽培品种至关重要。在这里,我们研究了高光照强度和线虫感染对番茄幼苗的综合影响。叶绿素荧光分析表明,在强光条件下,PSII量子产率和光化学荧光淬灭显著增强。胁迫相关标记基因的 qRT-PCR 分析表明,叶片和根部的表达模式不同,这表明防御和抗氧化反应强劲。尽管根部受到光照的保护,但根部仍出现了显著的分子变化,包括与氧化应激相关的基因下调和信号通路相关基因上调。转录组分析揭示了广泛的基因表达变化,其中光的影响占主导地位。值得注意的是,与单个刺激相比,光照和线虫反应协同诱导了更多的差异表达基因。对双重刺激下差异表达基因的功能分类突显了代谢途径、次生代谢产物的生物合成和氨基酸代谢的丰富性,而特定致病相关途径的重要性则有所下降。总之,我们的研究阐明了植物对综合胁迫的复杂反应,强调了在不断变化的环境条件下开发抗胁迫作物的综合方法的重要性。
{"title":"Identification of genes involved in the tomato root response to Globodera rostochiensis parasitism under varied light conditions.","authors":"Mateusz Matuszkiewicz, Magdalena Święcicka, Marek D Koter, Marcin Filipecki","doi":"10.1007/s13353-024-00897-6","DOIUrl":"10.1007/s13353-024-00897-6","url":null,"abstract":"<p><p>Understanding the intricate interplay between abiotic and biotic stresses is crucial for deciphering plant responses and developing resilient cultivars. Here, we investigate the combined effects of elevated light intensity and nematode infection on tomato seedlings. Chlorophyll fluorescence analysis revealed significant enhancements in PSII quantum yield and photochemical fluorescence quenching under high light conditions. qRT-PCR analysis of stress-related marker genes exhibited differential expression patterns in leaves and roots, indicating robust defense and antioxidant responses. Despite root protection from light, roots showed significant molecular changes, including downregulation of genes associated with oxidative stress and upregulation of genes involved in signaling pathways. Transcriptome analysis uncovered extensive gene expression alterations, with light exerting a dominant influence. Notably, light and nematode response synergistically induced more differentially expressed genes than individual stimuli. Functional categorization of differentially expressed genes upon double stimuli highlighted enrichment in metabolic pathways, biosynthesis of secondary metabolites, and amino acid metabolism, whereas the importance of specific pathogenesis-related pathways decreased. Overall, our study elucidates complex plant responses to combined stresses, emphasizing the importance of integrated approaches for developing stress-resilient crops in the face of changing environmental conditions.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"47-61"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11762221/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141982370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Bioinformatics to analyze the differentially expressed genes in different degrees of Alzheimer's disease and their roles in progress of the disease. 利用生物信息学分析不同程度阿尔茨海默病的不同表达基因及其在疾病进展中的作用。
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-02-01 Epub Date: 2024-02-05 DOI: 10.1007/s13353-024-00827-6
Yanfang Niu, Yunyun Zhang, Qin Zha, Jingfei Shi, Qiuyan Weng

Employing bioinformatics approaches, this investigation pinpointed pivotal differentially expressed genes (DEGs) across the spectrum of Alzheimer's disease (AD), from incipient to severe stages, using the GSE28146 dataset from the GEO repository. Analytical methods included DEG identification via the limma package in R, coupled with GO and KEGG pathway analyses through clusterProfiler, to discern biological processes and pathway involvements. Key findings spotlighted the roles of proteasome subunits PSMB4, PSMB8, PSMC4, and PSMD6 in the early stage, ribosomal proteins RPS3 and RPL11 during moderate AD, and mitochondrial components COX5B, COX6B2, and COX7A2 in severe AD, underscoring their importance in the disease's pathogenesis. Conclusively, these results not only delineate the dynamic genetic shifts accompanying AD progression but also propose critical biomarkers for potential therapeutic targeting, offering a consolidated basis for future AD research and treatment development. This offered a novel idea for analyzing the pathogenesis and development of AD and investigation of targeted drugs.

这项研究采用生物信息学方法,利用 GEO 数据库中的 GSE28146 数据集,精确定位了阿尔茨海默病(AD)从萌芽期到严重期各个阶段的关键差异表达基因(DEG)。分析方法包括通过R语言中的limma软件包识别DEG,并通过clusterProfiler进行GO和KEGG通路分析,以辨别生物过程和通路参与。主要发现突出了蛋白酶体亚基 PSMB4、PSMB8、PSMC4 和 PSMD6 在早期,核糖体蛋白 RPS3 和 RPL11 在中度 AD 中,线粒体成分 COX5B、COX6B2 和 COX7A2 在重度 AD 中的作用,强调了它们在疾病发病机制中的重要性。最后,这些结果不仅描述了伴随渐冻人症进展的动态基因变化,还提出了潜在治疗靶点的关键生物标志物,为未来渐冻人症的研究和治疗开发提供了坚实的基础。这为分析渐冻人症的发病机制和发展过程以及研究靶向药物提供了一个新思路。
{"title":"Bioinformatics to analyze the differentially expressed genes in different degrees of Alzheimer's disease and their roles in progress of the disease.","authors":"Yanfang Niu, Yunyun Zhang, Qin Zha, Jingfei Shi, Qiuyan Weng","doi":"10.1007/s13353-024-00827-6","DOIUrl":"10.1007/s13353-024-00827-6","url":null,"abstract":"<p><p>Employing bioinformatics approaches, this investigation pinpointed pivotal differentially expressed genes (DEGs) across the spectrum of Alzheimer's disease (AD), from incipient to severe stages, using the GSE28146 dataset from the GEO repository. Analytical methods included DEG identification via the limma package in R, coupled with GO and KEGG pathway analyses through clusterProfiler, to discern biological processes and pathway involvements. Key findings spotlighted the roles of proteasome subunits PSMB4, PSMB8, PSMC4, and PSMD6 in the early stage, ribosomal proteins RPS3 and RPL11 during moderate AD, and mitochondrial components COX5B, COX6B2, and COX7A2 in severe AD, underscoring their importance in the disease's pathogenesis. Conclusively, these results not only delineate the dynamic genetic shifts accompanying AD progression but also propose critical biomarkers for potential therapeutic targeting, offering a consolidated basis for future AD research and treatment development. This offered a novel idea for analyzing the pathogenesis and development of AD and investigation of targeted drugs.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":"73-85"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
HIF1A, EPAS1, and VEGFA: angiogenesis and hypoxia-related gene expression in endometrium and endometrial epithelial tumors.
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-01-31 DOI: 10.1007/s13353-025-00939-7
Monika Englert-Golon, Małgorzata Tokłowicz, Aleksandra Żbikowska, Stefan Sajdak, Małgorzata Kotwicka, Paweł Jagodziński, Andrzej Pławski, Mirosław Andrusiewicz

