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Genes, Volume 16, Issue 1 (January 2025) – 6 articles

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14 pages, 877 KiB  
Review
Hypoxia-Inducible Factor in Renal Cell Carcinoma: From Molecular Insights to Targeted Therapies
by Giandomenico Roviello, Irene De Gennaro, Ismaela Vascotto, Giulia Venturi, Alberto D’Angelo, Costanza Winchler, Adriana Guarino, Salvatore Cacioppo, Mikol Modesti, Marinella Micol Mela, Edoardo Francini, Laura Doni, Virginia Rossi, Elisabetta Gambale, Roberta Giorgione, Lorenzo Antonuzzo, Gabriella Nesi and Martina Catalano
Genes 2025, 16(1), 6; https://doi.org/10.3390/genes16010006 (registering DOI) - 24 Dec 2024
Abstract
Mutations of the von Hippel–Lindau (VHL) tumor suppressor gene occur frequently in clear cell renal cell carcinoma (RCC), the predominant histology of kidney cancer, and have been associated with its pathogenesis and progression. Alterations of VHL lead to impaired degradation of [...] Read more.
Mutations of the von Hippel–Lindau (VHL) tumor suppressor gene occur frequently in clear cell renal cell carcinoma (RCC), the predominant histology of kidney cancer, and have been associated with its pathogenesis and progression. Alterations of VHL lead to impaired degradation of hypoxia-inducible factor 1α (HIF1α) and HIF2α promoting neoangiogenesis, which is pivotal for cancer growth. As such, targeting the VHL-HIF axis holds relevant potential for therapeutic purposes. Belzutifan, an HIF-2α inhibitor, has been recently indicated for metastatic RCC and other antiangiogenic drugs directed against HIF-2α are currently under investigation. Further, clinical and preclinical studies of combination approaches for metastatic RCC including belzutifan with cyclin-dependent kinase 4–6 inhibitors, tyrosine kinase inhibitors, or immune checkpoint inhibitors achieved promising results or are ongoing. This review aims to summarize the existing evidence regarding the VHL/HIF pathway, and the approved and emerging treatment strategies that target this pivotal molecular axis and their mechanisms of resistance. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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22 pages, 1322 KiB  
Review
Genetic Etiology in Pelvic Organ Prolapse: Role of Connective Tissue Homeostasis, Hormone Metabolism, and Oxidative Stress
by Wenxuan Jiang, Rachel Yau Kar Cheung, Cheuk Yan Chung, Symphorosa Shing Chee Chan and Kwong Wai Choy
Genes 2025, 16(1), 5; https://doi.org/10.3390/genes16010005 - 24 Dec 2024
Abstract
Background: Pelvic organ prolapse (POP) has become a common health problem among the aging population and affects an increasing number of elderly women worldwide. Studies within family and twin pairs provided strong evidence for the contribution of genetic factors to POP. Given [...] Read more.
Background: Pelvic organ prolapse (POP) has become a common health problem among the aging population and affects an increasing number of elderly women worldwide. Studies within family and twin pairs provided strong evidence for the contribution of genetic factors to POP. Given the incomplete penetrance, polygenic traits, and small effect sizes of each variant in complex diseases, it is not always easy to evaluate the genetic susceptibility and molecular mechanisms involved in POP. Objectives: This review intends to comprehensively summarize the current studies on genetic variants associated with POP. Methods: We performed a comprehensive review to summarize the genetic findings from genome-linkage studies, genome-wide association studies, candidate association studies, and gene expression analyses. Results: We summarized genetic variants associated with connective tissue homeostasis, hormone metabolism, and oxidative stress, which were potentially related to the pathophysiology of POP. We also reviewed the limited polygenic risk score (PRS) studies generated for each individual’s genetic risk stratification and its integration into clinical risk factors for disease prediction. Conclusions: This pooled analysis provides moderate epidemiological credibility for associations of these genetic variants with POP to bridge the gap between genetic research and clinical medicine towards understanding the genetic etiology of POP. It also highlights the potential of PRS as a risk prediction model. Full article
(This article belongs to the Special Issue Genetic Advances and Challenges in Complex Diseases)
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16 pages, 469 KiB  
Article
Maximal Fat Oxidation During Exercise in Healthy Individuals: Lack of Genetic Association with the FTO rs9939609 Polymorphism
by Teresa García-Pastor, Iván Muñoz-Puente, Miriam Pérez-Pelayo, Isabel Púa, Justin D. Roberts and Juan Del Coso
Genes 2025, 16(1), 4; https://doi.org/10.3390/genes16010004 - 24 Dec 2024
Abstract
Background/Objectives: Previous studies suggest that there is a genetically determined component of fat oxidation at rest and during exercise. To date, the FTO gene has been proposed as a candidate gene to affect fat oxidation during exercise because of the association of [...] Read more.
