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Keywords = sex-specific genetic polymorphisms

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17 pages, 1042 KiB  
Article
Association of VAX1, MAFB, WNT3 with Non-Syndromic Cleft Lip with or without Cleft Palate in a Japanese Population
by Tran Phuong Thao, Teruyuki Niimi, Satoshi Suzuki, Toko Hayakawa, Chisato Sakuma, Ken Kitagawa, Hideto Imura, Hisataka Kondo, Nguyen Huu Tu, Tong Minh Son, Vo Truong Nhu Ngoc, Le Kha Anh, Pham Nguyen Gia Loc, Hiroo Furukawa, Nagana Natsume and Nagato Natsume
Genes 2025, 16(8), 862; https://doi.org/10.3390/genes16080862 - 24 Jul 2025
Viewed by 270
Abstract
Background/Objectives: Non-syndromic cleft lip with or without palate (NSCL/P) is a common, multifactorial congenital anomaly. As genetic associations can be population-specific, this study aimed to investigate single-nucleotide polymorphisms (SNPs) in the VAX1, MAFB, and WNT3 genes for association with NSCL/P in [...] Read more.
Background/Objectives: Non-syndromic cleft lip with or without palate (NSCL/P) is a common, multifactorial congenital anomaly. As genetic associations can be population-specific, this study aimed to investigate single-nucleotide polymorphisms (SNPs) in the VAX1, MAFB, and WNT3 genes for association with NSCL/P in a Japanese cohort. Methods: A case–control study was conducted with 310 Japanese patients with NSCL/P and 308 ethnically matched healthy controls from Aichi Gakuin Dental Hospital. We genotyped SNPs rs7078160 (VAX1), rs13041247 (MAFB), and rs3809857 (WNT3) using TaqMan assays. Associations were assessed using chi-squared tests, with results stratified by sex and corrected for multiple comparisons using the Bonferroni method. Results: The VAX1 rs7078160 A allele was significantly associated with an increased risk for NSCL/P (OR = 1.67, p < 0.00001). The association was particularly strong in females (OR = 1.93, p < 0.00001) but not significant in males after correction. The MAFB rs13041247 variant showed a nominal protective association with the NSCLO subtype that was not significant after Bonferroni correction. No significant association was found for WNT3. A notable gene–gene interaction was observed, where carrying risk alleles for both VAX1 and MAFB significantly increased overall NSCL/P risk (OR = 2.65, p = 0.00008). Conclusions: VAX1 rs7078160 is a significant risk factor for NSCL/P in the Japanese population, with a pronounced female-specific effect. A synergistic interaction between VAX1 and MAFB elevates disease risk, whereas WNT3 was not implicated in this cohort. These findings underscore the population-specific genetic architecture of NSCL/P. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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10 pages, 225 KiB  
Article
Gene-Sex Interaction in Non-Syndromic Orofacial Cleft Subtypes: A Case-Control Study Among the Vietnamese Population
by Le Kha Anh, Teruyuki Niimi, Satoshi Suzuki, Toko Hayakawa, Ken Kitagawa, Chisato Sakuma, Hideto Imura, Hisataka Kondo, Nguyen Huu Tu, Tong Minh Son, Vo Truong Nhu Ngoc, Tran Phuong Thao, Nguyen Minh Duc, Pham Nguyen Gia Loc, Hiroo Furukawa, Nagana Natsume and Nagato Natsume
Genes 2025, 16(8), 853; https://doi.org/10.3390/genes16080853 - 22 Jul 2025
Viewed by 244
Abstract
Background: Non-syndromic orofacial clefts (NSOFCs) are one of the common congenital malformations in Vietnam, with 1.4 per 1000 live births, with notable sex differences in occurrence. This case–control study aims to investigate potential sex-specific interactions of WNT3 and NOG polymorphisms across NSOFC subtypes [...] Read more.
