International Journal of Molecular Sciences

Research

35 pages, 3954 KiB

Open AccessArticle

Trophic Position of the White Worm (Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis

by Łukasz Gajda, Agata Daszkowska-Golec and Piotr Świątek

Int. J. Mol. Sci. 2024, 25(9), 4685; https://doi.org/10.3390/ijms25094685 - 25 Apr 2024

Cited by 1 | Viewed by 1119

Abstract

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no [...] Read more.

To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal’s digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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25 pages, 9210 KiB

Open AccessArticle

ISGF3 and STAT2/IRF9 Control Basal and IFN-Induced Transcription through Genome-Wide Binding of Phosphorylated and Unphosphorylated Complexes to Common ISRE-Containing ISGs

by Hanna Nowicka, Agata Sekrecka, Katarzyna Blaszczyk, Katarzyna Kluzek, Chan-Yu Chang, Joanna Wesoly, Chien-Kuo Lee and Hans A. R. Bluyssen

Int. J. Mol. Sci. 2023, 24(24), 17635; https://doi.org/10.3390/ijms242417635 - 18 Dec 2023

Cited by 5 | Viewed by 2438

Abstract

In addition to the canonical ISGF3 and non-canonical STAT2/IRF9 complexes, evidence is emerging of the role of their unphosphorylated counterparts in IFN-dependent and -independent ISG transcription. To better understand the relation between ISGF3 and U-ISGF3 and STAT2/IRF9 and U-STAT2/IRF9 in IFN-I-stimulated transcriptional responses, [...] Read more.

In addition to the canonical ISGF3 and non-canonical STAT2/IRF9 complexes, evidence is emerging of the role of their unphosphorylated counterparts in IFN-dependent and -independent ISG transcription. To better understand the relation between ISGF3 and U-ISGF3 and STAT2/IRF9 and U-STAT2/IRF9 in IFN-I-stimulated transcriptional responses, we performed RNA-Seq and ChIP-Seq, in combination with phosphorylation inhibition and antiviral experiments. First, we identified a group of ISRE-containing ISGs that were commonly regulated in IFNα-treated WT and STAT1-KO cells. Thus, in 2fTGH and Huh7.5 WT cells, early and long-term IFNα-inducible transcription and antiviral activity relied on the DNA recruitment of the ISGF3 components STAT1, STAT2 and IRF9 in a phosphorylation- and time-dependent manner. Likewise, in ST2-U3C and Huh-STAT1KO cells lacking STAT1, delayed IFN responses correlated with DNA binding of phosphorylated STAT2/IRF9 but not U-STAT2/IRF9. In addition, comparative experiments in U3C (STAT1-KO) cells overexpressing all the ISGF3 components (ST1-ST2-IRF9-U3C) revealed U-ISGF3 (and possibly U-STAT2/IRF9) chromatin interactions to correlate with phosphorylation-independent ISG transcription and antiviral activity. Together, our data point to the dominant role of the canonical ISGF3 and non-canonical STAT2/IRF9, without a shift to U-ISGF3 or U-STAT2/IRF9, in the regulation of early and prolonged ISG expression and viral protection. At the same time, they suggest the threshold-dependent role of U-ISFG3, and potentially U-STAT2/IRF9, in the regulation of constitutive and possibly long-term IFNα-dependent responses. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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20 pages, 5910 KiB

Open AccessArticle

Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761

by Jakub Skorupski, Florian Brandes, Christian Seebass, Wolfgang Festl, Przemysław Śmietana, Jennifer Balacco, Nivesh Jain, Tatiana Tilley, Linelle Abueg, Jonathan Wood, Ying Sims, Giulio Formenti, Olivier Fedrigo and Erich D. Jarvis

Int. J. Mol. Sci. 2023, 24(19), 14816; https://doi.org/10.3390/ijms241914816 - 1 Oct 2023

Viewed by 2932

Abstract

The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this [...] Read more.