Background/Objectives: Previous studies suggest that there is a genetically determined component of fat oxidation at rest and during exercise. To date, the FTO gene has been proposed as a candidate gene to affect fat oxidation during exercise because of the association of the “at-risk” A allele with different obesity-related factors such as increased body fat, higher appetite and elevated insulin and triglyceride levels. The A allele of the FTO gene may also be linked to obesity through a reduced capacity for fat oxidation during exercise, a topic that remains largely underexplored in the current literature. The aim of this study was to analyze the association between the FTO rs9939609 polymorphism with the rate of fat oxidation during exercise and metabolic syndrome criteria in healthy participants. Methods: A total of 80 healthy participants (41 men and 39 women) underwent comprehensive assessments, including measurements of anthropometric variables, blood pressure and blood measures of fasting glucose, triglycerides, low- and high-density lipoprotein cholesterol (LDL-c and HDL-c), insulin, interleukin-6 (IL-6) and C-reactive protein (CRP) concentrations. Additionally, the Homeostatic Model Assessment (HOMA-IR) was used to evaluate insulin resistance. Peak oxygen uptake (VO2peak) and maximal fat oxidation rate (MFO) were also measured during an incremental cycling test. FTO rs9939609 genotyping (TT, AT, AA) was performed using genomic DNA samples obtained from a buccal swab and measured with PCR. Results: There were 32 participants (40.0%) with the TT genotype; 31 (38.8%) with the AT genotype; and 17 (21.2%) with the AA genotype. Age, body characteristics, VO2peak, blood pressure and blood variables were similar across all three genotypes. However, serum insulin concentration and HOMA-IR were associated with the FTO rs9939609 genotype with higher values in AA with respect to AT and TT participants (p < 0.050). Still, MFO was similar in TT, AT and AA participants (0.35 ± 0.13, 0.37 ± 0.11, 0.33 ± 0.11 g/min, p = 0.702). In the dominant model, there was no statistical difference between TT and A allele carriers. However, the recessive model revealed that AA participants had higher values of body mass, body mass index, blood insulin concentration and HOMA-IR than T allele carriers (p < 0.050), with no differences in MFO. Conclusions: In our sample of healthy individuals, the FTO rs9939609 polymorphism was associated with several phenotypes associated with obesity and insulin resistance, particularly under the AA vs. T allele/recessive model. However, the FTO rs9939609 polymorphism was not associated with MFO during exercise as fat oxidation was similar across genotypes. This suggests that reduced fat oxidation during exercise is unlikely to be a cause of the obesogenic influence of the FTO AA genotype. Clinically, these findings suggest that the obesogenic effects of the FTO AA genotype are unlikely driven by impaired fat oxidation during exercise. Instead, attention should focus on mechanisms like appetite regulation and energy intake. Moreover, exercise interventions may still effectively mitigate obesity risk, as AA individuals retain normal fat oxidation capacity during exercise. Full article
(This article belongs to the Special Issue Molecular Genetics in Obesity and Metabolic Syndrome)
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11 pages, 610 KiB  
Article
Construction of Promoter Elements for Strong, Moderate, and Weak Gene Expression in Drosophila melanogaster
by Ksenia S. Kudryashova, Irina O. Deriglazova, Igor S. Osadchiy, Pavel Georgiev and Oksana Maksimenko
Genes 2025, 16(1), 3; https://doi.org/10.3390/genes16010003 - 24 Dec 2024
Abstract
Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms [...] Read more.