Background: Non-syndromic orofacial clefts (NSOFCs) are one of the common congenital malformations in Vietnam, with 1.4 per 1000 live births, with notable sex differences in occurrence. This case–control study aims to investigate potential sex-specific interactions of WNT3 and NOG polymorphisms across NSOFC subtypes in a Vietnamese population. Methods: A total of 720 participants were separated into 4 groups with a male/female ratio of 1:1 (160 individuals with cleft lip and palate (NSCLP), 160 with cleft lip only (NSCLO), 160 with cleft palate only (NSCPO), 240 healthy controls). Two single-nucleotide polymorphisms (SNPs), rs3809857 and rs227731, were genotyped by using the StepOnePlus Real-Time PCR System. Results: The most significant findings were found in the male NSCLO group under a recessive model of WNT3 rs3809857 after applying Bonferroni correction, as a five-fold protective factor with OR = 0.18 (95% confidence interval: 0.05–0.64, p = 0.0033). Additionally, the weak or moderate protective association between rs3809857 and male NSCLP was found with p < 0.05 under the dominant model. However, there were no significant findings in the female NSOFC subtypes associated with WNT3. Conversely, NOG rs227731 results showed a weak increased risk in female NSCLO and NSCPO with p < 0.05. Conclusion: this study identified the critical role of WNT3 rs3809857 in reducing NSCLO risk in males. These findings support the potential influence of sex as a modifying factor in the genetic susceptibility to non-syndromic orofacial clefts. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
9 pages, 204 KiB  
Article
Several Proinflammatory Genes’ Variability and Phenotypes of Atopic Dermatitis in Czech Adult AD Patients
by Vladimír Vašků and Anna Vašků
Genes 2025, 16(6), 703; https://doi.org/10.3390/genes16060703 - 12 Jun 2025
Viewed by 560
Abstract
Background: The etiopathogenesis of atopic dermatitis is complicated, and it includes aspects such as dysfunction of the skin barrier, changes in immune responses, IgE-mediated hypersensitivity, and many characteristics of the environment. Regarding skin barrier dysfunction, a number of genetic changes have been described. [...] Read more.
Background: The etiopathogenesis of atopic dermatitis is complicated, and it includes aspects such as dysfunction of the skin barrier, changes in immune responses, IgE-mediated hypersensitivity, and many characteristics of the environment. Regarding skin barrier dysfunction, a number of genetic changes have been described. This genetic predisposition could be related to the phenotypes of atopic dermatitis. Aim: In this study, several polymorphisms in five proinflammatory genes were associated with certain phenotypes of AD patients (genotype–phenotype study). Methods: In total, 89 unrelated AD Czech (Caucasian) patients were genotyped regarding five proinflammatory gene polymorphisms (angiotensinogen AGT M235T, AGT-6 G/A, TNF-α-238 G/A, TNF-β Fok1, IL-6-174 C/G and IL-6-596 G/A). Genotyping was performed using PCR and restriction analysis. For phenotypes, patients’ sex, age and personal and family history of atopy, aero- and food allergies and other complex diseases were evaluated. Results: A significant association with transepidermal water loss (TEWL) measured on the forearm was found with the AGT M235T polymorphism (p = 0.02). For the AG genotype of TNF-α-238 G/A, a six-times higher risk for a family history of diabetes mellitus compared to other examined aspects of family history was found (p = 0.02). A family history of thyreopathy was associated with the IL-6-174 G/C polymorphism when compared to a family history of other complex diseases. The GG genotype had a ten-times higher risk for a family history of thyreopathy compared to the other genotypes (p = 0.004). This result was highly specific (0.914). The GG genotype of IL-6-596 G/A was associated with a family history of thyreopathy, with the same result (p = 0.004). Moreover, the G allele of IL-6-174 G/C was associated with a family history of thyreopathy compared to AD patients without a positive family history of complex diseases (p = 0.03). In AD men, the MM genotype of the AGT M235T gene was found to be associated with food allergies (p = 0.004). This result was highly sensitive (0.833). A family history of cardiovascular disease in AD men was associated with AGT-6 G/A variability. The A allele was found to be six times more frequent in patients with a positive family history of cardiovascular disease (p = 0.02, with high sensitivity and specificity (0.700 and 0.735, respectively)). A family history of diabetes mellitus was associated with the TNF-β Fok1 polymorphism, where the B1 allele was almost six times more frequent in AD men with a positive family history of diabetes mellitus (p = 0.02), with high sensitivity (0.85). A significant association between TEWL measured on the forearm and the AGT M235T polymorphism was found when AD women were carriers of the MM genotype, with a median of 25 and range 4–61; those patients with the MT genotype had a median of 10 and range of 0.3–39; and patients with the TT genotype had a median of 5 and range of 3–40, p = 0.003. The polymorphism AGT-6 G/A was associated with different ages of eczema onset. The AG genotype was almost nine times more risky for the youngest group (0–7 years) compared to the oldest group (more than 18 years) (p = 0.02), with high specificity for this result. Conclusions: Our results in the field of cytokine signaling in the immune system in patients with atopic dermatitis are in agreement with those of GWASs. We suggest that cost-effective and simple PCR tests may be the best approach for the rapid and optimal collection of valid genetic information in clinical practice. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
17 pages, 1965 KiB  
Article
Genetic Variants in the NOD-like Receptor Signaling Pathway Are Associated with HIV-1/AIDS in a Northern Chinese Population
by Tingyu Pan, Yi Yang, Xia Zhang, Chenghong You, Jiawei Wu, Lidan Xu, Wei Ji, Xueyuan Jia, Jie Wu, Wenjing Sun, Songbin Fu, Xuelong Zhang and Yuandong Qiao
Int. J. Mol. Sci. 2025, 26(8), 3484; https://doi.org/10.3390/ijms26083484 - 8 Apr 2025
Viewed by 541
Abstract
The NOD-like receptor (NLR) signaling pathway may influence human immunodeficiency virus (HIV) clearance and CD4+ T cell recovery through inflammatory responses, but its specific mechanism requires further investigation. A deeper understanding of genetic variations can provide new insights into the biological mechanisms [...] Read more.