The European mink Mustela lutreola (Mustelidae) ranks among the most endangered mammalian species globally, experiencing a rapid and severe decline in population size, density, and distribution. Given the critical need for effective conservation strategies, understanding its genomic characteristics becomes paramount. To address this challenge, the platinum-quality, chromosome-level reference genome assembly for the European mink was successfully generated under the project of the European Mink Centre consortium. Leveraging PacBio HiFi long reads, we obtained a 2586.3 Mbp genome comprising 25 scaffolds, with an N50 length of 154.1 Mbp. Through Hi-C data, we clustered and ordered the majority of the assembly (>99.9%) into 20 chromosomal pseudomolecules, including heterosomes, ranging from 6.8 to 290.1 Mbp. The newly sequenced genome displays a GC base content of 41.9%. Additionally, we successfully assembled the complete mitochondrial genome, spanning 16.6 kbp in length. The assembly achieved a BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of 98.2%. This high-quality reference genome serves as a valuable genomic resource for future population genomics studies concerning the European mink and related taxa. Furthermore, the newly assembled genome holds significant potential in addressing key conservation challenges faced by M. lutreola. Its applications encompass potential revision of management units, assessment of captive breeding impacts, resolution of phylogeographic questions, and facilitation of monitoring and evaluating the efficiency and effectiveness of dedicated conservation strategies for the European mink. This species serves as an example that highlights the paramount importance of prioritizing endangered species in genome sequencing projects due to the race against time, which necessitates the comprehensive exploration and characterization of their genomic resources before their populations face extinction. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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30 pages, 2452 KiB

Open AccessArticle

Single-Nucleotide Polymorphisms in Genes Maintaining the Stability of Mitochondrial DNA Affect the Occurrence, Onset, Severity and Treatment of Major Depressive Disorder

by Piotr Czarny, Sylwia Ziółkowska, Łukasz Kołodziej, Cezary Watała, Paulina Wigner-Jeziorska, Katarzyna Bliźniewska-Kowalska, Katarzyna Wachowska, Małgorzata Gałecka, Ewelina Synowiec, Piotr Gałecki, Michał Bijak, Janusz Szemraj and Tomasz Śliwiński

Int. J. Mol. Sci. 2023, 24(19), 14752; https://doi.org/10.3390/ijms241914752 - 29 Sep 2023

Cited by 1 | Viewed by 1370

Abstract

One of the key features of major depressive disorder (MDD, depression) is increased oxidative stress manifested by elevated levels of mtROS, a hallmark of mitochondrial dysfunction, which can arise from mitochondrial DNA (mtDNA) damage. Thus, the current study explores possibility that the single-nucleotide [...] Read more.

One of the key features of major depressive disorder (MDD, depression) is increased oxidative stress manifested by elevated levels of mtROS, a hallmark of mitochondrial dysfunction, which can arise from mitochondrial DNA (mtDNA) damage. Thus, the current study explores possibility that the single-nucleotide polymorphisms (SNPs) of genes encoding the three enzymes that are thought to be implicated in the replication, repair or degradation of mtDNA, i.e., POLG, ENDOG and EXOG, have an impact on the occurrence, onset, severity and treatment of MDD. Five SNPs were selected: EXOG c.-188T > G (rs9838614), EXOG c.*627G > A (rs1065800), POLG c.-1370T > A (rs1054875), ENDOG c.-394T > C (rs2977998) and ENDOG c.-220C > T (rs2997922), while genotyping was performed on 538 DNA samples (277 cases and 261 controls) using TaqMan probes. All SNPs of EXOG and ENDOG modulated the risk of depression, but the strongest effect was observed for rs1065800, while rs9838614 and rs2977998 indicate that they might influence the severity of symptoms, and, to a lesser extent, treatment effectiveness. Although the SNP located in POLG did not affect occurrence of the disease, the result suggests that it may influence the onset and treatment outcome. These findings further support the hypothesis that mtDNA damage and impairment in its metabolism play a crucial role not only in the development, but also in the treatment of depression. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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15 pages, 335 KiB

Open AccessArticle

Genetic Factors of Teeth Impaction: Polymorphic and Haplotype Variants of PAX9, MSX1, AXIN2, and IRF6 Genes

by Grzegorz Trybek, Aleksandra Jaroń, Ewa Gabrysz-Trybek, Monika Rutkowska, Aleksandra Markowska, Krzysztof Chmielowiec, Jolanta Chmielowiec and Anna Grzywacz

Int. J. Mol. Sci. 2023, 24(18), 13889; https://doi.org/10.3390/ijms241813889 - 9 Sep 2023

Viewed by 1498

Abstract

In recent research, there has been a growing awareness of the role of genetic factors in the positioning and eruption of teeth in the maxilla and mandible. This study aimed to evaluate the potential of specific polymorphic markers of single nucleotide polymorphisms (SNPs) [...] Read more.

