Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.3 days after submission; acceptance to publication is undertaken in 2.6 days (median values for papers published in this journal in the first half of 2024).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.8 (2023);
5-Year Impact Factor:
3.3 (2023)
Latest Articles
The Molecular Basis of Multiple Morphological Abnormalities of Sperm Flagella and Its Impact on Clinical Practice
Genes 2024, 15(10), 1315; https://doi.org/10.3390/genes15101315 (registering DOI) - 13 Oct 2024
Abstract
Multiple morphological abnormalities of the sperm flagella (MMAF) is a specific form of severe flagellar or ciliary deficiency syndrome. MMAF is characterized by primary infertility with abnormal morphology in the flagella of spermatozoa, presenting with short, absent, bent, coiled, and irregular flagella. As
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Multiple morphological abnormalities of the sperm flagella (MMAF) is a specific form of severe flagellar or ciliary deficiency syndrome. MMAF is characterized by primary infertility with abnormal morphology in the flagella of spermatozoa, presenting with short, absent, bent, coiled, and irregular flagella. As a rare disease first named in 2014, studies in recent years have shed light on the molecular defects of MMAF that comprise the structure and biological function of the sperm flagella. Understanding the molecular genetics of MMAF may provide opportunities for the development of diagnostic and therapeutic strategies for this rare disease. This review aims to summarize current studies regarding the molecular pathogenesis of MMAF and describe strategies of genetic counseling, clinical diagnosis, and therapy for MMAF.
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(This article belongs to the Special Issue Molecular Basis of Rare Genetic Diseases)
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Open AccessArticle
Metagenomic Sequencing Elucidated the Microbial Diversity of Rearing Water Environments for Sichuan Taimen (Hucho bleekeri)
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Qinyao Wei, Zhaobin Song, Yeyu Chen, Huanchao Yang, Yanling Chen, Zhao Liu, Yi Yu, Quanyu Tu, Jun Du and Hua Li
Genes 2024, 15(10), 1314; https://doi.org/10.3390/genes15101314 (registering DOI) - 12 Oct 2024
Abstract
Background: Sichuan taimen (Hucho bleekeri) is a fish species endemic to China’s upper Yangtze River drainage and has significant value as an aquatic resource. It was listed as a first-class state-protected wild animal by the Chinese government due to its very
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Background: Sichuan taimen (Hucho bleekeri) is a fish species endemic to China’s upper Yangtze River drainage and has significant value as an aquatic resource. It was listed as a first-class state-protected wild animal by the Chinese government due to its very limited distribution and wild population at present. Methods: To elucidate the diversity of microorganisms in rearing water environments for H. bleekeri, metagenomic sequencing was applied to water samples from the Maerkang and Jiguanshan fish farms, where H. bleekeri were reared. Results: The results revealed that Pseudomonadota was the dominant phylum in the microbial communities of the water samples. Among the shared bacterial groups, Cyanobacteriota, Actinomycetota, Planctomycetota, Nitrospirota, and Verrucomicrobiota were significantly enriched in the water environment of Jiguanshan (p < 0.01), while Bacteroidota was more enriched in that of Maerkang (p < 0.01). Additionally, the Shannon diversity and Simpson index of the microbial community in the water environment of Maerkang were lower than in that of Jiguanshan. Conclusions: The present study demonstrated the similarities and differences in the microbial compositions of rearing water environments for H. bleekeri, which are expected to benefit the artificial breeding of H. bleekeri in the future.
Full article
(This article belongs to the Special Issue Research of Microbial Diversity and Functions in Environment and Host)
Open AccessReview
Role of Circulating microRNAs in Liver Disease and HCC: Focus on miR-122
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Francesco Colaianni, Veronica Zelli, Chiara Compagnoni, Martina Sara Miscione, Mario Rossi, Davide Vecchiotti, Monica Di Padova, Edoardo Alesse, Francesca Zazzeroni and Alessandra Tessitore
Genes 2024, 15(10), 1313; https://doi.org/10.3390/genes15101313 (registering DOI) - 12 Oct 2024
Abstract
miR-122 is the most abundant microRNA (miRNA) in the liver; it regulates several genes mainly involved in cell metabolism and inflammation. Host factors, diet, metabolic disorders and viral infection promote the development of liver diseases, including hepatocellular carcinoma (HCC). The downregulation of miR-122
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miR-122 is the most abundant microRNA (miRNA) in the liver; it regulates several genes mainly involved in cell metabolism and inflammation. Host factors, diet, metabolic disorders and viral infection promote the development of liver diseases, including hepatocellular carcinoma (HCC). The downregulation of miR-122 in tissue is a common feature of the progression of liver injury. In addition, the release of miR-122 in the bloodstream seems to be very promising for the early diagnosis of both viral and non-viral liver disease. Although controversial data are available on the role of circulating miR-122 as a single biomarker, high diagnostic accuracy has been observed using miR-122 in combination with other circulating miRNAs and/or proteins. This review is focused on comprehensively summarizing the most recent literature on the potential role of circulating miR-122, and related molecules, as biomarker(s) of metabolic liver diseases, hepatitis and HCC.