The NOD-like receptor (NLR) signaling pathway may influence human immunodeficiency virus (HIV) clearance and CD4+ T cell recovery through inflammatory responses, but its specific mechanism requires further investigation. A deeper understanding of genetic variations can provide new insights into the biological mechanisms underlying the occurrence and development of immunodeficiency syndrome (AIDS). By utilizing multiple bioinformatic analyses and functional annotations, we identified single-nucleotide polymorphisms (SNPs) in the NLR signaling pathway that may affect HIV-1 infection and AIDS progression. Then, a case–control study was performed to screen risk-related variants by genotyping candidate SNPs in a sample of 500 men who have sex with men (MSM) with HIV-1 and 500 healthy controls from the Han population in Northern China. The results revealed significant association between five SNPs (NLRP3 rs4612666, MAVS rs17857295, MAVS rs6084497, MAVS rs16989000, and JAK1 rs4244165) and HIV-1 infection. Interestingly, the gene–gene interaction model composed of five SNPs exhibited a cumulative effect on the disease. Specially, the increase in risk alleles carried by the samples elevated the risk of contracting HIV-1. In addition, three SNPs (IL1B rs1143623, STAT1 rs1467199 and STAT1 rs2066804) were associated with CD4+ T cell counts in patients with AIDS. Three SNPs (OAS1 rs1131454, NLRP3 rs10754558, and MAVS rs867335) were found to be related to the clinical staging of AIDS. This finding provides insights into the genetic variants in NLR signaling pathway genes in HIV-1 infection and AIDS progression among MSM in Northern China. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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17 pages, 3690 KiB  
Article
An In-Depth Characterization of SARS-CoV-2 Omicron Lineages and Clinical Presentation in Adult Population Distinguished by Immune Status
by Greta Marchegiani, Luca Carioti, Luigi Coppola, Marco Iannetta, Leonardo Alborghetti, Vincenzo Malagnino, Livia Benedetti, Maria Mercedes Santoro, Massimo Andreoni, Loredana Sarmati, Claudia Alteri, Francesca Ceccherini-Silberstein and Maria Concetta Bellocchi
Viruses 2025, 17(4), 540; https://doi.org/10.3390/v17040540 - 8 Apr 2025
Viewed by 620
Abstract
This retrospective study analyzed SARS-CoV-2 Omicron variability since its emergence, focusing on immunocompromised (IPs) and non-immunocompromised adult people (NIPs). Phylogenetic analysis identified at least five major Omicron lineage groups circulating in Central Italy, from December 2021 to December 2023: (a) BA.1 (34.0%), (b) [...] Read more.
This retrospective study analyzed SARS-CoV-2 Omicron variability since its emergence, focusing on immunocompromised (IPs) and non-immunocompromised adult people (NIPs). Phylogenetic analysis identified at least five major Omicron lineage groups circulating in Central Italy, from December 2021 to December 2023: (a) BA.1 (34.0%), (b) BA.2 + BA.4 (25.8%), (c) BA.5 + BF (10.8%), (d) BQ + BE + EF (9.2%), and (e) Recombinants (20.2%). The BA.2 + BA.4 lineages were more common in IPs compared to NIPs (30.9% vs. 17.8%, respectively; p = 0.011); conversely, Recombinants were less prevalent in IPs than in NIPs (16.0% vs. 27.1%, respectively; p = 0.018). High-abundant single nucleotide polymorphisms (SNPs; prevalence ≥ 40%) and non-synonymous SNPs (prevalence ≥ 20%) increased during the emergence of new variants, rising from BA.1 to Recombinants (54 to 92, and 43 to 70, respectively, both p < 0.001). Evaluating the genetic variability, 109 SNPs were identified as being involved in significant positive or negative associations in pairs (phi > 0.70, p < 0.001), with 19 SNPs associated in 3 distinct clusters (bootstrap > 0.96). Multivariate regression analysis showed that hospitalization was positively associated with one specific cluster, including S686R and A694S in Spike and L221F in Nucleocapsid (AOR: 2.74 [95% CI: 1.13–6.64, p = 0.025]), and with increased age (AOR:1.03 [95% CI: 1.00–1.06], p = 0.028). Conversely, negative associations with hospitalization were observed for female gender and previous vaccination status (AORs: 0.34 [95% CI: 0.14–0.83], p = 0.017 and 0.19 (95% CI: 0.06–0.63, p = 0.006, respectively). Interestingly, the S686R SNP located in a furin cleavage site suggests its potential pathogenetic role. The results show how Omicron genetic diversification significantly influences disease severity and hospitalization, together with age, sex, and vaccination status as key factors. Full article
(This article belongs to the Special Issue Coronaviruses Pathogenesis, Immunity, and Antivirals (2nd Edition))
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16 pages, 614 KiB  
Article
The Uneven Effect of Rare Diseases on Functional Status and Work Capacity
by Corina Oancea, Despina Mihaela Gherman, Florina Georgeta Popescu, Sorina Maria Aurelian and Corina Homentcovschi
Healthcare 2025, 13(6), 594; https://doi.org/10.3390/healthcare13060594 - 8 Mar 2025
Viewed by 1098
Abstract
Background: Rare diseases are defined as clinical conditions that affect only a small number of persons in a population, considered fewer than 1 per 2000 in the European Union or fewer than 1 per 1600 in the United States They are serious, often [...] Read more.