In recent research, there has been a growing awareness of the role of genetic factors in the positioning and eruption of teeth in the maxilla and mandible. This study aimed to evaluate the potential of specific polymorphic markers of single nucleotide polymorphisms (SNPs) located within the PAX9, MSX1, AXIN2, and IRF6 genes to determine the predisposition to tooth impaction. The study participants were divided into two groups: the first group consisted of individuals with at least one impacted secondary tooth. In contrast, the second group (control group) had no impacted teeth in their jaws. To analyze the genes, real-time PCR (polymerase chain reaction) and TaqMan probes were utilized to detect the selected polymorphisms. The findings suggest that disruptions in the structure and function of the mentioned genetic factors such as polymorphic and haplotype variants of PAX9, MSX1, AXIN2, and IRF6 genes, which play a direct role in tooth and periodontal tissue development, might be significant factors in tooth impaction in individuals with genetic variations. Therefore, it is reasonable to hypothesize that tooth impaction may be influenced, at least in part, by the presence of specific genetic markers, including different allelic variants of the PAX9, AXIN2, and IRF6 genes, and especially MSX1. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

10 pages, 407 KiB

Open AccessArticle

Report on the Effect of the Implementation of an Early Detection and Prevention of Cancer Program on Families at High Hereditary Risk—Concentrating on Patients Undergoing Genetic Diagnostics and Counseling in Central Poland

by Tadeusz Kałużewski, Izabela Kubiak, Michał Bednarek, Jordan Sałamunia, Dorota Kucharska, Łukasz Kępczyński, Marek Stempień, Tobiasz Kubicki, Radzisław Trzciński, Zofia Gordon-Sönmez, Anna Bartosińska-Dyc, Agnieszka Gach and Bogdan Kałużewski

Int. J. Mol. Sci. 2023, 24(17), 13178; https://doi.org/10.3390/ijms241713178 - 24 Aug 2023

Viewed by 1561

Abstract

Over a 46-month period, the objectives of the National Cancer Control Program (NCCP, pol. Narodowy Program Zwalczania Chorób Nowotworowych), coordinated by the Ministry of Health, were pursued by conducting genetic diagnostics on individuals at high risk of developing cancer. A total of 1097 [...] Read more.

Over a 46-month period, the objectives of the National Cancer Control Program (NCCP, pol. Narodowy Program Zwalczania Chorób Nowotworowych), coordinated by the Ministry of Health, were pursued by conducting genetic diagnostics on individuals at high risk of developing cancer. A total of 1097 individuals were enrolled in the study, leading to the identification of 128 cases of germline mutations. The implementation of the NCCP led to the identification of genetic mutations in 4.43% of the patients qualified for BRCA1 and BRCA2 screening tests, in 18.18% of those qualified for a comprehensive next-generation sequencing (NGS) panel in cases of breast and ovarian cancer, and in 17.36% of cases of colorectal and endometrial cancer. The research conducted allowed us to establish individualized preventive and therapeutic approaches for mutation carriers. However, the results prove that liberalizing the inclusion criteria for high-throughput diagnostics and the use of broad gene panels could significantly increase the percentage of detected carriers. This publication serves as a summary and discussion of the results obtained from the implementation of the NCCP as well as of the role of genetic consulting in personalized medicine. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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20 pages, 1971 KiB

Open AccessArticle

Effect of Allergen-Specific Immunotherapy on Transcriptomic Changes in Canine Atopic Dermatitis

by Alicja Majewska, Małgorzata Gajewska and Kourou Dembele

Int. J. Mol. Sci. 2023, 24(14), 11616; https://doi.org/10.3390/ijms241411616 - 18 Jul 2023

Cited by 1 | Viewed by 2065

Abstract

Canine atopic dermatitis (cAD) is a genetic, chronic, and recurrent inflammatory and pruritic skin disorder. Allergen-specific immunotherapy (ASIT) is presently recognized as the only clinically effective disease-modifying treatment for allergies. The aim of our study was to analyze the changes in gene expression [...] Read more.