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(This article belongs to the Section RNA)
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Open AccessArticle
Triplication of the PCDH19 Gene as a Novel Disease Mechanism Leading to Epileptic Encephalopathy Resembling Loss-of-Function Pathogenic Variants
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Alba Gabaldón-Albero, Patricia Smeyers, Sara Hernández-Muela, Mónica Roselló, Carmen Orellana, Sandra Monfort, Silvestre Oltra and Francisco Martínez
Genes 2024, 15(10), 1312; https://doi.org/10.3390/genes15101312 (registering DOI) - 12 Oct 2024
Abstract
Background/Objectives: Developmental and epileptic encephalopathy 9 (DEE9) (MIM #300088) affects heterozygous females and males with somatic pathogenic variants, while male carriers with hemizygous PCDH19 pathogenic variants are clinically unaffected. There are hundreds of pathogenic single nucleotide variants in the PCDH19 gene reported in
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Background/Objectives: Developmental and epileptic encephalopathy 9 (DEE9) (MIM #300088) affects heterozygous females and males with somatic pathogenic variants, while male carriers with hemizygous PCDH19 pathogenic variants are clinically unaffected. There are hundreds of pathogenic single nucleotide variants in the PCDH19 gene reported in the literature, which lead to the loss of function of the PCDH19 protein. To date, no phenotypes associated with overexpression or copy number gains have been described in this gene. Methods and results: We present a female patient with a de novo triplication in the Xq21.3–q22.1 chromosomal region, which includes the PCDH19 gene, which implies an unbalanced dose gain. This patient displayed a phenotype of epileptic encephalopathy compatible with DEE9. By comparison, another male patient with a similar duplication showed mild developmental delay and autism but never developed epilepsy. Conclusions: Here, we propose the dose gain of PCDH19 as a new pathogenic mechanism that results in a phenotype similar to that found in patients with loss-of-function variants in PCDH19, when present in a heterozygous state.
Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat
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Xiaohan Zhang, Yanan Yu, Yumeng Sun, Yan Bai, Yongjun Shu and Changhong Guo
Genes 2024, 15(10), 1311; https://doi.org/10.3390/genes15101311 - 11 Oct 2024
Abstract
Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution,
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Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations.
Full article
(This article belongs to the Special Issue Genes and Genomics of Plants Under Abiotic Stresses)
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Open AccessArticle
Whole Exome Sequencing and Panel-Based Analysis in 176 Spanish Children with Neurodevelopmental Disorders: Focus on Autism Spectrum Disorder and/or Intellectual Disability/Global Developmental Delay
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Ariadna Sánchez Suárez, Beatriz Martínez Menéndez, Eduardo Escolar Escamilla, Francisco J. Martínez Sarries, Miren Iranzu Esparza Garrido, Belén Gil-Fournier, Soraya Ramiro León, Bárbara Rubio Gribble, Juan F. Quesada Espinosa and Andrés J. Alcaraz Romero
Genes 2024, 15(10), 1310; https://doi.org/10.3390/genes15101310 - 11 Oct 2024
Abstract
Background: Neurodevelopmental disorders (NDDs) represent a significant challenge in pediatric genetics, often requiring advanced diagnostic tools for the accurate identification of genetic variants. Objectives: To determine the diagnostic yield of whole exome sequencing (WES) with targeted gene panels in children with neurodevelopmental disorders
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Background: Neurodevelopmental disorders (NDDs) represent a significant challenge in pediatric genetics, often requiring advanced diagnostic tools for the accurate identification of genetic variants. Objectives: To determine the diagnostic yield of whole exome sequencing (WES) with targeted gene panels in children with neurodevelopmental disorders (NDDs). Methods: This observational, prospective study included a total of 176 Spanish-speaking pediatric patients with neurodevelopmental disorders (NDDs), encompassing intellectual disability (ID), global developmental delay (GDD), and/or autism spectrum disorder (ASD). Participants were recruited from January 2019 to January 2023 at a University Hospital in Madrid, Spain. Clinical and sociodemographic variables were recorded, along with genetic study results. The age range of the subjects was 9 months to 16 years, and the percentage of males was 72.1%. The diagnostic yield of whole exome sequencing (WES) was calculated both before and after parental testing via Sanger DNA sequencing. Results: The study included 176 children: 67 (38.1%) with ID, 62 (35.2%) with ASD, and 47 (26.7%) with ASD + ID. The diagnostic yield of proband-only exome sequencing was 12.5% (22/176). By group, the diagnostic yield of proband-only exome sequencing was 3.2% in the ASD, 12.7% in the ASD + ID, and 20.8% in the ID group. Variants of uncertain significance (VUS) were found in 39.8% (70/176). After parental testing, some variants were reclassified as “likely pathogenic”, increasing the diagnostic yield by 4.6%, with an overall diagnostic yield of 17.1%. Diagnostic yield was higher in patients with syndromic ID (70.6%% vs. 29.4%; p = 0.036). Conclusions: A sequential approach utilizing WES followed by panel-based analysis, starting with the index case and, when appropriate, including the parents, proves to be a cost-effective strategy. WES is particularly suitable for complex conditions, as it allows for the identification of potentially causative genes beyond those covered by targeted panels, providing a more comprehensive analysis. Including parental testing enhances the diagnostic yield and improves accuracy, especially in cases with variants of uncertain significance (VUS), thereby advancing our understanding of NDDs.