Background: Rare diseases are defined as clinical conditions that affect only a small number of persons in a population, considered fewer than 1 per 2000 in the European Union or fewer than 1 per 1600 in the United States They are serious, often chronic and progressive conditions, characterized by a pronounced clinical polymorphism that crosses all medical specialties. Multiple areas of life beyond just physical health are affected with significant impact on patients, families, and healthcare systems. Objective: To analyze the socio-demographic, medical, and vocational characteristics that correlate with functional status and work disability as a measure of quality of life in rare diseases. Methods: An observational retrospective study of adults with rare diseases evaluated for eligibility for social insurance rights in the National Institute of Medical Assessment and Work Capacity Rehabilitation Bucharest (INEMRCM, the Romanian abbreviation) over a 5-year period was made. Descriptive analysis was used to present sample characteristics. Means and standard deviations (SD) were calculated to describe numerical variables, frequencies were used to describe categorical variables, and logistic regression analysis was conducted to evaluate potential predictors of work capacity. All statistical analyses were performed by PSPP.3 software. p < 0.05 was the cut-off for statistical significance with a 95% confidence interval. Results: 90 consecutive persons were included in the survey. The mean age of the group was 44.5 years ± SD 10.61 years, with a female/male ratio of 48/42 persons. The mean disease duration was 10.61 years ± SD 9.76 years. Men had more severe disease (73.81%); p = 0.018 and significantly younger retirement age, M/F = 39.10 ± 12.26/43.06 ± 9.32; p = 0.037. Less disabling diseases were predominant autoimmune conditions (85.71% of cases); genetic conditions had a more severe functional impact in 63.75% of cases; p = 0.037. People with multisystem diseases but with specific or targeted treatment can work more frequently (76.19%); those with visual impairment have more severe impairments (73.77%); p < 0.001. All individuals who received specific therapy had a better functional status, unlike only 37.21% of those who received symptomatic treatment or treatment for complications; p = 0.023. Logistic regression analysis indicated that the type of impairment and the availability of specific treatments could serve as predictors of a reduced likelihood of employment in rare disease cases. Education level and occupation were not correlated with functional impairment and work disability (NS). Conclusions: Several factors, including some that are modifiable, were associated with better outcomes, such as reduced disability and an increased potential for work participation. Sex, disease etiology, type of impairment, and treatment were all significantly linked to functional capacity. Among these, the type of impairment and the availability of specific treatments might be predictors of employment. Addressing these parameters requires a multidisciplinary team, involving specialized care and comprehensive support services to improve the overall quality of life of individuals affected by rare diseases. Full article
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8 pages, 781 KiB  
Article
Assessment of IL28 (rs12980275) and (rs8099917) Frequency in Recurrent Ocular Herpes Simplex Virus (HSV) Infection
by Borivoje Savic, Bozidar Savic, Tanja Kalezic, Bojana Dacic-Krnjaja, Veljko Milosevic, Sanja Petrovic Pajic, Vesna Maric, Tiana Petrovic and Svetlana Stanojlovic
Life 2025, 15(3), 389; https://doi.org/10.3390/life15030389 - 1 Mar 2025
Viewed by 798
Abstract
(1) Introduction: The main way of spreading the herpes simplex virus 1 (HSV-1) is through direct contact, as the virus enters the host via mucous membranes. Ocular infection can occur as a primary infection or as a recurrent one. The movement of HSV-1 [...] Read more.