Canine atopic dermatitis (cAD) is a genetic, chronic, and recurrent inflammatory and pruritic skin disorder. Allergen-specific immunotherapy (ASIT) is presently recognized as the only clinically effective disease-modifying treatment for allergies. The aim of our study was to analyze the changes in gene expression observed in the peripheral blood nuclear cells of cAD patients subjected to ASIT. Blood samples designated for transcriptomic analyses were collected from AD dogs twice, before and six months after ASIT, and also from healthy dogs. Statistical analysis revealed 521 differentially expressed transcripts, among which 241 transcripts represented genes with well-described functions. Based on the available literature, we chose nine differentially expressed genes (RARRES2, DPP10, SLPI, PLSCR4, MMP9, NTSR1, CBD103, DEFB122, and IL36G) which may be important in the context of the dysregulated immune response observed in cAD patients. The expressions of five out of the nine described genes (DPP10, PLSCR4, NTSR1, DEFB122, and IL36G) changed after the application of ASIT. The expressions of three of these genes returned to the level observed in the healthy control group. The genes listed above need further investigation to determine details of their role in the molecular mechanism of immune tolerance induction in response to allergen-specific immunotherapy. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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12 pages, 316 KiB

Open AccessArticle

Single-Nucleotide Polymorphisms in Base-Excision Repair-Related Genes Involved in the Risk of an Occurrence of Non-Alcoholic Fatty Liver Disease

by Sylwia Ziółkowska, Marcin Kosmalski, Łukasz Kołodziej, Aleksandra Jabłkowska, Janusz Zbigniew Szemraj, Tadeusz Pietras, Maciej Jabłkowski and Piotr Lech Czarny

Int. J. Mol. Sci. 2023, 24(14), 11307; https://doi.org/10.3390/ijms241411307 - 11 Jul 2023

Cited by 2 | Viewed by 1511

Abstract

Oxidative stress is one of the pillars crucial in the development of a non-alcoholic fatty liver disease (NAFLD) and may cause DNA damage. Since the main pathway responsible for the repair of oxidative DNA damage is the base-excision repair (BER) pathway, we examined [...] Read more.

Oxidative stress is one of the pillars crucial in the development of a non-alcoholic fatty liver disease (NAFLD) and may cause DNA damage. Since the main pathway responsible for the repair of oxidative DNA damage is the base-excision repair (BER) pathway, we examined the relationship between the presence of different genetic variants of BER-associated genes and the risk of NAFLD. The study evaluates seven single nucleotide polymorphisms (SNPs) within five genes, hOGG1, APEX1, NEIL1, LIG3, LIG1, in 150 NAFLD patients and 340 healthy controls. The genotyping was performed using TaqMan probes and the results were presented as odds ratio with its corresponding 95% confidence interval. The following SNPs were assessed in the study: hOGG1 (rs1052133), APEX1 (rs176094 and rs1130409), NEIL1 (rs4462560), LIG3 (rs1052536), LIG3 (rs4796030), and LIG1 (rs20579). Four of the investigated SNPs, i.e., rs176094, rs1130409, rs4462560 and rs4796030, were found to be associated with NAFLD risk. Furthermore, the occurrence of insulin resistance in patients with steatosis depended on various LIG3 genetic variants. The findings imply the impact of genes involved in BER on NAFLD and fatty liver-related insulin sensitivity. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

15 pages, 1963 KiB

Open AccessArticle

Gender Influences Gut Microbiota among Patients with Irritable Bowel Syndrome

by Paulina Pecyna, Marcin Gabryel, Dorota Mankowska-Wierzbicka, Dorota M. Nowak-Malczewska, Katarzyna Jaskiewicz, Marcelina M. Jaworska, Hanna Tomczak, Malgorzata Rydzanicz, Rafal Ploski, Marian Grzymislawski, Agnieszka Dobrowolska and Marzena Gajecka

Int. J. Mol. Sci. 2023, 24(13), 10424; https://doi.org/10.3390/ijms241310424 - 21 Jun 2023

Cited by 5 | Viewed by 2024

Abstract

Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disease that affects approximately 11% of the general population. The gut microbiota, among other known factors, plays a substantial role in its pathogenesis. The study aimed to characterize the gut microbiota differences between patients [...] Read more.

Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disease that affects approximately 11% of the general population. The gut microbiota, among other known factors, plays a substantial role in its pathogenesis. The study aimed to characterize the gut microbiota differences between patients with IBS and unaffected individuals, taking into account the gender aspect of the patients and the types of IBS determined on the basis of the Rome IV Criteria, the IBS-C, IBS-D, IBS-M, and IBS-U. In total, 121 patients with IBS and 70 unaffected individuals participated in the study; the derived stool samples were subjected to 16S rRNA amplicon sequencing. The gut microbiota of patients with IBS was found to be more diverse in comparison to unaffected individuals, and the differences were observed primarily among Clostridiales, Mogibacteriaceae, Synergistaceae, Coriobacteriaceae, Blautia spp., and Shuttleworthia spp., depending on the study subgroup and patient gender. There was higher differentiation of females’ gut microbiota compared to males, regardless of the disease status. No correlation between the composition of the gut microbiota and the type of IBS was found. Patients with IBS were characterized by more diverse gut microbiota compared to unaffected individuals. The gender criterion should be considered in the characterization of the gut microbiota. The type of IBS did not determine the identified differences in gut microbiota. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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11 pages, 763 KiB

Open AccessArticle

Association of the rs3864283 Polymorphism Located in the HINT1 Gene with Cigarette Use and Personality Traits

by Aleksandra Suchanecka, Agnieszka Boroń, Krzysztof Chmielowiec, Aleksandra Strońska-Pluta, Jolanta Masiak, Milena Lachowicz, Jolanta Chmielowiec and Anna Grzywacz

Int. J. Mol. Sci. 2023, 24(12), 10244; https://doi.org/10.3390/ijms241210244 - 16 Jun 2023

Cited by 2 | Viewed by 1222

Abstract

Nicotine is the major reinforcing component of tobacco and it is believed that the pharmacological effects of nicotine motivate the initiation and maintenance of a smoking habit. HINT1 appears to play a role in the modulation of the effects of drug abuse. Hence, [...] Read more.

Nicotine is the major reinforcing component of tobacco and it is believed that the pharmacological effects of nicotine motivate the initiation and maintenance of a smoking habit. HINT1 appears to play a role in the modulation of the effects of drug abuse. Hence, the aim of this study was the analysis of the association between the rs3864283 polymorphism of the HINT1 gene and cigarette use; the analysis of personality traits assessed by the means of the NEO-FFI Inventory; the analysis of anxiety measured by the STAI questionnaire; and the analysis of the interactions between the rs3864283 and both personality traits and anxiety. The study group consisted of 522 volunteers. Of these, 371 were cigarette users and 151 were never-smokers. The genomic DNA was isolated from venous blood using standard procedures. The results of both inventories, i.e., NEO-FFI and STAI., were reported as the sten scores. Genotyping was conducted with the real-time PCR method. Statistically significant differences were found in the frequency of rs3864283 genotypes and alleles in the tested sample of Cigarette Users when compared to the control group. The Cigarette Users compared to the control group obtained higher scores in the assessment of NEO-FFI extraversion scale, and significantly lower results were obtained for the NEO-FFI openness scale, the agreeableness scale, and the conscientiousness scale. There was a statistically significant effect of rs3864283 genotype interaction and Cigarette Use or not using (control group) on the extraversion scale. There was also a statistically significant effect of Cigarette Users or the control group on the extraversion scale score. The results obtained in the presented study indicated a significant association between the HINT1 rs3864283 variant and smoking status. Moreover, this is the first study incorporating genetic association of above-mentioned polymorphic site with interaction analysis of personality traits and anxiety. Overall, the results of this study suggest that HINT1 is an important genetic component associated with nicotine usage mechanisms. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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13 pages, 1015 KiB