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(This article belongs to the Topic Advances in Genetics and Precision Medicine in Human Diseases)
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Open AccessSystematic Review
Genetics of Calcific Aortic Stenosis: A Systematic Review
by
Vassilios S. Vassiliou, Nicholas Johnson, Kenneth Langlands and Vasiliki Tsampasian
Genes 2024, 15(10), 1309; https://doi.org/10.3390/genes15101309 - 10 Oct 2024
Abstract
Background: Calcific aortic stenosis is the most prevalent valvular abnormality in the Western world. Factors commonly associated with calcific aortic stenosis include advanced age, male sex, hypertension, diabetes and impaired renal function. This review synthesises the existing literature on genetic associations with calcific
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Background: Calcific aortic stenosis is the most prevalent valvular abnormality in the Western world. Factors commonly associated with calcific aortic stenosis include advanced age, male sex, hypertension, diabetes and impaired renal function. This review synthesises the existing literature on genetic associations with calcific aortic stenosis. Methods: A systematic search was conducted in the PubMed, Ovid and Cochrane libraries from inception to 21 July 2024 to identify human studies investigating the genetic factors involved in calcific aortic stenosis. From an initial pool of 1392 articles, 78 were selected for full-text review and 31 were included in the final qualitative synthesis. The risk of bias in these studies was assessed using the Newcastle Ottawa Scale. Results: Multiple genes have been associated with calcific aortic stenosis. These genes are involved in different biological pathways, including the lipid metabolism pathway (PLA, LDL, APO, PCSK9, Lp-PLA2, PONS1), the inflammatory pathway (IL-6, IL-10), the calcification pathway (PALMD, TEX41) and the endocrine pathway (PTH, VIT D, RUNX2, CACNA1C, ALPL). Additional genes such as NOTCH1, NAV1 and FADS1/2 influence different pathways. Mechanistically, these genes may promote a pro-inflammatory and pro-calcific environment in the aortic valve itself, leading to increased osteoblastic activity and subsequent calcific degeneration of the valve. Conclusions: Numerous genetic associations contribute to calcific aortic stenosis. Recognition of these associations can enhance risk stratification for individuals and their first-degree relatives, facilitate family screening, and importantly, pave the way for targeted therapeutic interventions focusing on the identified genetic factors. Understanding these genetic factors can also lead to gene therapy to prevent calcific aortic stenosis in the future.
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(This article belongs to the Special Issue Genomics and Genetics of Cardiovascular Diseases)
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Open AccessArticle
A Comparative Overview of the Role of Human Ribonucleases in Nonsense-Mediated mRNA Decay
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Paulo J. da Costa, Juliane Menezes, Raquel Guedes, Filipa P. Reis, Alexandre Teixeira, Margarida Saramago, Sandra C. Viegas, Cecília M. Arraiano and Luísa Romão
Genes 2024, 15(10), 1308; https://doi.org/10.3390/genes15101308 - 10 Oct 2024
Abstract
Eukaryotic cells possess surveillance mechanisms that detect and degrade defective transcripts. Aberrant transcripts include mRNAs with a premature termination codon (PTC), targeted by the nonsense-mediated decay (NMD) pathway, and mRNAs lacking a termination codon, targeted by the nonstop decay (NSD) pathway. The eukaryotic
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Eukaryotic cells possess surveillance mechanisms that detect and degrade defective transcripts. Aberrant transcripts include mRNAs with a premature termination codon (PTC), targeted by the nonsense-mediated decay (NMD) pathway, and mRNAs lacking a termination codon, targeted by the nonstop decay (NSD) pathway. The eukaryotic exosome, a ribonucleolytic complex, plays a crucial role in mRNA processing and turnover through its catalytic subunits PM/Scl100 (Rrp6 in yeast), DIS3 (Rrp44 in yeast), and DIS3L1. Additionally, eukaryotic cells have other ribonucleases, such as SMG6 and XRN1, that participate in RNA surveillance. However, the specific pathways through which ribonucleases recognize and degrade mRNAs remain elusive. In this study, we characterized the involvement of human ribonucleases, both nuclear and cytoplasmic, in the mRNA surveillance mechanisms of NMD and NSD. We performed knockdowns of SMG6, PM/Scl100, XRN1, DIS3, and DIS3L1, analyzing the resulting changes in mRNA levels of selected natural NMD targets by RT-qPCR. Additionally, we examined the levels of different human β-globin variants under the same conditions: wild-type, NMD-resistant, NMD-sensitive, and NSD-sensitive. Our results demonstrate that all the studied ribonucleases are involved in the decay of certain endogenous NMD targets. Furthermore, we observed that the ribonucleases SMG6 and DIS3 contribute to the degradation of all β-globin variants, with an exception for βNS in the former case. This is also the case for PM/Scl100, which affects all β-globin variants except the NMD-sensitive variants. In contrast, DIS3L1 and XRN1 show specificity for β-globin WT and NMD-resistant variants. These findings suggest that eukaryotic ribonucleases are target-specific rather than pathway-specific. In addition, our data suggest that ribonucleases play broader roles in mRNA surveillance and degradation mechanisms beyond just NMD and NSD.