(1) Introduction: The main way of spreading the herpes simplex virus 1 (HSV-1) is through direct contact, as the virus enters the host via mucous membranes. Ocular infection can occur as a primary infection or as a recurrent one. The movement of HSV-1 along the ophthalmic branch of the fifth cranial nerve from its latency phase in the trigeminal ganglion and its activation represent a process influenced by various symbiotic factors, such as environmental conditions and the host’s genetic characteristics. The aim of this study was to assess the frequency of IL28 (rs12980275) and (rs8099917) in recurrent ocular HSV infections. (2) Materials and methods: The study included 60 patients aged over 18, of both sexes, all of whom had a history of herpes simplex labialis (HSL). Patients were tested for HSV-1-specific IgG antibodies, and seropositive individuals were genotyped for single nucleotide polymorphisms (SNPs) rs12980275 and rs8099917. A total of 57 seropositive patients were included in the study. (3) Results: A statistically significant association was found between recurrent HSV keratitis (HSK) and heterozygous GT rs8099917 and homozygous TT rs8099917, as well as heterozygous AG rs12980275 and homozygous AA rs12980275 (p < 0.01). Interestingly, patients with homozygous GG polymorphism for both genotypes GG rs8099917 and GG rs12980275 did not develop recurrent HSV keratitis. (4) Conclusion: The most frequent SNP variations in patients with recurrent HSV disease were heterozygous AG rs12980275 (61.40%) and heterozygous GT rs8099917 (52.63%). Patients with recurrent HSV keratitis lacked the homozygous GG polymorphism in both GG rs8099917 and GG rs12980275 genotypes, suggesting that HSV-seropositive individuals expressing these genotypes may have lower predisposition to develop recurrent stromal HSV keratitis. Full article
(This article belongs to the Special Issue Cornea and Anterior Eye Diseases: 2nd Edition)
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38 pages, 1100 KiB  
Review
Emerging Biomarkers and Determinants of Lipoprotein Profiles to Predict CVD Risk: Implications for Precision Nutrition
by Catherine J. Andersen and Maria Luz Fernandez
Nutrients 2025, 17(1), 42; https://doi.org/10.3390/nu17010042 - 27 Dec 2024
Cited by 2 | Viewed by 3221
Abstract
Biomarkers constitute a valuable tool to diagnose both the incidence and the prevalence of chronic diseases and may help to inform the design and effectiveness of precision nutrition interventions. Cardiovascular disease (CVD) continues to be the foremost cause of death all over the [...] Read more.
Biomarkers constitute a valuable tool to diagnose both the incidence and the prevalence of chronic diseases and may help to inform the design and effectiveness of precision nutrition interventions. Cardiovascular disease (CVD) continues to be the foremost cause of death all over the world. While the reasons that lead to increased risk for CVD are multifactorial, dyslipidemias, plasma concentrations of specific lipoproteins, and dynamic measures of lipoprotein function are strong biomarkers to predict and document coronary heart disease incidence. The aim of this review is to provide a comprehensive evaluation of the biomarkers and emerging approaches that can be utilized to characterize lipoprotein profiles as predictive tools for assessing CVD risk, including the assessment of traditional clinical lipid panels, measures of lipoprotein efflux capacity and inflammatory and antioxidant activity, and omics-based characterization of lipoprotein composition and regulators of lipoprotein metabolism. In addition, we discuss demographic, genetic, metagenomic, and lifestyle determinants of lipoprotein profiles—such as age, sex, gene variants and single-nucleotide polymorphisms, gut microbiome profiles, dietary patterns, physical inactivity, obesity status, smoking and alcohol intake, and stress—which are likely to be essential factors to explain interindividual responses to precision nutrition recommendations to mitigate CVD risk. Full article
(This article belongs to the Special Issue Precision Nutrition and Human Health)
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12 pages, 1116 KiB  
Article
Metallothionein-1A (MT1A) Gene Variability May Play a Role in Female Frailty: A Preliminary Study
by Paolina Crocco, Francesco De Rango, Rossella La Grotta, Giuseppe Passarino, Giuseppina Rose and Serena Dato
Genes 2025, 16(1), 15; https://doi.org/10.3390/genes16010015 - 26 Dec 2024
Viewed by 992
Abstract
Background/Objectives: Frailty is a complex geriatric syndrome resulting in decreased physiological reserve. While genetics plays a role, the underlying mechanisms remain unsolved. Metallothioneins (MTs), metal-binding proteins with high affinity for zinc, an essential mineral for many physiological functions, are involved in processes including [...] Read more.