Open AccessArticle

Epigenetic Analysis of the Dopamine Transporter Gene DAT1 with a Focus on Personality Traits in Athletes

by Kinga Humińska-Lisowska, Krzysztof Chmielowiec, Aleksandra Strońska-Pluta, Jolanta Chmielowiec, Aleksandra Suchanecka, Jolanta Masiak, Monika Michałowska-Sawczyn, Agnieszka Boroń, Paweł Cięszczyk and Anna Grzywacz

Int. J. Mol. Sci. 2023, 24(10), 8931; https://doi.org/10.3390/ijms24108931 - 18 May 2023

Cited by 2 | Viewed by 1930

Abstract

Human phenotypes (traits) are determined by the selective use of a person’s unique genotype (DNA sequence), following exposure to environmental stimuli, such as exercise. Inducing profound changes in epigenetics may be an underlying factor of the beneficial effects of exercise. This study aimed [...] Read more.

Human phenotypes (traits) are determined by the selective use of a person’s unique genotype (DNA sequence), following exposure to environmental stimuli, such as exercise. Inducing profound changes in epigenetics may be an underlying factor of the beneficial effects of exercise. This study aimed to investigate the association between methylation in the promoter region of the DAT1 gene and personality traits measured by the NEO-FFI questionnaire in a group of athletes. The study group included 163 athletes, and the control group consisted of 232 non-athletes. The obtained results show several significant differences between the studied groups of subjects. The Extraversion scale and the Conscientiousness scale results of the NEO-FFI are significantly higher in the group of athletes compared to controls. The total methylation and the number of methylated islands in the promoter region of the DAT1 gene are higher in the study group. Pearson’s linear correlation between the total methylation, the number of methylated islands and the NEO-FFI shows significant results for the Extraversion and Agreeability scales. The total methylation and the number of methylated islands in the promoter region of the DAT1 gene are higher in the study group. Pearson’s linear correlation between the total methylation, the number of methylated islands and the NEO-FFI shows significant results for the Extraversion and Agreeability scales. Our analysis of the methylation status of individual CpG sites revealed a new direction of research into the biological aspects of regulating dopamine release and personality traits in people practicing sports. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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14 pages, 1021 KiB

Open AccessArticle

Staphylococcal Resistance Patterns, blaZ and SCCmec Cassette Genes in the Nasopharyngeal Microbiota of Pregnant Women

by Sylwia Andrzejczuk, Monika Cygan, Dominik Dłuski, Dagmara Stępień-Pyśniak and Urszula Kosikowska

Int. J. Mol. Sci. 2023, 24(9), 7980; https://doi.org/10.3390/ijms24097980 - 28 Apr 2023

Cited by 4 | Viewed by 2074

Abstract

Antimicrobial resistance in Staphylococcus spp. colonising the nasopharynx can create risk factors of therapeutic treatment failure or prophylaxis in pregnant women. Resistance is mostly encoded on plasmids (e.g., blaZ gene for penicillinase synthesis) or chromosomes (e.g., mecA and mecC for methicillin resistance). The [...] Read more.

Antimicrobial resistance in Staphylococcus spp. colonising the nasopharynx can create risk factors of therapeutic treatment failure or prophylaxis in pregnant women. Resistance is mostly encoded on plasmids (e.g., blaZ gene for penicillinase synthesis) or chromosomes (e.g., mecA and mecC for methicillin resistance). The mecA gene is part of the chromosomal mec gene cassette (SCCmec), which is also located on the plasmid. The disc diffusion method for the selected drugs (beta-lactams, fluoroquinolones, streptogramins, aminoglicosides, macrolides, oxasolidinones, tetracyclines and other groups) was used. PCR for blaZ, mecA and mecC genes and SCCmec cassette detection and typing were performed. S. aureus (54.4%) and S. epidermidis (27.9%) were the most prevalent and showed the highest diversity of resistance profiles. The blaZ, mecA and mecC genes were reported in 95.6%, 20.6% and 1.5% of isolates, respectively. The highest resistance was found to beta-lactams, commonly used during pregnancy. Resistance to a variety of antimicrobials, including benzylpenicillin resistance in blaZ-positive isolates, and the existence of a very high diversity of SCCmec cassette structures in all staphylococci selected from the nasopharyngeal microbiota of pregnant women were observed for the first time. Knowledge of the prevalence of antimicrobial-resistant staphylococci in the nasopharynx of pregnant women may be important for the appropriate treatment or prophylaxis of this group of patients. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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Review