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(This article belongs to the Special Issue Post-transcriptional Regulation in Mammals)
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Open AccessArticle
Germplasm Resources Evaluation of Cultured Largemouth Bass (Micropterus salmoides) in China Based on Whole Genome Resequencing
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Wenzhi Guan, Jieliang Jian, Baolong Niu, Xinhui Zhang, Jiongying Yu and Xiaojun Xu
Genes 2024, 15(10), 1307; https://doi.org/10.3390/genes15101307 - 10 Oct 2024
Abstract
Background: Largemouth bass (Micropterus salmoides), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status
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Background: Largemouth bass (Micropterus salmoides), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status of largemouth bass populations in China. Method: In this study, we conducted population genetic analyses on nine cultured largemouth bass populations using whole genome resequencing. Results: A total of 3.23 Tb of clean bases were generated, with average Q20 and Q30 values of 98.17% and 94.25%, respectively, and 2,140,534 high-quality SNPs were obtained. Relatively high genetic diversity was observed across all populations. Combined with linkage disequilibrium (LD) patterns, the Wanlu (WL) population possessed the highest genetic diversity, and the Longyou (LY) population possessed the lowest genetic diversity. Additionally, population structure analyses, including pairwise F-statistics, phylogenetic trees, PCA, and admixture analysis, revealed significant genetic differentiation, particularly between the WL, LY, and other 7 populations, while also indicating the occurrence of a common admixture event. Finally, TreeMix inferred migration events from the WL to the Chuanlu (CL) population and from the Taiwan breeding population (TWL) to the Guanglu (GL) population. Conclusions: These findings provide a critical foundation for developing conservation and breeding strategies for largemouth bass in China.
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(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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Open AccessArticle
Genome-Wide Characterization and Expression Profiling of Phytosulfokine Receptor Genes (PSKRs) in Triticum aestivum with Docking Simulations of Their Interactions with Phytosulfokine (PSK): A Bioinformatics Study
by
Hala Badr Khalil
Genes 2024, 15(10), 1306; https://doi.org/10.3390/genes15101306 - 9 Oct 2024
Abstract
Background/Objectives: The phytosulfokine receptor (PSKR) gene family plays a crucial role in regulating plant growth, development, and stress response. Here, the PSKR gene family was characterized in Triticum aestivum L. The study aimed to bridge knowledge gaps and clarify the functional
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Background/Objectives: The phytosulfokine receptor (PSKR) gene family plays a crucial role in regulating plant growth, development, and stress response. Here, the PSKR gene family was characterized in Triticum aestivum L. The study aimed to bridge knowledge gaps and clarify the functional roles of TaPSKRs to create a solid foundation for examining the structure, functions, and regulatory aspects. Methods: The investigation involved genome-wide identification of PSKRs through collection and chromosomal assignment, followed by phylogenetic analysis and gene expression profiling. Additionally, interactions with their interactors were stimulated and analyzed to elucidate their function. Results: The wide-genome inspection of all TaPSKRs led to 25 genes with various homeologs, resulting in 57 TaPSKR members distributed among the A, B, and D subgenomes. Investigating the expression of 61 TaPSKR cDNAs in RNA-seq datasets generated from different growth stages at 14, 21, and 60 days old and diverse tissues such as leaves, shoots, and roots provided further insight into their functional purposes. The expression profile of the TaPSKRs resulted in three key clusters. Gene cluster 1 (GC 1) is partially associated with root growth, suggesting that specific TaPSKRs control root development. The GC 2 cluster targeted genes that show high levels of expression in all tested leaf growth stages and the early developmental stage of the shoots and roots. Furthermore, the GC 3 cluster was composed of genes that are constantly expressed, highlighting their crucial role in regulating various processes during the entire life cycle of wheat. Molecular docking simulations showed that phytosulfokine type α (PSK-α) interacted with all TaPSKRs and had a strong binding affinity with certain TaPSKR proteins, encompassing TaPSKR1A, TaPSKR3B, and TaPSKR13A, that support their involvement in PSK signaling pathways. The crucial arbitration of the affinity may depend on interactions between wheat PSK-α and PSKRs, especially in the LRR domain region. Conclusions: These discoveries deepened our knowledge of the role of the TaPSKR gene family in wheat growth and development, opening up possibilities for further studies to enhance wheat durability and yield via focused innovation approaches.
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(This article belongs to the Special Issue Quality Gene Mining and Breeding of Wheat)
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Open AccessReview
PERM1—An Emerging Transcriptional Regulator of Mitochondrial Biogenesis: A Systematic Review
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Eveline Soares Menezes, Zeyu Wu, John R. M. Renwick, Andres Moran-MacDonald and Brendon J. Gurd
Genes 2024, 15(10), 1305; https://doi.org/10.3390/genes15101305 - 9 Oct 2024
Abstract
Background/Objectives: This systematic review aims to explore the role of PERM1 across different organisms, tissues, and cellular functions, with a particular focus on its involvement in regulating skeletal muscle mitochondrial biogenesis. Methods: This systematic review follows The PRISMA 2020 Statement. We used the