Background/Objectives: Frailty is a complex geriatric syndrome resulting in decreased physiological reserve. While genetics plays a role, the underlying mechanisms remain unsolved. Metallothioneins (MTs), metal-binding proteins with high affinity for zinc, an essential mineral for many physiological functions, are involved in processes including oxidative stress and inflammation. We investigated the impact of genetic variations in MTs on frailty. Methods: 448 subjects (235 females and 213 males, median age of 76 years) were categorized into three frailty groups (non-frail/pre-frail/frail), by hierarchical cluster analysis based on cognitive status (MMSE), functional capacity (ADL), and physical strength (HGS). Subjects were analyzed for selected SNPs in MT1A, MT1B, MT2A, and MT3 genes by PCR-RFLP. Results: An association was found between the rs8052394-A/G (Lys51Arg) polymorphism in the MT1A gene and frailty in females both in binary (OR = 0.345, p = 0.037) and multinomial logistic regression (OR = 0.343, p = 0.036) corrected for age and sex, with carriers of the minor G-allele less likely to transition from non-frail to pre-frail status. Additionally, a significant association with albumin levels (beta = 0.231; p = 0.027) and a trend of association with CRP levels (beta = −1.563; p = 0.097) were observed for this SNP in non-frail females, both indicative of a low inflammatory status. However, Bonferroni correction for multiple SNPs and physiological parameters tested renders these results statistically non-significant. Conclusions: Although its associations do not survive Bonferroni correction, this exploratory study suggests a sex-specific influence of MT1A variability in frailty, likely affecting zinc availability, aligning with ongoing research on sex differences in frailty risk and progression. Larger studies are needed to validate these findings and clarify the mechanisms behind MTs’ variability in frailty progression. Full article
(This article belongs to the Special Issue Genetic Variation in Age-Related Changes)
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13 pages, 2198 KiB  
Article
Study of Variation of ACOX1 Gene Among Different Horse Breeds Maintained in Iran
by Shayan Boozarjomehri Amnieh, Ali Hassanpour, Sina Moghaddam, Fatemeh Sakhaee and Katarzyna Ropka-Molik
Animals 2024, 14(24), 3566; https://doi.org/10.3390/ani14243566 - 10 Dec 2024
Viewed by 1156
Abstract
The ACOX1 gene is vital for fatty acid metabolism and is linked to environmental stress and physical exertion adaptation. The p.Asp237Ser variant (rs782885985) in ACOX1 is associated with increased enzyme activity and reactive oxygen species (ROS) levels. This study examined the ACOX1 polymorphism [...] Read more.
The ACOX1 gene is vital for fatty acid metabolism and is linked to environmental stress and physical exertion adaptation. The p.Asp237Ser variant (rs782885985) in ACOX1 is associated with increased enzyme activity and reactive oxygen species (ROS) levels. This study examined the ACOX1 polymorphism across six horse breeds in Iran: Arabian, Thoroughbred, KWPN, Caspian, Kurdish, and Turkmen. The goal was to identify differences in ACOX1 genotype distribution, potentially serving as genetic markers under selection pressure related to breed-specific traits. In a sample of 324 horses, genomic DNA was analyzed using PCR-RFLP, revealing three genotypes (TT, TG, GG). The GG genotype was most common in Kurdish and Arabian horses (86% and 70%, respectively), while the TT genotype was prevalent in Turkmen (24%) and Thoroughbred horses (23%). The T allele’s frequency in Thoroughbred and Turkmen horses suggests that ACOX1 may be under selection pressure for phenotypic traits. Differences in genotype distribution were confirmed among breeds, with no sex-based association. The study concludes that ACOX1 is a potential genetic marker for horse performance and adaptability, emphasizing the importance of genetic diversity in breeding programs. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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21 pages, 4143 KiB  
Article
Roadmap and Considerations for Genome Editing in a Non-Model Organism: Genetic Variations and Off-Target Profiling
by Hanin Wattad, Jonathan Molcho, Rivka Manor, Simy Weil, Eliahu D. Aflalo, Vered Chalifa-Caspi and Amir Sagi
Int. J. Mol. Sci. 2024, 25(23), 12530; https://doi.org/10.3390/ijms252312530 - 22 Nov 2024
Cited by 1 | Viewed by 1465
Abstract
The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved. Here, we demonstrated a generalized roadmap for a de novo genome annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed the typical genome editing [...] Read more.
The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved. Here, we demonstrated a generalized roadmap for a de novo genome annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed the typical genome editing challenges arising from genetic variations, such as a high frequency of single nucleotide polymorphisms, differences in sex chromosomes, and repetitive sequences that can lead to off-target events. For the genome editing of M. rosenbergii, our laboratory recently adapted the CRISPR/Cas genome editing approach to embryos and the embryonic primary cell culture. In this continuation study, an annotation pipeline was trained to predict the gene models by leveraging the available genomic, transcriptomic, and proteomic data, and enabling accurate gene prediction and guide design for knock-outs. A next-generation sequencing analysis demonstrated a high frequency of genetic variations in genes on both autosomal and sex chromosomes, which have been shown to affect the accuracy of editing analyses. To enable future applications based on the CRISPR/Cas tool in non-model organisms, we also verified the reliability of editing efficiency and tracked off-target frequencies. Despite the lack of comprehensive information on non-model organisms, this study provides an example of the feasibility of selecting and editing specific genes with a high degree of certainty. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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20 pages, 7174 KiB  
Article
Genome-Wide Association Studies (GWAS) and Transcriptome Analysis Reveal Male Heterogametic Sex-Determining Regions and Candidate Genes in Northern Snakeheads (Channa argus)
by Haiyang Liu, Jin Zhang, Tongxin Cui, Weiwei Xia, Qing Luo, Shuzhan Fei, Xinping Zhu, Kunci Chen, Jian Zhao and Mi Ou
Int. J. Mol. Sci. 2024, 25(20), 10889; https://doi.org/10.3390/ijms252010889 - 10 Oct 2024
Cited by 3 | Viewed by 1846
Abstract
The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to [...] Read more.