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29 pages, 2107 KiB

Open AccessReview

The Role of Genetic Polymorphisms in Diabetic Retinopathy: Narrative Review

by Edyta Sienkiewicz-Szłapka, Ewa Fiedorowicz, Angelika Król-Grzymała, Natalia Kordulewska, Dominika Rozmus, Anna Cieślińska and Andrzej Grzybowski

Int. J. Mol. Sci. 2023, 24(21), 15865; https://doi.org/10.3390/ijms242115865 - 1 Nov 2023

Cited by 2 | Viewed by 2366

Abstract

Diabetic retinopathy (DR) is renowned as a leading cause of visual loss in working-age populations with its etiopathology influenced by the disturbance of biochemical metabolic pathways and genetic factors, including gene polymorphism. Metabolic pathways considered to have an impact on the development of [...] Read more.

Diabetic retinopathy (DR) is renowned as a leading cause of visual loss in working-age populations with its etiopathology influenced by the disturbance of biochemical metabolic pathways and genetic factors, including gene polymorphism. Metabolic pathways considered to have an impact on the development of the disease, as well as genes and polymorphisms that can affect the gene expression, modify the quantity and quality of the encoded product (protein), and significantly alter the metabolic pathway and its control, and thus cause changes in the functioning of metabolic pathways. In this article, the screening of chromosomes and the most important genes involved in the etiology of diabetic retinopathy is presented. The common databases with manuscripts published from January 2000 to June 2023 have been taken into consideration and chosen. This article indicates the role of specific genes in the development of diabetic retinopathy, as well as polymorphic changes within the indicated genes that may have an impact on exacerbating the symptoms of the disease. The collected data will allow for a broader look at the disease and help to select candidate genes that can become markers of the disease. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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20 pages, 997 KiB

Open AccessReview

Chromosome 22q11.2 Deletion Syndrome: A Comprehensive Review of Molecular Genetics in the Context of Multidisciplinary Clinical Approach

by Aleksandra Szczawińska-Popłonyk, Eyal Schwartzmann, Zuzanna Chmara, Antonina Głukowska, Tomasz Krysa, Maksymilian Majchrzycki, Maurycy Olejnicki, Paulina Ostrowska and Joanna Babik

Int. J. Mol. Sci. 2023, 24(9), 8317; https://doi.org/10.3390/ijms24098317 - 5 May 2023

Cited by 10 | Viewed by 4342

Abstract

The 22q11.2 deletion syndrome is a multisystemic disorder characterized by a marked variability of phenotypic features, making the diagnosis challenging for clinicians. The wide spectrum of clinical manifestations includes congenital heart defects—most frequently conotruncal cardiac anomalies—thymic hypoplasia and predominating cellular immune deficiency, laryngeal [...] Read more.

The 22q11.2 deletion syndrome is a multisystemic disorder characterized by a marked variability of phenotypic features, making the diagnosis challenging for clinicians. The wide spectrum of clinical manifestations includes congenital heart defects—most frequently conotruncal cardiac anomalies—thymic hypoplasia and predominating cellular immune deficiency, laryngeal developmental defects, midline anomalies with cleft palate and velar insufficiency, structural airway defects, facial dysmorphism, parathyroid and thyroid gland hormonal dysfunctions, speech delay, developmental delay, and neurocognitive and psychiatric disorders. Significant progress has been made in understanding the complex molecular genetic etiology of 22q11.2 deletion syndrome underpinning the heterogeneity of clinical manifestations. The deletion is caused by chromosomal rearrangements in meiosis and is mediated by non-allelic homologous recombination events between low copy repeats or segmental duplications in the 22q11.2 region. A range of genetic modifiers and environmental factors, as well as the impact of hemizygosity on the remaining allele, contribute to the intricate genotype-phenotype relationships. This comprehensive review has been aimed at highlighting the molecular genetic background of 22q11.2 deletion syndrome in correlation with a clinical multidisciplinary approach. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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18 pages, 3561 KiB