Endometrial cancer (EC) is the second most frequent gynecological malignancy and the sixth most common women's cancer worldwide. EC incidence rate is increasing rapidly. Apart from the classical, we should consider angiogenesis and hypoxia-related genes as a reason for EC manifestation and progression. We compared the patterns of HIF1A, EPAS1, and VEGFA (genes of interest - GOIs) mRNA expression in 92 cases. HIF1A and VEGFA levels were higher in EC patients than in controls. VEGFA differed significantly between controls and both tumor grades G2 and G3, and we observed a positive correlation for HIF1A and VEGFA with EC grading. VEGFA levels were significantly higher in post-menopausal compared to pre-menopausal patients. All GOIs demonstrated strong correlations in pre-menopausal cases and weak correlations in post-menopausal cases. A positive correlation was observed in pre-menopausal controls for all GOIs and in post-menopausal patients for only EPAS1 and VEGFA. HIF1A and EPAS1 positively correlated with VEGFA in post-menopausal EC cases. Multiple linear regression analyses revealed that menopause, body mass index (BMI), and HIF1A expression are significant stimulating factors for EC occurrence. HIF1A levels were higher in EC patients after BMI and comorbidity number adjustment. The gene-to-gene relation could be seen as either a diagnostic or a therapeutic target in EC. Physicians should inform patients about modifiable risk factors such as BMI. Second, more attention should be paid to diagnosing patients with comorbidities in older age and after menopause. These factors should be considered in designing angiogenesis and hypoxia-related gene-targeting therapies.

{"title":"HIF1A, EPAS1, and VEGFA: angiogenesis and hypoxia-related gene expression in endometrium and endometrial epithelial tumors.","authors":"Monika Englert-Golon, Małgorzata Tokłowicz, Aleksandra Żbikowska, Stefan Sajdak, Małgorzata Kotwicka, Paweł Jagodziński, Andrzej Pławski, Mirosław Andrusiewicz","doi":"10.1007/s13353-025-00939-7","DOIUrl":"https://doi.org/10.1007/s13353-025-00939-7","url":null,"abstract":"<p><p>Endometrial cancer (EC) is the second most frequent gynecological malignancy and the sixth most common women's cancer worldwide. EC incidence rate is increasing rapidly. Apart from the classical, we should consider angiogenesis and hypoxia-related genes as a reason for EC manifestation and progression. We compared the patterns of HIF1A, EPAS1, and VEGFA (genes of interest - GOIs) mRNA expression in 92 cases. HIF1A and VEGFA levels were higher in EC patients than in controls. VEGFA differed significantly between controls and both tumor grades G2 and G3, and we observed a positive correlation for HIF1A and VEGFA with EC grading. VEGFA levels were significantly higher in post-menopausal compared to pre-menopausal patients. All GOIs demonstrated strong correlations in pre-menopausal cases and weak correlations in post-menopausal cases. A positive correlation was observed in pre-menopausal controls for all GOIs and in post-menopausal patients for only EPAS1 and VEGFA. HIF1A and EPAS1 positively correlated with VEGFA in post-menopausal EC cases. Multiple linear regression analyses revealed that menopause, body mass index (BMI), and HIF1A expression are significant stimulating factors for EC occurrence. HIF1A levels were higher in EC patients after BMI and comorbidity number adjustment. The gene-to-gene relation could be seen as either a diagnostic or a therapeutic target in EC. Physicians should inform patients about modifiable risk factors such as BMI. Second, more attention should be paid to diagnosing patients with comorbidities in older age and after menopause. These factors should be considered in designing angiogenesis and hypoxia-related gene-targeting therapies.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 diversity and selection signatures in sheep breeds.
IF 2 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-01-30 DOI: 10.1007/s13353-025-00941-z
Julia Lisboa Rodrigues, Larissa Graciano Braga, Rafael Nakamura Watanabe, Flávio Schramm Schenkel, Donagh Pearse Berry, Marcos Eli Buzanskas, Danísio Prado Munari

Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.

{"title":"Genetic diversity and selection signatures in sheep breeds.","authors":"Julia Lisboa Rodrigues, Larissa Graciano Braga, Rafael Nakamura Watanabe, Flávio Schramm Schenkel, Donagh Pearse Berry, Marcos Eli Buzanskas, Danísio Prado Munari","doi":"10.1007/s13353-025-00941-z","DOIUrl":"https://doi.org/10.1007/s13353-025-00941-z","url":null,"abstract":"<p><p>Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.</p>","PeriodicalId":14891,"journal":{"name":"Journal of Applied Genetics","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143065734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
期刊
Journal of Applied Genetics
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1