Background/Objectives: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, as many regulatory proteins need to be expressed in small quantities, and excessive expression can have harmful effects on cells and organisms. Therefore, it is important to select the right promoter when creating transgenic organisms for research and practical applications. Methods: In this study, we used the Drosophila melanogaster genome as a source of natural promoter sequences for RNA polymerase II. These sequences were extracted and used to create a set of promoters that are suitable for practical application. The promoters were tested in a model system using fluorescent reporter genes in S2 cells and transgenic lines of Drosophila. Results: We assessed the expression levels of fluorescent reporter genes to rank the tested promoters from strongest to weakest. Six individual promoters of different sizes were established and compared. Additionally, we designed and tested three pairs of bidirectional promoters that could be used to simultaneously express two proteins. Conclusions: Based on our findings, we grouped the tested promoters into three categories: strong, moderate, and weak. These promoters can be utilized in transgenic model systems for protein production at different levels, from high to low. Bidirectional promoters, constructed “head-to-head”, meaning oppositely directed with the minimum distance between them, represent a novel tool for the co-expression of proteins. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
15 pages, 6261 KiB  
Article
Metabolomics and WGCNA Analyses Reveal the Underlying Mechanisms of Resistance to Botrytis cinerea in Hazelnut
by Jun Sun, Liyuan Lu, Juanjuan Liu, Yanhong Cui, Hanqi Liu, Yue Zhang, Zeyang Zheng and Weicong Yang
Genes 2025, 16(1), 2; https://doi.org/10.3390/genes16010002 - 24 Dec 2024
Abstract
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To [...] Read more.
Background: Hazelnut (Corylus), a significant woody oil tree species in economic forests, faces production constraints due to biotic stresses, with Hazelnut Husk Brown Rot, caused by the pathogenic necrotrophic fungus Botrytis cinerea (B. cinerea), being the most severe. To date, limited information is available regarding the resistance of hazelnuts to B. cinerea. To better understand the mechanisms of resistance to B. cinerea. in hazelnut, we conducted metabolomics and WGCNA analyses of a B. cinerea-resistant Ping’ou hybrid hazelnut variety (Dawei; DW) and a susceptible variety (Qiuxiang; QX). Methods: In this study, metabolomics and weighted gene co-expression network analysis (WGCNA, weighted correlation network analysis) were applied to elucidate the resistance mechanisms underlying different hazelnut varieties to B. cinerea. Our study focused on the metabolome profiles of DW and QX plants after 72 h of B. cinerea infection. Results: Venn analysis of QX_0 vs. DW_0 and QX_72 vs. DW_72 revealed 120 differential accumulation metabolites (DAMs) that were upregulated. Among these metabolites, the concentrations of flavonoids and phenolic acids in DW were significantly higher than those in QX, respectively, suggesting that the elevated levels of these compounds contribute substantially to the resistance of hazelnut against B. cinerea. 3,4-hydroxyphenyllactic acid and phloretin were significantly more abundant in accumulation in DW than in QX after infection by B. cinerea. Conclusions: This study provides that the elevated levels of these compounds (flavonoids and phenolic acids) contribute substantially to the resistance of hazelnut against B. cinerea. Furthermore, 3,4-hydroxyphenyllactic acid and phloretin were identified as pivotal metabolites in modulating the resistance of hazelnut to B. cinerea. Through WGCNA analyses, we identified four transcription factors (WRKY19, HSFC1, ERF071, and RAP2-1) that are most likely to regulate the synthesis of 3,4-dihydroxyphenyllactic acid and phloretin. This study provides crucial insights for further investigation into the regulatory network of metabolites associated with hazelnut resistance to B. cinerea. Full article
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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5 pages, 141 KiB  
Editorial
Genetic and Epigenetic Insights into Pregnancy-Related Complications
by Nihar R. Nayak, Akhilesh Srivastava, Manoj Kumar Jena, Anthony Odibo and Gary Sutkin
Genes 2025, 16(1), 1; https://doi.org/10.3390/genes16010001 - 24 Dec 2024
Abstract
Placental dysfunction is a leading cause of numerous pregnancy complications, including preeclampsia, preterm birth, fetal growth restrictions, placental abruption, and late spontaneous abortion [...] Full article
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