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Background/Objectives: This systematic review aims to explore the role of PERM1 across different organisms, tissues, and cellular functions, with a particular focus on its involvement in regulating skeletal muscle mitochondrial biogenesis. Methods: This systematic review follows The PRISMA 2020 Statement. We used the Covidence systematic review software for abstract/title screening, full-text review, and data extraction. The review included studies that examined PERM1 expression or activity in skeletal muscle, heart, and adipose tissue and/or cells, from mice, rats, and humans, and involved exercise or disease models. Risk of bias was assessed using the Cochrane Collaboration tool, and the data were extracted and synthesized qualitatively, with bioinformatic analyses performed using the MetaMEx database. Results: Twenty-one studies were included in our data extraction process, where 10 studies involved humans, 21 involved mice, four involved rats, and 11 involved cells. Conclusions: PERM1 in skeletal muscle increases with endurance exercise, affecting muscle function and oxidative metabolism, but its role in humans is not well understood. In cardiac tissue, PERM1 is vital for function and mitochondrial biogenesis purposes, but decreases with disease and pressure overload. Our review synthesizes the current understanding of PERM1’s function, raises awareness of its role in mitochondrial regulation, and identifies key areas for future research in the field.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Chromosome 15q11-q13 Duplication Syndrome: A Review of the Literature and 14 New Cases
by
Maria Bisba, Christina Malamaki, Pantelis Constantoulakis and Spiros Vittas
Genes 2024, 15(10), 1304; https://doi.org/10.3390/genes15101304 - 8 Oct 2024
Abstract
The 15q11.2q13 chromosomal region is particularly susceptible to chromosomal rearrangements due to low-copy repeats (LCRs) located inside this area. Specific breakpoints (BP1-BP5) that lead to deletions and duplications of variable size have been identified. Additionally, this specific region contains several imprinted genes, giving
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The 15q11.2q13 chromosomal region is particularly susceptible to chromosomal rearrangements due to low-copy repeats (LCRs) located inside this area. Specific breakpoints (BP1-BP5) that lead to deletions and duplications of variable size have been identified. Additionally, this specific region contains several imprinted genes, giving rise to complex syndromes (Prader–Willi, Angelman and 15q11-q13 duplication syndromes). 15q11.2-q13 duplication syndrome has been associated with neurodevelopmental disorders (hypotonia, developmental delay, speech delay and seizures) and ASD but is characterized by variable expressivity and reduced penetrance, features that make genetic counseling a complex procedure especially in prenatal cases. In the present study, a total of 14 pre- and postnatal cases were diagnosed as 15q11.2q13 duplication carriers using Affymetrix CytoScan 750 K array-CGH, and our analysis combined these with 120 cases existing in the literature. The inheritance pattern of the cases of this study is unknown, but as a review of the literature revealed, 62.96% of the affected carriers inherited the duplicated area from their mother. The combined results of this analysis (the present study and the literature) show that in the majority of the cases, the phenotype is a compound phenotype, with clinical characteristics that include ASD, intellectual disability, developmental delay and an absence of speech. The aim of this paper is to deliver new possibilities to genetic counseling that can be provided in prenatal and postnatal cases as the phenotype of 15q11.2q13 microduplication carriers cannot be fully predicted; so, clinical diagnoses should be a combination of molecular findings and clinical manifestations that are present.
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(This article belongs to the Special Issue Molecular Genetics of Neurodevelopmental Disorders)
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Open AccessArticle
Genetic Insights into the Giant Keyhole Limpet (Megathura crenulata), an Eastern Pacific Coastal Endemic: Complete Mitogenome, Phylogenetics, Phylogeography, and Historical Demography
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Brenda Bonett-Calzada, Fausto Valenzuela-Quiñonez, Miguel A. Del Río-Portilla, Natalia J. Bayona-Vásquez, Carmen E. Vargas-Peralta, John R. Hyde and Fabiola Lafarga-De la Cruz
Genes 2024, 15(10), 1303; https://doi.org/10.3390/genes15101303 - 8 Oct 2024
Abstract
Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called
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Background: The giant keyhole limpet Megathura crenulata is a gastropod mollusk (Fissurella superfamily) that is endemic to the eastern Pacific coast from southern California, USA, to Baja California Sur, Mexico. M. crenulata is socioeconomically important as it produces a potent immune-stimulating protein, called Keyhole Limpet Hemocyanin, which is extracted in vivo and utilized for vaccine development. However, ecological studies are scarce and genetic knowledge of the species needs to be improved. Our objectives were to assemble and annotate the mitogenome of M. crenulata, and to assess its phylogenetic relationships with other marine gastropods and to evaluate its population genetic diversity and structure. Methods: Samples were collected for mitogenome assembly (n = 3) spanning its geographic range, Puerto Canoas (PCA) and Punta Eugenia (PEU), Mexico, and California (CAL), USA. Total DNA was extracted from gills sequenced using Illumina paired-end 150-bp-read sequencing. Reads were cleaned, trimmed, assembled de novo, and annotated. In addition, 125 samples from eight locations were analyzed for genetic diversity and structure analysis at the 16s rRNA and COX1 genes. Results: The M. crenulata mitogenomes had lengths of 16,788 bp (PCA) and 16,787 bp (PEU) and were composed of 13 protein-coding regions, 22 tRNAs, two rRNAs, and the D-Loop region. In terms of phylogeographic diversity and structure, we found a panmictic population that has experienced recent demographic expansion with low nucleotide diversity (0.002), high haplotypic diversity (0.915), and low φST (0.047). Conclusions: Genetic insights into the giant keyhole limpet provides tools for its management and conservation by delimiting fishing regions with low genetic diversity and/or genetically discrete units.