The Northern snakehead (Channa argus) is a significant economic aquaculture species in China. Exhibiting sexual dimorphism in the growth rate between females and males, mono-sex breeding holds substantial value for aquaculture. This study employed GWAS and transcriptome analysis were applied to identify sex determination genomic regions and develop sex-specific markers. A total of 270 single-nucleotide polymorphisms (SNPs) and 31 insertion-deletions (InDels) were identified as being sexually dimorphic through GWAS and fixation index (Fst) scanning. Based on GWAS results, two sex-specific InDel markers were developed, effectively distinguishing genetic sex for XX females, XY males, and YY super-males via (polymerase chain reaction) PCR amplification. A major genomic segment of approximately 115 kb on chromosome 3 (Chr 03) was identified as the sex-determination region. A comparative transcriptome analysis of gonads for three sexes identified 158 overlapping differentially expressed genes (DEGs). Additionally, three sex-related candidate genes were identified near the sex determination region, including id2, sox11, and rnf144a. Further studies are required to elucidate the functions of these genes. Overall, two sex-specific InDel markers support a male heterogametic XX/XY sex-determination system in Northern snakeheads and three candidate genes offer new insights into sex determination and the evolution of sex chromosomes in teleost fish. Full article
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17 pages, 1607 KiB  
Article
Influence of Genetic Polymorphisms on the Age at Cancer Diagnosis in a Homogenous Lynch Syndrome Cohort of Individuals Carrying the MLH1:c.1528C>T South African Founder Variant
by Lutricia Ndou, Ramadhani Chambuso, Ursula Algar, Paul Goldberg, Adam Boutall and Raj Ramesar
Biomedicines 2024, 12(10), 2201; https://doi.org/10.3390/biomedicines12102201 - 27 Sep 2024
Cited by 1 | Viewed by 1596
Abstract
Background: High variability in the age at cancer diagnosis in Lynch syndrome (LS) patients is widely observed, even among relatives with the same germline pathogenic variant (PV) in the mismatch repair (MMR) genes. Genetic polymorphisms and lifestyle factors are thought to contribute to [...] Read more.
Background: High variability in the age at cancer diagnosis in Lynch syndrome (LS) patients is widely observed, even among relatives with the same germline pathogenic variant (PV) in the mismatch repair (MMR) genes. Genetic polymorphisms and lifestyle factors are thought to contribute to this variability. We investigated the influence of previously reported genetic polymorphisms on the age at cancer diagnosis in a homogenous LS cohort with a South African founder germline PV c.1528C>T in the MLH1 gene. Methods: A total of 359 LS variant heterozygotes (LSVH) from 60 different families were genotyped for specific genetic polymorphisms in GSTM1, GSTT1, CYP1A1, CYP17, PPP2R2B, KIF20A, TGFB1, XRCC5, TNF, BCL2, CHFR, CDC25C, ATM, TTC28, CDC25C, HFE, and hTERT genes using Multiplex Polymerase Chain Reaction and MassArray methods. Kaplan–Meier survival analysis, univariate and multivariate Cox proportional hazards gamma shared frailty models adjusted for sex were used to estimate the association between age at cancer diagnosis and polymorphism genotypes. A p-value < 0.05 after correcting for multiple testing using the Benjamini–Hochberg method was considered significant at a 95% confidence interval. Results: We identified three genotypes in the cell-cycle regulation, DNA repair, and xenobiotic-metabolism genes significantly associated with age at cancer diagnosis in this cohort. The CYP1A1 rs4646903 risk (GG) and CDC25C rs3734166 polymorphic (GA+AA) genotypes were significantly associated with an increased risk of a younger age at cancer diagnosis (Adj HR: 2.03 [1.01–4.08], p = 0.034 and Adj HR: 1.53 [1.09–2.14], p = 0.015, respectively). LSVH who were heterozygous for the XRCC5 rs1051685 SNP showed significant protection against younger age at cancer diagnosis (Adj HR: 0.69 [CI, 0.48–0.99], p = 0.043). The risk of a younger age at any cancer diagnosis was significantly high in LS carriers of one to two risk genotypes (Adj HR: 1.49 [CI: 1.06–2.09], corrected p = 0.030), while having one to two protective genotypes significantly reduced the risk of developing any cancer and CRC at a younger age (Adj HR: 0.52 [CI: 0.37–0.73], and Adj HR: 0.51 [CI: 0.36–0.74], both corrected p < 0.001). Conclusions: Polymorphism genotypes in the cell-cycle regulation, DNA repair, and xenobiotic metabolizing genes may influence the age at cancer diagnosis in a homogenous LS cohort with a South African founder germline PV c.1528C>T in the MLH1 gene. Full article
(This article belongs to the Section Molecular Genetics and Genetic Diseases)
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17 pages, 1841 KiB  
Review
Vitamin D in Primary Sjogren’s Syndrome (pSS) and the Identification of Novel Single-Nucleotide Polymorphisms Involved in the Development of pSS-Associated Diseases
by Siarhei A. Dabravolski, Alexey V. Churov, Irina A. Starodubtseva, Dmitry F. Beloyartsev, Tatiana I. Kovyanova, Vasily N. Sukhorukov and Nikolay A. Orekhov
Diagnostics 2024, 14(18), 2035; https://doi.org/10.3390/diagnostics14182035 - 13 Sep 2024
Cited by 4 | Viewed by 2670
Abstract
Sjögren’s syndrome (SS) is a chronic autoimmune disorder characterised by lymphocytic infiltration of the exocrine glands, which leads to dryness of the eyes and mouth; systemic manifestations such as arthritis, vasculitis, and interstitial lung disease; and increased risks of lymphoma and cardiovascular diseases. [...] Read more.