Open AccessCase Report

Specific Deletions of Chromosomes 3p, 5q, 13q, and 21q among Patients with G2 Grade of Non-Small Cell Lung Cancer

by Agata Kolecka-Bednarczyk, Magdalena Frydrychowicz, Bartłomiej Budny, Marcin Ruciński, Claudia Dompe, Piotr Gabryel, Bartosz J. Płachno, Marek Ruchała, Katarzyna Ziemnicka, Paweł Zieliński and Joanna Budna-Tukan

Int. J. Mol. Sci. 2024, 25(16), 8642; https://doi.org/10.3390/ijms25168642 - 8 Aug 2024

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Abstract

Non-small cell lung cancer (NSCLC) leads as a primary cause of cancer-related premature mortality in Western populations. This study leverages cutting-edge gene-expression-profiling technologies to perform an in-depth molecular characterization of NSCLC specimens, with the objective of uncovering tumor-specific genomic alterations. By employing DNA [...] Read more.

Non-small cell lung cancer (NSCLC) leads as a primary cause of cancer-related premature mortality in Western populations. This study leverages cutting-edge gene-expression-profiling technologies to perform an in-depth molecular characterization of NSCLC specimens, with the objective of uncovering tumor-specific genomic alterations. By employing DNA microarray analysis, our research aims to refine the classification of NSCLC for early detection, guide molecular-targeted treatment approaches, enhance prognostication, and broaden the scientific understanding of the disease’s biology. We identified widespread genomic abnormalities in our samples, including the recurrent loss of chromosomal regions 3p, 5q, 13q, and 21q and the gain of 12p. Furthermore, utilizing Metascape for bioinformatic analysis revealed critical biological pathways disrupted in NSCLC, offering promising leads for novel therapeutic interventions. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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Open AccessBrief Report

The Epidermal Transcriptome Analysis of a Novel c.639_642dup LORICRIN Variant-Delineation of the Loricrin Keratoderma Pathology

by Katarzyna Wertheim-Tysarowska, Katarzyna Osipowicz, Bartłomiej Gielniewski, Bartosz Wojtaś, Alicja Szabelska-Beręsewicz, Joanna Zyprych-Walczak, Adriana Mika, Andrzej Tysarowski, Katarzyna Duk, Agnieszka Magdalena Rygiel, Katarzyna Niepokój, Katarzyna Woźniak, Cezary Kowalewski, Jolanta Wierzba and Aleksandra Jezela-Stanek

Int. J. Mol. Sci. 2023, 24(11), 9459; https://doi.org/10.3390/ijms24119459 - 29 May 2023

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Abstract

Loricrin keratoderma (LK) is a rare autosomal dominant genodermatosis caused by LORICRIN gene mutations. The pathogenesis of the disease is not yet fully understood. So far, only 10 pathogenic variants in LORICRIN have been described, with all of them but one being deletions [...] Read more.

Loricrin keratoderma (LK) is a rare autosomal dominant genodermatosis caused by LORICRIN gene mutations. The pathogenesis of the disease is not yet fully understood. So far, only 10 pathogenic variants in LORICRIN have been described, with all of them but one being deletions or insertions. The significance of rare nonsense variants remains unclear. Furthermore, no data regarding the RNA expression in affected patients are available. The aim of this study is to describe the two variants in the LORICRIN gene found in two distinct families: the novel pathogenic variant c.639_642dup and a rare c.10C > T (p.Gln4Ter) of unknown significance. We also present the results of the transcriptome analysis of the lesional loricrin keratoderma epidermis of a patient with c.639_642dup. We show that in the LK lesion, the genes associated with epidermis development and keratocyte differentiation are upregulated, while genes engaged in cell adhesion, differentiation developmental processes, ion homeostasis and transport, signaling and cell communication are downregulated. In the context of the p.Gln4Ter clinical significance evaluation, we provide data indicating that LORICRIN haploinsufficiency has no skin consequences. Our results give further insight into the pathogenesis of LK, which may have therapeutic implications in the future and important significance in the context of genetic counseling. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland 2.0)

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