Full article
(This article belongs to the Special Issue Molecular Evolution, Mitochondrial Genomics and Mitochondrial Genome Expression in Animals: 2024–2025)
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Open AccessArticle
Prognostic Role of Specific KRAS Mutations Detected in Aspiration and Liquid Biopsies from Patients with Pancreatic Cancer
by
Tereza Hálková, Bohuš Bunganič, Eva Traboulsi, Marek Minárik, Miroslav Zavoral and Lucie Benešová
Genes 2024, 15(10), 1302; https://doi.org/10.3390/genes15101302 - 7 Oct 2024
Abstract
Background/Objectives: Although the overall survival prognosis of patients in advanced stages of pancreatic ductal adenocarcinoma (PDAC) is poor, typically ranging from days to months from diagnosis, there are rare cases of patients remaining in therapy for longer periods of time. Early estimations of
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Background/Objectives: Although the overall survival prognosis of patients in advanced stages of pancreatic ductal adenocarcinoma (PDAC) is poor, typically ranging from days to months from diagnosis, there are rare cases of patients remaining in therapy for longer periods of time. Early estimations of survival prognosis would allow rational decisions on complex therapy interventions, including radical surgery and robust systemic therapy regimens. Understandably, there is great interest in finding prognostic markers that can be used for patient stratification. We determined the role of various KRAS mutations in the prognosis of PDAC patients using biopsy samples and circulating tumor DNA. Methods: A total of 118 patients with PDAC, clinically confirmed by endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNB), were included in the study. DNA was extracted from cytological slides following a standard cytology evaluation to ensure adequacy (viability and quantity) and to mark the tumor cell fraction. Circulating tumor DNA (ctDNA) was extracted from plasma samples of 45 patients in stage IV of the disease. KRAS mutations in exons 12 and 13 were detected by denaturing capillary electrophoresis (DCE), revealing a minute presence of mutation-specific heteroduplexes. Kaplan–Meier survival curves were calculated for individual KRAS mutation types. Results:KRAS mutations were detected in 90% of tissue (106/118) and 44% of plasma (20/45) samples. All mutations were localized at exon 2, codon 12, with G12D (GGT > GAT) being the most frequent at 44% (47/106) and 65% (13/20), followed by other types including G12V (GGT > GTT) at 31% (33/106) and 10% (2/20), G12R (GGT > CGT) at 17% (18/106) and 10% (2/20), G12C (GGT/TGT) at 5% (5/106) and 0% (0/20) and G12S (GGT/AGT) at 1% (1/106) and 5% (1/20) in tissue and plasma samples, respectively. Two patients had two mutations simultaneously (G12V + G12S and G12D + G12S) in both types of samples (2%, 2/106 and 10%, 2/20 in tissue and plasma samples, respectively). The median survival of patients with the G12D mutation in tissues was less than half that of other patients (median survival 101 days, 95% CI: 80–600 vs. 228 days, 95% CI: 184–602), with a statistically significant overall difference in survival (p = 0.0080, log-rank test), and furthermore it was less than that of all combined patients with other mutation types (101 days, 95% CI: 80–600 vs. 210 days, 95% CI: 161–602, p = 0.0166). For plasma samples, the survival of patients with this mutation was six times shorter than that of patients without the G12D mutation (27 days, 95% CI: 8–334 vs. 161 days, 95% CI: 107–536, p = 0.0200). In contrast, patients with detected KRAS G12R in the tissue survived nearly twice as long as other patients in the aggregate (286 days, 95% CI: 70–602 vs. 162 days, 95% CI: 122–600, p = 0.0374) or patients with other KRAS mutations (286 days, 95% CI: 70–602 vs. 137 days, 95% CI: 107–600, p = 0.0257). Conclusions: Differentiation of specific KRAS mutations in EUS-FNB and ctDNA (above all, the crucial G12D and G12R) is feasible in routine management of PDAC patients and imperative for assessment of prognosis.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
The Complete Chloroplast Genome of Meconopsis simplicifolia and Its Genetic Comparison to Other Meconopsis Species
by
Min Sun, Zhidan Zhu and Rui Li
Genes 2024, 15(10), 1301; https://doi.org/10.3390/genes15101301 - 6 Oct 2024
Abstract
Background: Chloroplasts, due to their high conservation and lack of recombination, serve as important genetic resources for the classification and evolutionary analysis of closely related species that are difficult to distinguish based on their morphological features. Meconopsis simplicifolia (M. simplicifolia), an endangered
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Background: Chloroplasts, due to their high conservation and lack of recombination, serve as important genetic resources for the classification and evolutionary analysis of closely related species that are difficult to distinguish based on their morphological features. Meconopsis simplicifolia (M. simplicifolia), an endangered herb within the Meconopsis genus, has demonstrated therapeutic potential in treating various diseases. However, the highly polymorphic morphology of this species poses a challenge for accurate identification. Methods: In this study, the complete chloroplast genome of M. simplicifolia was sequenced and assembled using Illumina sequencing technology. Simple sequence repeats (SSRs) and repetitive sequences were characterized. In addition, a comparative analysis was conducted with the chloroplast genomes of six other Meconopsis species. Results: The chloroplast genome of M. simplicifolia has a quadripartite circular structure with a total length of 152,772 bp. It consists of a large single-copy region of 83,824 bp and a small single-copy region of 17,646 bp, separated by a pair of inverted repeat sequences (IRa and IRb, 25,651 bp). The genome contains 131 genes, 33 SSRs, and 27 long repetitive sequences. Comparative analysis with six other chloroplast genomes of Meconopsis revealed that M. simplicifolia is closely related to M. betonicifolia and that the rpl2 (ribosomal protein L2) gene in the IRb region has been deleted. This deletion is of significant importance for future taxonomic studies of M. simplicifolia. Conclusions: This study provides a valuable reference for the identification of M. simplicifolia and contributes to a deeper understanding of the phylogeny and evolution of the Meconopsis genus.