Sjögren’s syndrome (SS) is a chronic autoimmune disorder characterised by lymphocytic infiltration of the exocrine glands, which leads to dryness of the eyes and mouth; systemic manifestations such as arthritis, vasculitis, and interstitial lung disease; and increased risks of lymphoma and cardiovascular diseases. SS predominantly affects women, with a strong genetic component linked to sex chromosomes. Genome-wide association studies (GWASs) have identified numerous single-nucleotide polymorphisms (SNPs) associated with primary SS (pSS), revealing insights into its pathogenesis. The adaptive and innate immune systems are crucial to SS’s development, with viral infections implicated as environmental triggers that exacerbate autoimmune responses in genetically susceptible individuals. Moreover, recent research has highlighted the role of vitamin D in modulating immune responses in pSS patients, suggesting its potential therapeutic implications. In this review, we focus on the recently identified SNPs in genes like OAS1, NUDT15, LINC00243, TNXB, and THBS1, which have been associated with increased risks of developing more severe symptoms and other diseases such as fatigue, lymphoma, neuromyelitis optica spectrum disorder (NMOSD), dry eye syndrome (DES), and adverse drug reactions. Future studies should focus on larger, multi-ethnic cohorts with standardised protocols to validate findings and identify new associations. Integrating genetic testing into clinical practise holds promise for improving SS management and treatment strategies, enabling personalised interventions based on comprehensive genetic profiles. By focusing on specific SNPs, vitamin D, and their implications, future research can lead to more effective and personalised approaches for managing pSS and its complications. Full article
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13 pages, 2311 KiB  
Article
Genetic Differences between Male and Female Pattern Hair Loss in a Korean Population
by Jihyun Lee, Ja-Eun Choi, Joohun Ha, Youngjoo Kim, Changhyun Lee and Kyung-Won Hong
Life 2024, 14(8), 939; https://doi.org/10.3390/life14080939 - 26 Jul 2024
Cited by 3 | Viewed by 3196
Abstract
Studies on androgenetic alopecia (AGA or patterned hair loss (PHL)) have suggested different underlying pathological mechanisms between males and females. While many genetic factors for male hair loss have been identified through genome-wide association studies (GWASs), the genetic determinants of female hair loss [...] Read more.
Studies on androgenetic alopecia (AGA or patterned hair loss (PHL)) have suggested different underlying pathological mechanisms between males and females. While many genetic factors for male hair loss have been identified through genome-wide association studies (GWASs), the genetic determinants of female hair loss remain unclear. In this study, we analyzed approximately 1000 individuals (436 males and 568 females) to identify sex-specific genetic factors. We conducted three independent GWASs for the total, male-only, and female-only groups, identifying three novel loci (rs7814359, rs2163085, and rs4793158 of the TSNARE1, FZD1, and GJC1 genes, respectively). rs7814359 showed a significant genome-wide association with AGA in the combined sex group and a weak association in both the male-only and female-only groups. The single nucleotide polymorphism (SNP) rs2163085 showed a significant genome-wide association with AGA in the combined group and notable significance in females. The rs4793158 SNP showed a suggestive association with AGA in both the combined and female-only groups. TSNARE1, related to rs7814359, is involved in vesicle transport. FZD1 is a key regulator of the Wnt signaling pathway. GJC1 is a gap junction protein. The associations of FZD1 and GJC1 with female-specific AGA suggest that sex hormones, such as estrogen, may influence FPHL through these genes. These findings will contribute to our understanding of the sex-specific pathophysiology of AGA. Full article
(This article belongs to the Section Genetics and Genomics)
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