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(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)
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Open AccessBrief Report
Novel Variant in ANO5 Muscular Dystrophy: Identification by Whole Genome Sequencing and Quad Analysis
by
Mario Ćuk, Busra Unal, Luka Lovrenčić, McKenzie Walker, Connor P. Hayes, Feruza Abraamyan, Maja Prutki, Goran Krakar, Lidija Srkoč-Majčica and Arezou A. Ghazani
Genes 2024, 15(10), 1300; https://doi.org/10.3390/genes15101300 - 6 Oct 2024
Abstract
Background: The phenotypic spectrum of ANO5 muscle disease ranges widely from elevated creatine kinase (CK) levels in the serum of asymptomatic individuals to progressive muscular dystrophy. Due to overlapping clinical features among muscular dystrophies, the diagnosis of ANO5 muscle disease is established by
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Background: The phenotypic spectrum of ANO5 muscle disease ranges widely from elevated creatine kinase (CK) levels in the serum of asymptomatic individuals to progressive muscular dystrophy. Due to overlapping clinical features among muscular dystrophies, the diagnosis of ANO5 muscle disease is established by molecular genetic tests. Early diagnosis is crucial for the clinical management of symptoms and to mitigate cardiac and musculoskeletal complications. Methods: Quad-joint analysis was performed on whole genome sequencing (WGS) data obtained from an 18-year-old female with mild myalgia and elevated CK and her unaffected parents and sister. The phenotype-driven analysis was performed to prioritize genomic alterations related to the phenotype. The zygosity-based analysis investigated compound heterozygous and de novo status for all variants. Results: The quad-joint WGS analysis revealed a novel pathogenic heterozygous variant, ANO5:c.1770_1773del (p.Phe593Metfs*15), that was paternally inherited. A second and known pathogenic heterozygous variant, ANO5:c.148C>T (p.Arg50*), was also present that was maternally inherited. The genome finding led to the diagnosis of autosomal recessive ANO5 muscle disease and an early personalized clinical management for the patient regarding her cardiac and musculoskeletal health. Conclusions: This is the first report of the ANO5:c.1770_1773del variant in the literature. This report highlights the spectrum of ANO5 muscle disease and describes the role of quad-joint WGS in the early diagnosis and preventive clinical management of ANO5 muscle disease.
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(This article belongs to the Special Issue Application of Next-Generation Sequencing in Genetic Diseases Diagnosis)
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Open AccessReview
Genomic Multicopy Loci Targeted by Current Forensic Quantitative PCR Assays
by
Richard Jäger
Genes 2024, 15(10), 1299; https://doi.org/10.3390/genes15101299 - 5 Oct 2024
Abstract
Modern forensic DNA quantitation assays provide information on the suitability of a DNA extract for a particular type of analysis, on the amount of sample to put into the analysis in order to yield an optimal (or best possible) result, and on the
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Modern forensic DNA quantitation assays provide information on the suitability of a DNA extract for a particular type of analysis, on the amount of sample to put into the analysis in order to yield an optimal (or best possible) result, and on the requirement for optional steps to improve the analysis. To achieve a high sensitivity and specificity, these assays are based on quantitative PCR (qPCR) and analyze target DNA loci that are present in multiple copies distributed across the genome. These target loci allow the determination of the amount of DNA, the degree of DNA degradation, and the proportion of DNA from male contributors. In addition, internal control DNA of a known amount is analyzed in order to inform about the presence of PCR inhibitors. These assays are nowadays provided as commercial kits that have been technically validated and are compatible with common qPCR instruments. In this review, the principles of forensic qPCR assays will be explained, followed by information on the nature of DNA loci targeted by modern forensic qPCR assays. Finally, we critically draw attention to the current trend of manufacturers not to disclose the exact nature of the target loci of their commercial kits.
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(This article belongs to the Special Issue Genetic Tools and Techniques in Forensic Science—an In-Depth Look at the Process of Quantification of Forensic Samples)
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Open AccessCase Report
G6PD Potenza: A Novel Pathogenic Variant Broadening the Mutational Landscape in the Italian Population
by
Claudio Ricciardi Tenore, Eugenia Tulli, Claudia Calò, Roberto Bertozzi, Jessica Evangelista, Giulia Maneri, Martina Rinelli, Francesca Brisighelli, Alessia Perrucci, Elisa De Paolis, Andrea Urbani, Maria De Bonis and Angelo Minucci
Genes 2024, 15(10), 1298; https://doi.org/10.3390/genes15101298 - 4 Oct 2024
Abstract
Background: Glucose 6 phosphate dehydrogenase (G6PD) is a rate-limiting enzyme of the pentose phosphate pathway. The loss of G6PD activity in red blood cells increases the risk of acute haemolytic anaemia under oxidative stress induced by infections, some medications, or fava beans.
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Background: Glucose 6 phosphate dehydrogenase (G6PD) is a rate-limiting enzyme of the pentose phosphate pathway. The loss of G6PD activity in red blood cells increases the risk of acute haemolytic anaemia under oxidative stress induced by infections, some medications, or fava beans. More than 200 single missense mutations are known in the G6PD gene. A 41-year-old woman with a family history of favism coming from the Basilicata region (Italy) was evaluated at our hospital for G6PD abnormalities. Methods: DNA was extracted from a peripheral blood sample and genotyped for the most common G6PD pathogenic variants (PVs). Positive results obtained by Restriction Fragment Length Polymorphism (RFLP), as per practice in our laboratory, were then reconfirmed in Sanger sequencing. Results: RFLP analysis highlighted a variant compatible with the G6PD Cassano variant. Confirmatory testing by Sanger unexpectedly identified a novel variant: c.1357G>A, p.(Val453Met) (NM_001360016.2); the same variant was found in the patient’s mother. In silico models predicted a deleterious effect of this variant at the protein level. The novel G6PD variant was named “G6PD Potenza” on the basis of the patient’s regional origin. Conclusions: This case describes a novel G6PD variant. It also highlights how the Sanger sequencing technique still represents an indispensable confirmatory standard method for variants that could be misinterpreted by only using a “first-level” approach, such as the RFLP. We stress that the evaluation of clinical manifestations in G6PD-deficient patients is of primary importance for the classification of each new G6PD mutation, in agreement with the new WHO guidelines.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Genomic and Transcriptional Analysis of the Necroptosis Pathway Elements RIPK and MLKL in Sea Cucumber, Holothuria leucospilota
by
Rong Chen, Qianying Huang, Yingzhu Rao, Junyan Wang, Ruiming Yu, Shuangxin Peng, Kaiyi Huang, Yihang Huang, Xiangxing Zhu, Dongsheng Tang, Xiaoli Zhang, Tiehao Lin, Ting Chen and Aifen Yan
Genes 2024, 15(10), 1297; https://doi.org/10.3390/genes15101297 - 3 Oct 2024
Abstract
Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in
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Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in sea cucumber remains limited. Methods: We searched the genomes of sea cucumber Holothuria leucospilota for genes encoding RIPKs and MLKL, performed phylogenetic tree, motif and functional domain analyses, and examined tissue distribution and embryonic development patterns using qPCR. Results: RIPK5 (Hl-RIPK5), RIPK7 (Hl-RIPK7) and MLKL (Hl-MLKL) were identified in sea cucumber H. leucospilota. Hl-RIPK5 and Hl-RIPK7 were mainly expressed in coelomocytes, suggesting that they play a role in innate immunity, whereas Hl-MLKL exhibited relatively low expression across tissues. During embryonic development, Hl-MLKL was highly expressed from the 2-cell stage to the morula stage, while Hl-RIPK5 and Hl-RIPK7 were primarily expressed after the morula stage, indicating different roles in embryonic development. In primary coelomocytes, Hl-RIPK5 transcriptional activity was significantly depressed by LPS, poly(I:C), or pathogen Vibrio harveyi. Hl-RIPK7 expression levels were unchanged following the same challenges. Hl-MLKL mRNA levels were significantly decreased with poly(I:C) or V. harveyi, but did not change with LPS. Conclusions: These findings provide valuable insights into the evolutionary tree and characterization of RIPK and MLKL genes in sea cucumber, contributing to the broader understanding of the RIPK gene family and MLKL in ancient echinoderms.
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(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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Expression of HMGB1, TGF-β1, BIRC3, ADAM17, CDKN1A, and FTO in Relation to Left Ventricular Remodeling in Patients Six Months after the First Myocardial Infarction: A Prospective Study
by
Jovana Kuveljic, Ana Djordjevic, Ivan Zivotic, Milica Dekleva, Ana Kolakovic, Maja Zivkovic, Aleksandra Stankovic and Tamara Djuric
Genes 2024, 15(10), 1296; https://doi.org/10.3390/genes15101296 - 2 Oct 2024
Abstract
Background: After myocardial infarction (MI), adverse left ventricular (LV) remodeling may occur. This is followed by LV hypertrophy and eventually heart failure. The remodeling process is complex and goes through multiple phases. The aim of this study was to investigate the expression of
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Background: After myocardial infarction (MI), adverse left ventricular (LV) remodeling may occur. This is followed by LV hypertrophy and eventually heart failure. The remodeling process is complex and goes through multiple phases. The aim of this study was to investigate the expression of HMGB1, TGF-β1, BIRC3, ADAM17, CDKN1A, and FTO, each involved in a specific step of LV remodeling, in association with the change in the echocardiographic parameters of LV structure and function used to assess the LV remodeling process in the peripheral blood mononuclear cells (PBMCs) of patients six months after the first MI. The expression of selected genes was also determined in PBMCs of controls. Methods: The study group consisted of 99 MI patients, who were prospectively followed-up for 6 months, and 25 controls. Cardiac parameters, measured via conventional 2D echocardiography, were evaluated at two time points: 3–5 days and 6 months after MI. The mRNA expression six-months-post-MI was detected using TaqMan® technology (Applied Biosystems, Thermo Fisher Scientific, Waltham, MA, USA). Results:HMGB1 mRNA was significantly higher in patients with adverse LV remodeling six-months-post-MI than in patients without adverse LV remodeling (p = 0.04). HMGB1 mRNA was significantly upregulated in patients with dilated LV end-diastolic diameter (LVEDD) (p = 0.03); dilated LV end-diastolic volume index (LVEDVi) (p = 0.03); severely dilated LV end-systolic volume index (LVESVi) (p = 0.006); impaired LV ejection fraction (LVEF) (p = 0.01); and LV enlargement (p = 0.03). It was also significantly upregulated in PBMCs from patients compared to controls (p = 0.005). TGF-β1 and BIRC3 mRNA were significantly lower in patients compared to controls (p = 0.02 and p = 0.05, respectively). Conclusions: Our results suggest that HMGB1 is involved in adverse LV remodeling six-months-post-MI, even on the mRNA level. Further research and validation are needed.
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(This article belongs to the Special Issue Genetic and Genomic Research of Cardiovascular Diseases)
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